Merge devel with master branch

ChemFlow/bin/LigFlow

@@ -50,9 +50,26 @@ source ${CHEMFLOW_HOME}/src/ChemFlow_functions.bash
 ChemFlow_echo_software_header
 
 # Programm
-ChemFlow_set_defaults 'LigFlow'   # Set default values for docking parameters.
-LigFlow_CLI "$@"        # Read the command line.
-ChemFlow_validate_input  # Sanity check. (parameters and input files)
+ChemFlow_set_defaults 'LigFlow' # Set default values for docking parameters.
+LigFlow_CLI "$@"        	# Read the command line.
+ChemFlow_validate_input  	# Sanity check. (parameters and input files)
+
+
+#
+# Another dirty fix by DIEGO - PLEASE FIX THIS PORCAPUTTANA!!!
+#
+if [ -z "$(command -v antechamber)" ] ; then
+    echo "AmberTools 17+ is not installed or on PATH" ; exit 1;
+fi
+
+if [ "${CHARGE}" == "resp" ] && [ -z "$(command -v g09)" ] ; then
+    echo "Gaussian is not installed or on PATH" ; exit 1
+fi
+
+if [ -z "$(command -v g09)" ] ; then
+exit 0
+fi
+
 
 RUNDIR=${WORKDIR}/${PROJECT}.chemflow/LigFlow/
 

ChemFlow/bin/SmilesTo3D.py

@@ -75,10 +75,10 @@ def Generate3D(mol):
 				else:
 					AllChem.MMFFOptimizeMolecule(m_H)
 	# Keep hydrogens or not
-	if args.hydrogen:
-		m = m_H
-	else:
+	if args.no_hydrogen:
 		m = Chem.RemoveHs(m_H)
+	else:
+		m = m_H
 	return m
 
 def ExThreadSubmit(smiles, args):
@@ -148,7 +148,7 @@ def OutputSDF(structures, args):
 
 	group_output = parser.add_argument_group('OUTPUT arguments')
 	group_output.add_argument("-o", "--output", metavar='filename', required=True, type=str, help="Path to the output SDF file")
-	group_output.add_argument("--hydrogen", action="store_true", help="Output with all hydrogen atoms" )
+	group_output.add_argument("-noh", "--no-hydrogen", action="store_true", help="Remove hydrogen atoms from the output" )
 	group_output.add_argument("-v", "--verbose", action="store_true", help="Increase terminal output verbosity")
 
 	group_args = parser.add_argument_group('Other arguments')

ChemFlow/bin/bounding_shape.py

@@ -114,7 +114,7 @@ def bounding_box(XYZ, padding):
 			if d > dmax:
 				dmax = d
 		dmax += padding
-		size.append(dmax)
+		size.append(dmax*2)
 	return center, size
 
 if __name__ == '__main__':
@@ -169,14 +169,14 @@ def bounding_box(XYZ, padding):
 		center, size = bounding_box(XYZ, args.padding)
 		print(' '.join(['{:.3f}'.format(x) for x in center + size]))
 		if args.pymol:
-			print('pseudoatom a1, pos={}'.format([center[0]+size[0],center[1]+size[1],center[2]+size[2]]))
-			print('pseudoatom a2, pos={}'.format([center[0]+size[0],center[1]+size[1],center[2]-size[2]]))
-			print('pseudoatom a3, pos={}'.format([center[0]+size[0],center[1]-size[1],center[2]-size[2]]))
-			print('pseudoatom a4, pos={}'.format([center[0]+size[0],center[1]-size[1],center[2]+size[2]]))
-			print('pseudoatom a5, pos={}'.format([center[0]-size[0],center[1]-size[1],center[2]+size[2]]))
-			print('pseudoatom a6, pos={}'.format([center[0]-size[0],center[1]-size[1],center[2]-size[2]]))
-			print('pseudoatom a7, pos={}'.format([center[0]-size[0],center[1]+size[1],center[2]-size[2]]))
-			print('pseudoatom a8, pos={}'.format([center[0]-size[0],center[1]+size[1],center[2]+size[2]]))
+			print('pseudoatom a1, pos={}'.format([center[0]+size[0]/2,center[1]+size[1]/2,center[2]+size[2]/2]))
+			print('pseudoatom a2, pos={}'.format([center[0]+size[0]/2,center[1]+size[1]/2,center[2]-size[2]/2]))
+			print('pseudoatom a3, pos={}'.format([center[0]+size[0]/2,center[1]-size[1]/2,center[2]-size[2]/2]))
+			print('pseudoatom a4, pos={}'.format([center[0]+size[0]/2,center[1]-size[1]/2,center[2]+size[2]/2]))
+			print('pseudoatom a5, pos={}'.format([center[0]-size[0]/2,center[1]-size[1]/2,center[2]+size[2]/2]))
+			print('pseudoatom a6, pos={}'.format([center[0]-size[0]/2,center[1]-size[1]/2,center[2]-size[2]/2]))
+			print('pseudoatom a7, pos={}'.format([center[0]-size[0]/2,center[1]+size[1]/2,center[2]-size[2]/2]))
+			print('pseudoatom a8, pos={}'.format([center[0]-size[0]/2,center[1]+size[1]/2,center[2]+size[2]/2]))
 			print('distance d12, a1, a2')
 			print('distance d23, a2, a3')
 			print('distance d34, a3, a4')

ChemFlow/src/ChemFlow_functions.bash

@@ -13,7 +13,7 @@ echo "
 #          + ||de Strasbourg +              ++  +     +   +            #
 #          +++++++++++++++++++              ++  +     +   + LAB        #
 #                                                                      #
-#         Laboratoire d'Ingenierie de la Fonction Moleculaire          #
+#         Laboratoire d'Ingenierie des Fonctions Moleculaires          #
 #                                                                      #
 # Marco Cecchini - cecchini@unistra.fr                                 #
 # Diego E. B. Gomes - dgomes@pq.cnpq.br                                #
@@ -134,6 +134,7 @@ case "${WORKFLOW}" in
             if [ "$(basename ${RECEPTOR_FILE} | cut -d. -f2 )" != "mol2" ] ; then
                 ERROR_MESSAGE="Plants rescoring requires a mol2 file as receptor input"; ChemFlow_error ;
             fi
+            check_center
         ;;
         "vina")
             SCORE_PROGRAM="VINA" ;
@@ -143,23 +144,20 @@ case "${WORKFLOW}" in
             if [ "${VINA_MODE}" != "local_only" ] && [ "${VINA_MODE}" != "score_only" ] ; then
                 ERROR_MESSAGE="Vina rescoring mode ${VINA_MODE} does not exist"; ChemFlow_error ;
             fi
+            check_center
         ;;
-        "mmgbsa") # mmgbsa as scoring function is only allowed for ScoreFlow.
+        "mmgbsa"|"mmpbsa") # mmgbsa as scoring function is only allowed for ScoreFlow.
             SCORE_PROGRAM="AMBER"
             RECEPTOR_NAME="$(basename ${RECEPTOR_FILE} .pdb)"
             if [ "$(basename ${RECEPTOR_FILE} | cut -d. -f2 )" != "pdb" ] ; then
-                ERROR_MESSAGE="mmgbsa rescoring requires a PDB file as receptor input"; ChemFlow_error ;
+                ERROR_MESSAGE="MM(PB,GB)SA rescoring requires a PDB file as receptor input"; ChemFlow_error ;
             fi
         ;;
         *)
             ERROR_MESSAGE="SCORING_FUNCTION ${SCORING_FUNCTION} not implemented"; ChemFlow_error ;
         ;;
     esac
 
-    if [ "${SCORING_FUNCTION}" != "mmgbsa"  ] ; then
-        # Center is not required for mmgbsa rescoring.
-        check_center
-    fi
 ;;
 esac
 
@@ -170,14 +168,22 @@ if [ -z "${POSTPROCESS}" ] && [ -z "${ARCHIVE}" ] ; then
     case "${JOB_SCHEDULLER}" in
     "None") ;;
     "PBS"|"SLURM")
-        if [ -z ${NC_CHANGED} ] ; then
-            NCORES=16
-        fi
+#        if [ -z ${NC_CHANGED} ] ; then
+#            NCORES=16
+#        fi
+       echo "Using ${JOB_SCHEDULLER}"
     ;;
     *) ERROR_MESSAGE="Invalid JOB_SCHEDULLER" ; ChemFlow_error ;
        ;;
     esac
 
+
+    # AmberTools must be installed because we use AnteChamber everywhere
+    if  [ -z "$(command -v antechamber)" ] ; then
+        ERROR_MESSAGE="AmberTools 17+ is not installed or on PATH" ; ChemFlow_error ;
+    fi
+
+
     # Check program locations ---------------------------------------------------
     case "${DOCK_PROGRAM}" in
     "PLANTS")
@@ -189,7 +195,7 @@ if [ -z "${POSTPROCESS}" ] && [ -z "${ARCHIVE}" ] ; then
         if  [ -z "$(command -v vina)" ] ; then
             ERROR_MESSAGE="Autodock Vina is not installed or on PATH" ; ChemFlow_error ;
         fi
-        if [ -z "$(command -v ${mgltools_folder}/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py)" ] ; then
+        if [ -z "$(command -v prepare_ligand4.py)" ] ; then
             ERROR_MESSAGE="MglTools is not installed or on PATH" ; ChemFlow_error ;
         fi
     ;;
@@ -205,7 +211,7 @@ if [ -z "${POSTPROCESS}" ] && [ -z "${ARCHIVE}" ] ; then
         if  [ -z "$(command -v vina)" ] ; then
             ERROR_MESSAGE="Autodock Vina is not installed or on PATH" ; ChemFlow_error ;
         fi
-        if [ -z "$(command -v ${mgltools_folder}/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py)" ] ; then
+        if [ -z "$(command -v prepare_ligand4.py)" ] ; then
             ERROR_MESSAGE="MglTools is not installed or on PATH" ; ChemFlow_error ;
         fi
     ;;
@@ -231,7 +237,12 @@ if [ -z "${POSTPROCESS}" ] && [ -z "${ARCHIVE}" ] ; then
                 fi
             fi
         else
+
             AMBER_EXEC="pmemd.cuda"
+            if [ "${CUDA_PRECISION}" == "DOUBLE" ] ; then
+                AMBER_EXEC="pmemd.cuda_DPFP"
+            fi
+
         fi
      ;;
     esac
@@ -297,6 +308,7 @@ ChemFlow_set_defaults(){
 #
 #        Author: Dona de Francquen
 #===============================================================================
+
 # General options
 WORKDIR="${PWD}"
 PROTOCOL="default"