diff --git a/.idea/ChemFlow.iml b/.idea/ChemFlow.iml
new file mode 100644
index 0000000..6711606
--- /dev/null
+++ b/.idea/ChemFlow.iml
@@ -0,0 +1,11 @@
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 0000000..105ce2d
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..65531ca
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+
+
+
+
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..922d239
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..94a25f7
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/CHEMFLOW_LOGO.PNG b/CHEMFLOW_LOGO.PNG
new file mode 100644
index 0000000..7d2b742
Binary files /dev/null and b/CHEMFLOW_LOGO.PNG differ
diff --git a/ChemFlow/bin/LigFlow b/ChemFlow/bin/LigFlow
index f5a5391..7f942df 100755
--- a/ChemFlow/bin/LigFlow
+++ b/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/
diff --git a/ChemFlow/bin/SmilesTo3D.py b/ChemFlow/bin/SmilesTo3D.py
index e312918..55fcaaa 100755
--- a/ChemFlow/bin/SmilesTo3D.py
+++ b/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')
diff --git a/ChemFlow/bin/bounding_shape.py b/ChemFlow/bin/bounding_shape.py
index e4217f9..7ddb272 100755
--- a/ChemFlow/bin/bounding_shape.py
+++ b/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')
diff --git a/ChemFlow/src/ChemFlow_functions.bash b/ChemFlow/src/ChemFlow_functions.bash
index 7561a0a..4a139a5 100644
--- a/ChemFlow/src/ChemFlow_functions.bash
+++ b/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 ${RECEPTOR_FILE} | cut -d. -f2 )" != "mol2" ] ; then
ERROR_MESSAGE="Plants rescoring requires a mol2 file as receptor input"; ChemFlow_error ;
fi
+ check_center
;;
"vina")
SCORE_PROGRAM="VINA" ;
@@ -143,12 +144,13 @@ case "${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 ${RECEPTOR_FILE} | cut -d. -f2 )" != "pdb" ] ; then
- ERROR_MESSAGE="mmgbsa rescoring requires a PDB file as receptor input"; ChemFlow_error ;
+ ERROR_MESSAGE="MM(PB,GB)SA rescoring requires a PDB file as receptor input"; ChemFlow_error ;
fi
;;
*)
@@ -156,10 +158,6 @@ case "${WORKFLOW}" in
;;
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"
diff --git a/ChemFlow/src/DockFlow_functions.bash b/ChemFlow/src/DockFlow_functions.bash
index 3a5c0bf..19ee232 100644
--- a/ChemFlow/src/DockFlow_functions.bash
+++ b/ChemFlow/src/DockFlow_functions.bash
@@ -38,7 +38,8 @@ DockFlow_dock() {
# Always work here
cd ${RUNDIR}
-DockFlow_update_ligand_list
+#DockFlow_update_ligand_list
+DockFlow_update_ligand_list_DEV
NDOCK=${#LIGAND_LIST[@]}
if [ ${NDOCK} == 0 ] ; then
@@ -83,7 +84,7 @@ case ${JOB_SCHEDULLER} in
--center_x ${DOCK_CENTER[0]} --center_y ${DOCK_CENTER[1]} --center_z ${DOCK_CENTER[2]} \
--size_x ${DOCK_LENGTH[0]} --size_y ${DOCK_LENGTH[1]} --size_z ${DOCK_LENGTH[2]} \
--energy_range ${ENERGY_RANGE} --exhaustiveness ${EXHAUSTIVENESS} \
- --out ${RUNDIR}/${LIGAND}/VINA/output.pdbqt --log ${RUNDIR}/${LIGAND}/VINA/output.log ${VINA_EXTRA} &>/dev/null " >> dock.xargs
+ --out ${RUNDIR}/${LIGAND}/VINA/output.pdbqt --log ${RUNDIR}/${LIGAND}/VINA/output.log ${VINA_EXTRA} --cpu 1 &>/dev/null " >> dock.xargs
done
;;
esac
@@ -165,6 +166,55 @@ unset LIGAND_LIST
LIGAND_LIST=(${DOCK_LIST[@]})
}
+DockFlow_update_ligand_list_DEV() {
+# Creation of the docking list, checkpoint calculations.
+DOCK_LIST=""
+case ${DOCK_PROGRAM} in
+"PLANTS")
+ # If the folder exists but there's no "bestranking.csv" its incomplete.
+ FILE="bestranking.csv"
+;;
+"VINA")
+ # If the folder exists but there's no "output.pdbqt" its incomplete.
+ FILE="output.pdbqt"
+;;
+esac
+
+
+if [ "${OVERWRITE}" == "no" ] ; then # Useless to update ligand list if we overwrite
+
+ counter=0
+ for LIGAND in ${LIGAND_LIST[@]} ; do
+ if [ -d ${LIGAND}/${DOCK_PROGRAM} ] && [ ! -f ${LIGAND}/${DOCK_PROGRAM}/${FILE} ] ; then
+# echo "[ NOTE ] ${RECEPTOR_NAME} and ${LIGAND} incomplete... redoing it !"
+ rm -rf ${LIGAND}/${DOCK_PROGRAM}
+ DOCK_LIST[${counter}]="$LIGAND"
+ fi
+ if [ -f ${LIGAND}/${DOCK_PROGRAM}/${FILE} ] ; then
+ if [ $(wc -l ${LIGAND}/${DOCK_PROGRAM}/${FILE} | cut -d' ' -f1) -lt 2 ] ; then
+# echo "[ NOTE ] ${RECEPTOR_NAME} and ${LIGAND} incomplete... redoing it !"
+ rm -rf ${LIGAND}/${DOCK_PROGRAM}
+ DOCK_LIST[${counter}]="$LIGAND"
+ fi
+ fi
+ if [ ! -d ${LIGAND}/${DOCK_PROGRAM} ] ; then
+ DOCK_LIST[${counter}]="$LIGAND"
+ # Still unused.
+ fi
+
+ let counter++
+ done
+else
+ DOCK_LIST=(${LIGAND_LIST[@]})
+fi
+
+unset LIGAND_LIST
+LIGAND_LIST=(${DOCK_LIST[@]})
+}
+
+
+
+
DockFlow_write_plants_HPC() {
#=== FUNCTION ================================================================
@@ -279,7 +329,6 @@ DockFlow_prepare_receptor() {
# PARAMETERS: ${DOCK_PROGRAM}
# ${RUNDIR}
# ${RECEPTOR_FILE}
-# ${mgltools_folder} (should be in the path)
#
# Author: Dona de Francquen
#
@@ -289,10 +338,9 @@ DockFlow_prepare_receptor() {
cp ${RECEPTOR_FILE} ${RUNDIR}/receptor.mol2
if [ ${DOCK_PROGRAM} == 'VINA' ] && [ ! -f ${RUNDIR}/receptor.pdbqt ] ; then
- ${mgltools_folder}/bin/python \
- ${mgltools_folder}/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py \
+ pythonsh $(command -v prepare_receptor4.py) \
-r ${RUNDIR}/receptor.mol2 \
- -o ${RUNDIR}/receptor.pdbqt
+ -o ${RUNDIR}/receptor.pdbqt &>/dev/null
fi
}
@@ -314,11 +362,12 @@ DockFlow_prepare_ligands() {
#
# Author: Dona de Francquen
#
-# UPDATE: fri. july 6 14:49:50 CEST 2018
+# UPDATE: Ter Nov 5 12:10:24 -03 2019
#
#===============================================================================
cd ${RUNDIR}
+echo "[Preparing ligands]"
# Create ligand folder into the project
for LIGAND in ${LIGAND_LIST[@]} ; do
if [ ! -d ${LIGAND} ] ; then
@@ -331,18 +380,22 @@ for LIGAND in ${LIGAND_LIST[@]} ; do
case ${DOCK_PROGRAM} in
"PLANTS")
if [ ! -f ${LIGAND}/ligand.mol2 ] ; then
- cp ${WORKDIR}/${PROJECT}.chemflow/LigFlow/original/${LIGAND}.mol2 ${LIGAND}/ligand.mol2
+ echo "cp ${WORKDIR}/${PROJECT}.chemflow/LigFlow/original/${LIGAND}.mol2 ${LIGAND}/ligand.mol2"
fi
;;
"VINA")
if [ ! -f ${LIGAND}/ligand.pdbqt ] ; then
- ${mgltools_folder}/bin/python ${mgltools_folder}/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py \
+ echo "pythonsh $(command -v prepare_ligand4.py) \
-l ${WORKDIR}/${PROJECT}.chemflow/LigFlow/original/${LIGAND}.mol2 \
- -o ${LIGAND}/ligand.pdbqt
+ -o ${LIGAND}/ligand.pdbqt &>/dev/null"
fi
;;
esac
-done
+done > LigFlow.xargs
+
+cat LigFlow.xargs | xargs -P${NCORES} -I '{}' bash -c '{}'
+
+echo "[ DONE ]"
}
@@ -515,6 +568,11 @@ if [ ! -z ${POSTPROCESS_ALL} ] ; then
fi
+# First, a clean up.
+if [ -f ${RUNDIR}/docked_ligands.mol2 ] ; then
+ rm -rf ${RUNDIR}/docked_ligands.mol2
+fi
+
for LIGAND in ${LIGAND_LIST[@]}; do
if [ ! -f ${LIGAND}/PLANTS/docked_ligands.mol2 ] ; then
echo "[ ERROR ] Plants result for ligand ${LIGAND} does not exists."
@@ -522,7 +580,10 @@ for LIGAND in ${LIGAND_LIST[@]}; do
else
# Fill the DockFlow.csv file
echo -ne "PostDock: ${PROTOCOL} - ${LIGAND} \r"
- head -${DOCK_POSES} ${LIGAND}/PLANTS/ranking.csv | awk -v protocol=${PROTOCOL} -v target=${RECEPTOR_NAME} -v ligand=${LIGAND} -F, '!/LIGAND_ENTRY/ {print "PLANTS",protocol,target,ligand,$1,$2}' >> DockFlow.csv
+# head -${DOCK_POSES} ${LIGAND}/PLANTS/ranking.csv | awk -v protocol=${PROTOCOL} -v target=${RECEPTOR_NAME} -v ligand=${LIGAND} -F, '!/LIGAND_ENTRY/ {print "PLANTS",protocol,target,ligand,$1,$2}' >> DockFlow.csv
+# Patch by Kgalentino & Dgomes
+ awk -F, -v protocol=${PROTOCOL} -v target=${RECEPTOR_NAME} -v ligand=${LIGAND} -v dock_poses=${DOCK_POSES} '!/LIGAND/{cc++; if(cc<=dock_poses){gsub(".*_entry_00001_conf_","",$1); print "PLANTS",protocol,target,ligand, $1,$2}}' ${LIGAND}/PLANTS/ranking.csv >> DockFlow.csv
+
# Create the docked_ligands.mol2, a file containing every conformations of every ligands.
OLDIFS=$IFS
@@ -546,7 +607,7 @@ done
# rename the ligand in the created file
if [ -f docked_ligands.mol2 ] && [ -f DockFlow.csv ] ; then
sed -i 's/\.*_entry_[[:digit:]]*//' docked_ligands.mol2
- sed -i 's/[a-zA-Z0-9]*_entry_[[:digit:]]*_conf_//' DockFlow.csv
+# Patch by Kgalentino & Dgomes sed -i 's/[a-zA-Z0-9]*_entry_[[:digit:]]*_conf_//' DockFlow.csv
fi
}
@@ -660,10 +721,12 @@ for PROTOCOL in ${PROTOCOL_LIST[@]} ; do
for RECEPTOR in ${RECEPTOR_LIST[@]} ; do
RUNDIR="${WORKDIR}/${PROJECT}.chemflow/DockFlow/${PROTOCOL}/${RECEPTOR}"
cd ${RUNDIR}
- if [ "${OVERWRITE}" == 'yes' ] ; then
+
+# You should always overwrite docked_ligands.mol2 and DockFlow.csv
+# if [ "${OVERWRITE}" == 'yes' ] ; then
rm -rf ${RUNDIR}/docked_ligands.mol2
rm -rf ${RUNDIR}/DockFlow.csv
- fi
+# fi
# Cleanup
if [ ! -f ${RUNDIR}/DockFlow.csv ] ; then
@@ -686,13 +749,16 @@ else
echo "[ DockFlow ] Done with post-processing."
# Archiving.
- echo -n "[ DockFlow ] Archive the docking results (folders) in TAR files? [y/n] "
- read opt
- case ${opt} in
- "y"|"yes"|"Yes"|"Y"|"YES")
- DockFlow_archive
- ;;
- esac
+ if [ ! -z ${ARCHIVE} ] ; then
+ echo -n "[ DockFlow ] Archive the docking results (folders) in TAR files? [y/n] "
+ read opt
+ case ${opt} in
+ "y"|"yes"|"Yes"|"Y"|"YES")
+ DockFlow_archive
+ ;;
+ esac
+ fi
+
fi
unset FAIL
@@ -772,6 +838,8 @@ JOB SCHEDULLER: ${JOB_SCHEDULLER}
OVERWRITE: ${OVERWRITE}
"
+if [ "${YESTOALL}" != 'yes' ] ; then
+
echo -n "
Continue [y/n]? "
read opt
@@ -779,6 +847,8 @@ case $opt in
"Y"|"YES"|"Yes"|"yes"|"y") ;;
*) echo "Exiting" ; exit 0 ;;
esac
+
+fi
}
@@ -841,6 +911,7 @@ DockFlow -r receptor.mol2 -l ligand.mol2 -p myproject --center X Y Z [--protocol
[ Additional ]
--overwrite : Overwrite results
+ --yes : Yes to all questions
[ Options for docking program ]
*--center LIST : xyz coordinates of the center of the binding site, separated by a space
@@ -998,6 +1069,9 @@ while [[ $# -gt 0 ]]; do
ARCHIVE='yes'
ARCHIVE_ALL="yes"
;;
+ "--yes")
+ YESTOALL='yes'
+ ;;
*)
unknown="$1" # unknown option
echo "Unknown flag \"$unknown\""
diff --git a/ChemFlow/src/GUI/GUI.py b/ChemFlow/src/GUI/GUI.py
index 39ba074..112e2d3 100755
--- a/ChemFlow/src/GUI/GUI.py
+++ b/ChemFlow/src/GUI/GUI.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
from PyQt5 import QtGui, QtWidgets
-from PyQt5.QtWidgets import QFileDialog, QMainWindow
+from PyQt5.QtWidgets import QFileDialog, QMainWindow, QDesktopWidget
from PyQt5.QtCore import QProcess, QByteArray, QRegExp
from webbrowser import open as browser_open
from time import strftime, gmtime
@@ -15,7 +15,7 @@
from DockingClasses import DialogDockVina, DialogDockPlants
from ScoringClasses import DialogScoreVina, DialogScorePlants, DialogScoreMmgbsa
from ExecutionClasses import DialogRunLocal, DialogRunPbs, DialogRunSlurm
-from ToolsClasses import DialogToolBoundingShape, DialogToolSmilesTo3D
+from ToolsClasses import DialogToolBoundingShape
from qt_creator.UImainwindow import Ui_MainWindow
@@ -23,6 +23,11 @@ class Main(QMainWindow, Ui_MainWindow):
def __init__(self, parent=None):
super().__init__(parent)
self.setupUi(self)
+ # show the main window at the center of the screen
+ qtRectangle = self.frameGeometry()
+ centerPoint = QDesktopWidget().availableGeometry().center()
+ qtRectangle.moveCenter(centerPoint)
+ self.move(qtRectangle.topLeft())
# set window icon and logo
icon = QtGui.QIcon()
logo_path = os.path.realpath(os.path.join(WORKDIR, "img", "logo.png"))
@@ -32,6 +37,7 @@ def __init__(self, parent=None):
# set other icons
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(os.path.realpath(os.path.join(WORKDIR, "img", "run.png"))), QtGui.QIcon.Normal, QtGui.QIcon.Off)
+ self.commandLinkButton_smiles_run.setIcon(icon)
self.commandLinkButton_ligflow_run.setIcon(icon)
self.commandLinkButton_docking_run.setIcon(icon)
self.commandLinkButton_scoring_run.setIcon(icon)
@@ -49,6 +55,7 @@ def __init__(self, parent=None):
self.actionAbout.triggered.connect(self.about)
self.actionGitHub.triggered.connect(self.github)
self.actionReport_issue.triggered.connect(self.report_issue)
+ self.actionDocumentation.triggered.connect(self.documentation)
self.actionTutorial.triggered.connect(self.tutorial)
self.actionDebug_mode.triggered.connect(self.debug_mode)
self.actionLogfile.triggered.connect(self.read_logs)
@@ -63,6 +70,8 @@ def __init__(self, parent=None):
self.pushButton_docking_lig.clicked.connect(self.browse_ligand)
self.pushButton_scoring_rec.clicked.connect(self.browse_receptor)
self.pushButton_scoring_lig.clicked.connect(self.browse_ligand)
+ self.pushButton_smiles_input.clicked.connect(self.select_smiles_input)
+ self.lineEdit_smiles_input.textChanged.connect(lambda text: self.set_smiles_output(text))
## Protocol
self.pushButton_docking_configure_protocol.clicked.connect(self.configure_docking_protocol)
self.pushButton_scoring_configure_protocol.clicked.connect(self.configure_scoring_protocol)
@@ -71,6 +80,7 @@ def __init__(self, parent=None):
self.pushButton_docking_configure_job_queue.clicked.connect(self.configure_workflow_execution)
self.pushButton_scoring_configure_job_queue.clicked.connect(self.configure_workflow_execution)
## Actions
+ self.commandLinkButton_smiles_run.clicked.connect(self.run_smiles)
self.commandLinkButton_ligflow_run.clicked.connect(self.run_ligflow)
self.commandLinkButton_docking_run.clicked.connect(self.run_docking)
self.commandLinkButton_docking_postprocess.clicked.connect(self.run_docking_postprocess)
@@ -80,6 +90,7 @@ def __init__(self, parent=None):
self.commandLinkButton_scoring_archive.clicked.connect(self.run_scoring_archive)
self.commandLinkButton_tools_run.clicked.connect(self.run_tools)
self.action_buttons = [
+ self.commandLinkButton_smiles_run,
self.commandLinkButton_ligflow_run,
self.commandLinkButton_docking_run,
self.commandLinkButton_docking_postprocess,
@@ -133,8 +144,11 @@ def report_issue(self):
def tutorial(self):
"""Open the tutorial section in a web browser"""
- # TODO update link when commit to master branch
- browser_open('https://github.com/IFMlab/ChemFlow/blob/devel/tutorial/TUTORIAL.rst')
+ browser_open('https://chemflow-docs.readthedocs.io/en/latest/tutorial.html')
+
+ def documentation(self):
+ """Open the documentation in a web browser"""
+ browser_open('http://chemflow.cc')
def debug_mode(self):
"""Activate the debug mode. Prints commands instead of running them"""
@@ -208,6 +222,21 @@ def browse_ligand(self):
self.lineEdit_docking_lig.setText(self.input['Ligand'])
self.lineEdit_scoring_lig.setText(self.input['Ligand'])
+ def select_smiles_input(self):
+ filetypes = "All Files (*)"
+ value, _ = QFileDialog.getOpenFileName(None,"Select input SMILES file", os.getcwd(), filetypes)
+ if value:
+ self.lineEdit_smiles_input.setText(value)
+
+ def set_smiles_output(self, text):
+ """Suggest path to SDF output file automatically from SMILES input file"""
+ output = self.lineEdit_smiles_output.text()
+ output_dir = os.path.dirname(output)
+ input_dir = os.path.dirname(text)
+ if (output_dir[:len(input_dir)] in input_dir) or (output in EMPTY_VALUES):
+ filename, file_extension = os.path.splitext(text)
+ self.lineEdit_smiles_output.setText('{}.sdf'.format(filename))
+
def configure_docking_protocol(self):
'''Configure the docking protocol'''
self.input['docking_software'] = self.comboBox_docking_software.currentText()
@@ -247,11 +276,11 @@ def configure_scoring_protocol(self):
def configure_workflow_execution(self):
'''Configure how the workflow is going to run on the local machine'''
# get the selected execution mode
- if self.tabWidget.currentIndex() == 0: # LigFlow
+ if self.tabWidget.currentIndex() == self.tabWidget.indexOf(self.tab_LigFlow): # LigFlow
self.input['JobQueue'] = self.comboBox_ligflow_job_queue.currentText()
- elif self.tabWidget.currentIndex() == 1: # DockFlow
+ elif self.tabWidget.currentIndex() == self.tabWidget.indexOf(self.tab_DockFlow): # DockFlow
self.input['JobQueue'] = self.comboBox_docking_job_queue.currentText()
- elif self.tabWidget.currentIndex() == 2: # ScoreFlow
+ elif self.tabWidget.currentIndex() == self.tabWidget.indexOf(self.tab_ScoreFlow): # ScoreFlow
self.input['JobQueue'] = self.comboBox_scoring_job_queue.currentText()
# launch appropriate dialog
@@ -271,11 +300,11 @@ def configure_workflow_execution(self):
if workflow_execution:
for kw in workflow_execution:
self.input[kw] = workflow_execution[kw]
- if self.tabWidget.currentIndex() == 0: # LigFlow
+ if self.tabWidget.currentIndex() == self.tabWidget.indexOf(self.tab_LigFlow): # LigFlow
self.ligflow_execution = True
- elif self.tabWidget.currentIndex() == 1: # DockFlow
+ elif self.tabWidget.currentIndex() == self.tabWidget.indexOf(self.tab_DockFlow): # DockFlow
self.docking_execution = True
- elif self.tabWidget.currentIndex() == 2: # ScoreFlow
+ elif self.tabWidget.currentIndex() == self.tabWidget.indexOf(self.tab_ScoreFlow): # ScoreFlow
self.scoring_execution = True
def check_ligflow_required_args(self):
@@ -333,6 +362,37 @@ def check_scoring_required_args(self):
missing.append('- Protocol name')
return missing
+ def run_smiles(self):
+ """Run SmilesTo3D.py to create a single 3D conformation per SMILES"""
+ missing = []
+ self.input['InputFile'] = self.lineEdit_smiles_input.text()
+ self.input['OutputFile'] = self.lineEdit_smiles_output.text()
+ self.input['SmilesColumn'] = self.spinBox_smiles_col.value()
+ self.input['NamesColumn'] = self.spinBox_names_col.value()
+ self.input['NThreads'] = self.spinBox_nthreads.value()
+ self.input['Header'] = self.checkBox_header.isChecked()
+ self.input['NoHydrogen'] = self.checkBox_hydrogen.isChecked()
+ self.input['Verbose'] = self.checkBox_verbose.isChecked()
+ self.input['MPI'] = self.checkBox_mpi.isChecked()
+ value = self.comboBox_delimiter.currentText()
+ if value == 'Tab':
+ delimiter = '\t'
+ elif value == 'Space':
+ delimiter = ' '
+ else:
+ delimiter = value
+ self.input['Delimiter'] = delimiter
+ self.input['Method'] = self.comboBox_method.currentText().lower()
+ if self.input['InputFile'] in EMPTY_VALUES:
+ missing.append('- Input SMILES file')
+ if self.input['OutputFile'] in EMPTY_VALUES:
+ missing.append('- Output SDF file')
+ if missing:
+ missingParametersDialog(*missing)
+ else:
+ # Execute
+ self.execute_command(self.build_smiles_command())
+
def run_ligflow(self):
'''Run ligand preparation with LigFlow'''
# search for missing configuration
@@ -467,8 +527,6 @@ def describe_tools(self, tool):
"""Set the description label for ChemFlow tools"""
if tool == 'Bounding shape':
self.label_tools_description.setText('Reads a mol2 file and returns the center and radius/size of the smallest shape containing all the atoms of the given molecule.')
- elif tool == 'SMILES to 3D':
- self.label_tools_description.setText('Generates 3D structures in SDF format from SMILES, using RDKIT.')
else:
self.label_tools_description.setText('')
@@ -482,8 +540,6 @@ def configure_tools(self):
self.input['Tool'] = tool
if tool == 'Bounding shape':
tool_dialog = DialogToolBoundingShape()
- elif tool == 'SMILES to 3D':
- tool_dialog = DialogToolSmilesTo3D()
tool_dialog.exec_()
try:
tool_parameters = tool_dialog.values
@@ -500,6 +556,7 @@ def run_tools(self):
except KeyError:
errorDialog(message="Please configure a ChemFlow tool first")
else:
+ # Bounding shape
if self.input['Tool'] == 'Bounding shape':
command = ['bounding_shape.py']
command.append(self.input['InputFile'])
@@ -507,25 +564,28 @@ def run_tools(self):
command.extend(['--padding', self.input['Padding']])
if self.input['PyMOL']:
command.append('--pymol')
- elif self.input['Tool'] == 'SMILES to 3D':
- command = ['SmilesTo3D.py']
- command.extend(['-i', self.input['InputFile']])
- command.extend(['-o', self.input['OutputFile']])
- command.extend(['-sc', self.input['SmilesColumn']])
- command.extend(['-nc', self.input['NamesColumn']])
- command.extend(['-d', self.input['Delimiter']])
- command.extend(['-m', self.input['Method']])
- command.extend(['-nt', self.input['NThreads']])
- if self.input['Header']:
- command.append('--header')
- if self.input['AllHydrogens']:
- command.append('--hydrogen')
- if self.input['Verbose']:
- command.append('-v')
- if self.input['MPI']:
- command.append('--mpi')
+ # Run
self.execute_command(command)
+ def build_smiles_command(self):
+ command = ['SmilesTo3D.py']
+ command.extend(['-i', self.input['InputFile']])
+ command.extend(['-o', self.input['OutputFile']])
+ command.extend(['-sc', self.input['SmilesColumn']])
+ command.extend(['-nc', self.input['NamesColumn']])
+ command.extend(['-d', '\"' + self.input['Delimiter'] + '\"'])
+ command.extend(['-m', self.input['Method']])
+ command.extend(['-nt', self.input['NThreads']])
+ if self.input['Header']:
+ command.append('--header')
+ if self.input['NoHydrogen']:
+ command.append('-noh')
+ if self.input['Verbose']:
+ command.append('-v')
+ if self.input['MPI']:
+ command.append('--mpi')
+ return command
+
def build_ligflow_command(self):
command = ['LigFlow']
# Project
@@ -730,6 +790,7 @@ def process_started(self):
self.display(command)
self.summary_text = ''
self.display('[ ChemFlow ] {} was spawned with PID {}'.format(self.process.program(), self.process.processId()))
+ self.statusBar.showMessage('Running {}'.format(self.process.program()), 3000)
# Prevent user from launching other commands
for button in self.action_buttons:
button.setEnabled(False)
@@ -738,6 +799,7 @@ def process_finished(self, status):
"""Routine launched when a QProcess is finished"""
self.display('[ ChemFlow ] {} process ended with exit status {}'.format(self.process.program(), status))
self.pushButton_kill.setEnabled(False)
+ self.statusBar.showMessage('Finished running {}'.format(self.process.program()), 3000)
# Allow user to send new commands
for button in self.action_buttons:
button.setEnabled(True)
diff --git a/ChemFlow/src/GUI/ToolsClasses.py b/ChemFlow/src/GUI/ToolsClasses.py
index 9131b0d..a116dae 100644
--- a/ChemFlow/src/GUI/ToolsClasses.py
+++ b/ChemFlow/src/GUI/ToolsClasses.py
@@ -2,7 +2,6 @@
from PyQt5.QtWidgets import QDialog, QFileDialog
from PyQt5.QtCore import QSettings
from qt_creator.UItool_boundingshape import Ui_ToolBoundingShape
-from qt_creator.UItool_smiles_to_3d import Ui_ToolSmilesTo3d
from utils import (
WORKDIR, INI_FILE, EMPTY_VALUES,
guiSave, guiRestore,
@@ -45,70 +44,3 @@ def select_input(self):
value, _ = QFileDialog.getOpenFileName(None,"Select MOL2 file", os.getcwd(), filetypes)
if value:
self.lineEdit_path.setText(value)
-
-
-class DialogToolSmilesTo3D(QDialog, Ui_ToolSmilesTo3d):
- def __init__(self, parent=None):
- super().__init__(parent)
- self.setupUi(self)
- # Buttons
- self.pushButton_ok.clicked.connect(self.validate)
- self.pushButton_cancel.clicked.connect(self.cancel)
- self.pushButton_input.clicked.connect(self.select_input)
- self.lineEdit_input.textChanged.connect(lambda text: self.set_output(text))
- # Settings
- self.values = {}
- self.settings = QSettings(INI_FILE, QSettings.IniFormat)
- guiRestore(self, self.settings)
-
- def closeEvent(self, event):
- guiSave(self, self.settings)
- QDialog.closeEvent(self, event)
-
- def validate(self):
- missing = []
- self.values['InputFile'] = self.lineEdit_input.text()
- self.values['OutputFile'] = self.lineEdit_output.text()
- self.values['SmilesColumn'] = self.spinBox_smiles_col.value()
- self.values['NamesColumn'] = self.spinBox_names_col.value()
- self.values['NThreads'] = self.spinBox_nthreads.value()
- self.values['Header'] = self.checkBox_header.isChecked()
- self.values['AllHydrogens'] = self.checkBox_hydrogen.isChecked()
- self.values['Verbose'] = self.checkBox_verbose.isChecked()
- self.values['MPI'] = self.checkBox_mpi.isChecked()
- value = self.comboBox_delimiter.currentText()
- if value == 'Tab':
- delimiter = '\t'
- elif value == 'Space':
- delimiter = ' '
- else:
- delimiter = value
- self.values['Delimiter'] = delimiter
- self.values['Method'] = self.comboBox_delimiter.currentText().lower()
- if self.values['InputFile'] in EMPTY_VALUES:
- missing.append('- Input SMILES file')
- if self.values['OutputFile'] in EMPTY_VALUES:
- missing.append('- Output SDF file')
- if len(missing):
- missingParametersDialog(*missing)
- else:
- self.close()
-
- def cancel(self):
- del self.values
- self.close()
-
- def select_input(self):
- filetypes = "All Files (*)"
- value, _ = QFileDialog.getOpenFileName(None,"Select input SMILES file", os.getcwd(), filetypes)
- if value:
- self.lineEdit_input.setText(value)
-
- def set_output(self, text):
- """Suggest path to output file automatically from input file"""
- output = self.lineEdit_output.text()
- output_dir = os.path.dirname(output)
- input_dir = os.path.dirname(text)
- if (output_dir[:len(input_dir)] in input_dir) or (output in EMPTY_VALUES):
- filename, file_extension = os.path.splitext(text)
- self.lineEdit_output.setText('{}.sdf'.format(filename))
diff --git a/ChemFlow/src/GUI/qss/dark.css b/ChemFlow/src/GUI/qss/dark.css
index f868cc8..e6b38d7 100644
--- a/ChemFlow/src/GUI/qss/dark.css
+++ b/ChemFlow/src/GUI/qss/dark.css
@@ -1,6 +1,9 @@
/*
Custom theme settings
*/
+QMenuBar {
+ border-bottom: 1px solid red;
+}
QTabBar::tab {
border-top-left-radius: 2px;
border-top-right-radius: 2px;
@@ -48,6 +51,13 @@ QPushButton:disabled {
background-color: #474747;
color: #8e8e8e;
}
+QCheckBox::indicator:disabled {
+ background-color: #8e8e8e;
+}
+QLabel:disabled,
+QCheckBox:disabled {
+ color: #8e8e8e;
+}
QLabel,
QCheckBox {
background-color: transparent;
diff --git a/ChemFlow/src/GUI/qt_creator/UImainwindow.py b/ChemFlow/src/GUI/qt_creator/UImainwindow.py
index 6ff0125..f65bf10 100644
--- a/ChemFlow/src/GUI/qt_creator/UImainwindow.py
+++ b/ChemFlow/src/GUI/qt_creator/UImainwindow.py
@@ -32,6 +32,145 @@ def setupUi(self, MainWindow):
self.tabWidget = QtWidgets.QTabWidget(self.centralWidget)
self.tabWidget.setGeometry(QtCore.QRect(10, 70, 641, 423))
self.tabWidget.setObjectName("tabWidget")
+ self.tab_Smiles = QtWidgets.QWidget()
+ self.tab_Smiles.setObjectName("tab_Smiles")
+ self.label_9 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_9.setGeometry(QtCore.QRect(11, 95, 67, 17))
+ self.label_9.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+ self.label_9.setObjectName("label_9")
+ self.comboBox_method = QtWidgets.QComboBox(self.tab_Smiles)
+ self.comboBox_method.setGeometry(QtCore.QRect(90, 228, 85, 27))
+ self.comboBox_method.setObjectName("comboBox_method")
+ self.comboBox_method.addItem("")
+ self.comboBox_method.addItem("")
+ self.comboBox_method.addItem("")
+ self.checkBox_verbose = QtWidgets.QCheckBox(self.tab_Smiles)
+ self.checkBox_verbose.setGeometry(QtCore.QRect(349, 194, 151, 22))
+ self.checkBox_verbose.setObjectName("checkBox_verbose")
+ self.spinBox_smiles_col = QtWidgets.QSpinBox(self.tab_Smiles)
+ self.spinBox_smiles_col.setGeometry(QtCore.QRect(158, 57, 48, 27))
+ self.spinBox_smiles_col.setMinimum(1)
+ self.spinBox_smiles_col.setProperty("value", 1)
+ self.spinBox_smiles_col.setObjectName("spinBox_smiles_col")
+ self.comboBox_delimiter = QtWidgets.QComboBox(self.tab_Smiles)
+ self.comboBox_delimiter.setGeometry(QtCore.QRect(90, 89, 85, 27))
+ self.comboBox_delimiter.setObjectName("comboBox_delimiter")
+ self.comboBox_delimiter.addItem("")
+ self.comboBox_delimiter.addItem("")
+ self.comboBox_delimiter.addItem("")
+ self.comboBox_delimiter.addItem("")
+ self.comboBox_delimiter.addItem("")
+ self.label_10 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_10.setGeometry(QtCore.QRect(94, 288, 91, 20))
+ self.label_10.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
+ self.label_10.setObjectName("label_10")
+ self.checkBox_mpi = QtWidgets.QCheckBox(self.tab_Smiles)
+ self.checkBox_mpi.setGeometry(QtCore.QRect(349, 289, 131, 22))
+ self.checkBox_mpi.setObjectName("checkBox_mpi")
+ self.lineEdit_smiles_input = QtWidgets.QLineEdit(self.tab_Smiles)
+ self.lineEdit_smiles_input.setGeometry(QtCore.QRect(92, 30, 441, 21))
+ font = QtGui.QFont()
+ font.setPointSize(9)
+ self.lineEdit_smiles_input.setFont(font)
+ self.lineEdit_smiles_input.setObjectName("lineEdit_smiles_input")
+ self.checkBox_header = QtWidgets.QCheckBox(self.tab_Smiles)
+ self.checkBox_header.setGeometry(QtCore.QRect(90, 120, 171, 22))
+ self.checkBox_header.setObjectName("checkBox_header")
+ self.checkBox_hydrogen = QtWidgets.QCheckBox(self.tab_Smiles)
+ self.checkBox_hydrogen.setGeometry(QtCore.QRect(90, 194, 221, 22))
+ self.checkBox_hydrogen.setObjectName("checkBox_hydrogen")
+ self.spinBox_names_col = QtWidgets.QSpinBox(self.tab_Smiles)
+ self.spinBox_names_col.setGeometry(QtCore.QRect(300, 57, 48, 27))
+ self.spinBox_names_col.setMinimum(1)
+ self.spinBox_names_col.setProperty("value", 2)
+ self.spinBox_names_col.setObjectName("spinBox_names_col")
+ self.label_rec_2 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_rec_2.setGeometry(QtCore.QRect(13, 10, 51, 17))
+ font = QtGui.QFont()
+ font.setBold(True)
+ font.setWeight(75)
+ self.label_rec_2.setFont(font)
+ self.label_rec_2.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
+ self.label_rec_2.setObjectName("label_rec_2")
+ self.label_11 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_11.setGeometry(QtCore.QRect(11, 32, 67, 17))
+ self.label_11.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+ self.label_11.setObjectName("label_11")
+ self.label_12 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_12.setGeometry(QtCore.QRect(13, 261, 81, 17))
+ font = QtGui.QFont()
+ font.setBold(True)
+ font.setWeight(75)
+ self.label_12.setFont(font)
+ self.label_12.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
+ self.label_12.setObjectName("label_12")
+ self.spinBox_nthreads = QtWidgets.QSpinBox(self.tab_Smiles)
+ self.spinBox_nthreads.setGeometry(QtCore.QRect(190, 284, 48, 27))
+ self.spinBox_nthreads.setMinimum(1)
+ self.spinBox_nthreads.setProperty("value", 1)
+ self.spinBox_nthreads.setObjectName("spinBox_nthreads")
+ self.label_18 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_18.setGeometry(QtCore.QRect(246, 60, 51, 20))
+ font = QtGui.QFont()
+ font.setItalic(True)
+ self.label_18.setFont(font)
+ self.label_18.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
+ self.label_18.setObjectName("label_18")
+ self.pushButton_smiles_input = QtWidgets.QPushButton(self.tab_Smiles)
+ self.pushButton_smiles_input.setGeometry(QtCore.QRect(538, 29, 91, 23))
+ self.pushButton_smiles_input.setObjectName("pushButton_smiles_input")
+ self.label_19 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_19.setGeometry(QtCore.QRect(13, 143, 67, 17))
+ font = QtGui.QFont()
+ font.setBold(True)
+ font.setWeight(75)
+ self.label_19.setFont(font)
+ self.label_19.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
+ self.label_19.setObjectName("label_19")
+ self.label_20 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_20.setGeometry(QtCore.QRect(13, 234, 71, 17))
+ font = QtGui.QFont()
+ font.setBold(True)
+ font.setWeight(75)
+ self.label_20.setFont(font)
+ self.label_20.setObjectName("label_20")
+ self.lineEdit_smiles_output = QtWidgets.QLineEdit(self.tab_Smiles)
+ self.lineEdit_smiles_output.setGeometry(QtCore.QRect(92, 165, 391, 21))
+ font = QtGui.QFont()
+ font.setPointSize(9)
+ self.lineEdit_smiles_output.setFont(font)
+ self.lineEdit_smiles_output.setObjectName("lineEdit_smiles_output")
+ self.label_21 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_21.setGeometry(QtCore.QRect(10, 169, 67, 17))
+ self.label_21.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+ self.label_21.setObjectName("label_21")
+ self.label_22 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_22.setGeometry(QtCore.QRect(-33, 60, 111, 20))
+ self.label_22.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+ self.label_22.setObjectName("label_22")
+ self.line_6 = QtWidgets.QFrame(self.tab_Smiles)
+ self.line_6.setGeometry(QtCore.QRect(0, 320, 640, 3))
+ self.line_6.setFrameShadow(QtWidgets.QFrame.Sunken)
+ self.line_6.setFrameShape(QtWidgets.QFrame.HLine)
+ self.line_6.setObjectName("line_6")
+ self.commandLinkButton_smiles_run = QtWidgets.QCommandLinkButton(self.tab_Smiles)
+ self.commandLinkButton_smiles_run.setGeometry(QtCore.QRect(230, 330, 181, 51))
+ font = QtGui.QFont()
+ font.setPointSize(14)
+ self.commandLinkButton_smiles_run.setFont(font)
+ icon = QtGui.QIcon()
+ icon.addPixmap(QtGui.QPixmap("../img/run.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
+ self.commandLinkButton_smiles_run.setIcon(icon)
+ self.commandLinkButton_smiles_run.setIconSize(QtCore.QSize(36, 36))
+ self.commandLinkButton_smiles_run.setObjectName("commandLinkButton_smiles_run")
+ self.label_23 = QtWidgets.QLabel(self.tab_Smiles)
+ self.label_23.setGeometry(QtCore.QRect(94, 62, 61, 17))
+ font = QtGui.QFont()
+ font.setItalic(True)
+ self.label_23.setFont(font)
+ self.label_23.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
+ self.label_23.setObjectName("label_23")
+ self.tabWidget.addTab(self.tab_Smiles, "")
self.tab_LigFlow = QtWidgets.QWidget()
self.tab_LigFlow.setObjectName("tab_LigFlow")
self.pushButton_ligflow_lig = QtWidgets.QPushButton(self.tab_LigFlow)
@@ -96,8 +235,6 @@ def setupUi(self, MainWindow):
font = QtGui.QFont()
font.setPointSize(14)
self.commandLinkButton_ligflow_run.setFont(font)
- icon = QtGui.QIcon()
- icon.addPixmap(QtGui.QPixmap("../img/run.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.commandLinkButton_ligflow_run.setIcon(icon)
self.commandLinkButton_ligflow_run.setIconSize(QtCore.QSize(36, 36))
self.commandLinkButton_ligflow_run.setObjectName("commandLinkButton_ligflow_run")
@@ -397,7 +534,6 @@ def setupUi(self, MainWindow):
self.comboBox_tools.setFrame(True)
self.comboBox_tools.setObjectName("comboBox_tools")
self.comboBox_tools.addItem("")
- self.comboBox_tools.addItem("")
self.label_tools_description = QtWidgets.QLabel(self.tab_Tools)
self.label_tools_description.setGeometry(QtCore.QRect(20, 94, 595, 211))
self.label_tools_description.setText("")
@@ -457,6 +593,7 @@ def setupUi(self, MainWindow):
MainWindow.setCentralWidget(self.centralWidget)
self.menuBar = QtWidgets.QMenuBar(MainWindow)
self.menuBar.setGeometry(QtCore.QRect(0, 0, 662, 25))
+ self.menuBar.setNativeMenuBar(False)
self.menuBar.setObjectName("menuBar")
self.menuProject = QtWidgets.QMenu(self.menuBar)
self.menuProject.setObjectName("menuProject")
@@ -492,13 +629,16 @@ def setupUi(self, MainWindow):
self.actionDefault_theme.setObjectName("actionDefault_theme")
self.actionDark_theme = QtWidgets.QAction(MainWindow)
self.actionDark_theme.setObjectName("actionDark_theme")
+ self.actionDocumentation = QtWidgets.QAction(MainWindow)
+ self.actionDocumentation.setObjectName("actionDocumentation")
self.menuProject.addAction(self.actionNew_project)
self.menuProject.addAction(self.actionLoad_project)
self.menuProject.addSeparator()
self.menuProject.addAction(self.actionExit)
+ self.menuHelp.addAction(self.actionDocumentation)
+ self.menuHelp.addAction(self.actionTutorial)
self.menuHelp.addAction(self.actionGitHub)
self.menuHelp.addAction(self.actionReport_issue)
- self.menuHelp.addAction(self.actionTutorial)
self.menuHelp.addSeparator()
self.menuHelp.addAction(self.actionDebug_mode)
self.menuHelp.addAction(self.actionLogfile)
@@ -516,7 +656,20 @@ def setupUi(self, MainWindow):
self.tabWidget.setCurrentIndex(0)
self.comboBox_tools.setCurrentIndex(-1)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
- MainWindow.setTabOrder(self.tabWidget, self.lineEdit_ligflow_lig)
+ MainWindow.setTabOrder(self.tabWidget, self.lineEdit_smiles_input)
+ MainWindow.setTabOrder(self.lineEdit_smiles_input, self.pushButton_smiles_input)
+ MainWindow.setTabOrder(self.pushButton_smiles_input, self.spinBox_smiles_col)
+ MainWindow.setTabOrder(self.spinBox_smiles_col, self.spinBox_names_col)
+ MainWindow.setTabOrder(self.spinBox_names_col, self.comboBox_delimiter)
+ MainWindow.setTabOrder(self.comboBox_delimiter, self.checkBox_header)
+ MainWindow.setTabOrder(self.checkBox_header, self.lineEdit_smiles_output)
+ MainWindow.setTabOrder(self.lineEdit_smiles_output, self.checkBox_hydrogen)
+ MainWindow.setTabOrder(self.checkBox_hydrogen, self.checkBox_verbose)
+ MainWindow.setTabOrder(self.checkBox_verbose, self.comboBox_method)
+ MainWindow.setTabOrder(self.comboBox_method, self.spinBox_nthreads)
+ MainWindow.setTabOrder(self.spinBox_nthreads, self.checkBox_mpi)
+ MainWindow.setTabOrder(self.checkBox_mpi, self.commandLinkButton_smiles_run)
+ MainWindow.setTabOrder(self.commandLinkButton_smiles_run, self.lineEdit_ligflow_lig)
MainWindow.setTabOrder(self.lineEdit_ligflow_lig, self.pushButton_ligflow_lig)
MainWindow.setTabOrder(self.pushButton_ligflow_lig, self.comboBox_charges)
MainWindow.setTabOrder(self.comboBox_charges, self.comboBox_ligflow_job_queue)
@@ -561,6 +714,42 @@ def retranslateUi(self, MainWindow):
_translate = QtCore.QCoreApplication.translate
MainWindow.setWindowTitle(_translate("MainWindow", "ChemFlow"))
self.label_logo_text.setText(_translate("MainWindow", "ChemFlow"))
+ self.label_9.setText(_translate("MainWindow", "Delimiter"))
+ self.comboBox_method.setToolTip(_translate("MainWindow", "