def GenerateMACCS166KeysFingerprints(Mols):
"""Generate MACCS166Keys fingerprints."""
MiscUtil.PrintInfo("\nGenerating MACCS166Keys fingerprints...")
# Generate ExplicitBitVect fingerprints...
MolsFingerprints = [
rdMolDescriptors.GetMACCSKeysFingerprint(Mol) for Mol in Mols
]
return MolsFingerprints
def SetupContoursInfo():
"""Setup contour info for generating contour plots."""
MiscUtil.PrintInfo(
"\nProcessing phi and psi densities for contour plots...")
OptionsInfo["PlotTypesInfo"]["PhiPsiContourInfo"] = {}
for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
PhiPsiContourInfo = SetupPhiAndPsiContourInfo(PlotType)
OptionsInfo["PlotTypesInfo"]["PhiPsiContourInfo"][
PlotType] = PhiPsiContourInfo
def ProcessMoleculesUsingSingleProcess(Mols, GroupsPatternMols, Writer,
GroupOutfilesWriters):
"""Process and search molecules using a single process."""
MiscUtil.PrintInfo("\nSearching functional groups...")
Compute2DCoords = OptionsInfo["OutfileParams"]["Compute2DCoords"]
CombineMatchResults = OptionsInfo["CombineMatchResults"]
SetSMILESMolProps = OptionsInfo["OutfileParams"]["SetSMILESMolProps"]
GroupsPatternsMatchCountList = [0] * len(
OptionsInfo["SpecifiedFunctionalGroups"])
(MolCount, ValidMolCount, RemainingMolCount) = [0] * 3
FirstMol = True
for Mol in Mols:
MolCount += 1
if Mol is None:
continue
if RDKitUtil.IsMolEmpty(Mol):
MolName = RDKitUtil.GetMolName(Mol, MolCount)
MiscUtil.PrintWarning("Ignoring empty molecule: %s" % MolName)
continue
ValidMolCount += 1
if FirstMol:
FirstMol = False
if SetSMILESMolProps:
if Writer is not None:
RDKitUtil.SetWriterMolProps(Writer, Mol)
for GroupOutfileWriter in GroupOutfilesWriters:
if GroupOutfileWriter is not None:
RDKitUtil.SetWriterMolProps(GroupOutfileWriter, Mol)
# Match molecule against functional group patterns...
MolMatched, GroupsPatternMatchStatusList = MatchMolecule(
Mol, GroupsPatternMols)
# Update functional group match count...
for GroupIndex, MatchStatus in enumerate(GroupsPatternMatchStatusList):
if MatchStatus:
GroupsPatternsMatchCountList[GroupIndex] += 1
if not MolMatched:
continue
RemainingMolCount += 1
WriteMolecule(Writer, GroupOutfilesWriters, Mol, Compute2DCoords,
CombineMatchResults, GroupsPatternMatchStatusList)
return (MolCount, ValidMolCount, RemainingMolCount,
GroupsPatternsMatchCountList)
def RemoveSalts():
"""Identify and remove salts from molecules"""
# Setup a molecule reader...
MiscUtil.PrintInfo("\nProcessing file %s..." % OptionsInfo["Infile"])
Mols = RDKitUtil.ReadMolecules(OptionsInfo["Infile"], **OptionsInfo["InfileParams"])
# Set up a molecule writer...
Writer = SetupMoleculeWriter()
MolCount, ValidMolCount, SaltsMolCount = ProcessMolecules(Mols, Writer)
if Writer is not None:
Writer.close()
MiscUtil.PrintInfo("\nTotal number of molecules: %d" % MolCount)
MiscUtil.PrintInfo("Number of valid molecules: %d" % ValidMolCount)
MiscUtil.PrintInfo("Number of ignored molecules: %d" % (MolCount - ValidMolCount))
MiscUtil.PrintInfo("\nNumber of molecules coontaining salts: %d" % (SaltsMolCount))
def SetupMoleculeWriter():
"""Setup a molecule writer."""
Writer = RDKitUtil.MoleculesWriter(OptionsInfo["Outfile"],
**OptionsInfo["OutfileParams"])
if Writer is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " %
OptionsInfo["Outfile"])
MiscUtil.PrintInfo("Generating file %s..." % OptionsInfo["Outfile"])
return Writer
def PerformMutagenesis():
"""Mutate specified residues across chains and generate an output file."""
MiscUtil.PrintInfo("\nApplying mutations...")
# Load macromolecule from input file...
MolName = OptionsInfo["InfileRoot"]
LoadMolecule(OptionsInfo["Infile"], MolName)
# Apply mutations...
for Mutation, ChainID, ResNum, NewBaseName in OptionsInfo["SpecifiedMutationsInfo"] :
ApplyMutation(Mutation, MolName, ChainID, ResNum, NewBaseName)
# Generate output file...
Outfile = OptionsInfo["Outfile"]
MiscUtil.PrintInfo("\nGenerating output file %s..." % Outfile)
pymol.cmd.save(Outfile, MolName)
# Delete macromolecule...
DeleteMolecule(MolName)
def SetupPAINSPatternMols(PAINSPatterns):
"""Set up PAINS pattern mols for substructure search"""
MiscUtil.PrintInfo(
"\nSetting up PAINS pattern molecules for performins substructure search..."
)
PatternMols = []
for Pattern in PAINSPatterns:
PatternMol = Chem.MolFromSmarts(Pattern)
PatternMols.append(PatternMol)
return PatternMols
def main():
"""Start execution of the script"""
MiscUtil.PrintInfo("\n%s (RDK v%s; %s): Starting...\n" %
(ScriptName, rdBase.rdkitVersion, time.asctime()))
(WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
# Retrieve command line arguments and options...
RetrieveOptions()
# Process and validate command line arguments and options...
ProcessOptions()
# Perform actions required by the script...
PerformFunctionalGroupsSearch()
MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
MiscUtil.PrintInfo(
"Total time: %s" %
MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["CombineMatches"] = Options["--combineMatches"]
OptionsInfo["CombineMatchResults"] = True
if re.match("^No$", Options["--combineMatches"], re.I):
OptionsInfo["CombineMatchResults"] = False
if Options["--outfile"]:
FileDir, FileName, FileExt = MiscUtil.ParseFileName(
Options["--outfile"])
OptionsInfo["OutfileBasename"] = FileName
OptionsInfo["OutfileExt"] = FileExt
OptionsInfo["CombineOperator"] = Options["--combineOperator"]
OptionsInfo["AndCombineOperatorMode"] = True
if re.match("^or$", Options["--combineOperator"], re.I):
OptionsInfo["AndCombineOperatorMode"] = False
OptionsInfo["GroupNamesFile"] = None
if not re.match("^auto$", Options["--groupNamesFile"], re.I):
OptionsInfo["GroupNamesFile"] = Options["--groupNamesFile"]
OptionsInfo["FunctionalGroups"] = Options["--functionalGroups"]
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"], Options["--infile"],
Options["--outfile"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["CountMode"] = False
if re.match("^count$", Options["--mode"], re.I):
OptionsInfo["CountMode"] = True
OptionsInfo["MPMode"] = True if re.match("^yes$", Options["--mp"],
re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters(
"--mpParams", Options["--mpParams"])
OptionsInfo["UseChirality"] = False
if re.match("^yes$", Options["--useChirality"], re.I):
OptionsInfo["UseChirality"] = True
def SetupMoleculeWriters():
"""Setup molecule writers."""
Writer = None
WriterFiltered = None
if OptionsInfo["CountMode"]:
return (Writer, WriterFiltered)
Writer = RDKitUtil.MoleculesWriter(OptionsInfo["Outfile"], **OptionsInfo["OutfileParams"])
if Writer is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " % OptionsInfo["Outfile"])
MiscUtil.PrintInfo("Generating file %s..." % OptionsInfo["Outfile"])
if OptionsInfo["OutfileFilteredMode"]:
WriterFiltered = RDKitUtil.MoleculesWriter(OptionsInfo["OutfileFiltered"], **OptionsInfo["OutfileParams"])
if WriterFiltered is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " % OptionsInfo["OutfileFiltered"])
MiscUtil.PrintInfo("Generating file %s..." % OptionsInfo["OutfileFiltered"])
return (Writer, WriterFiltered)
def PerformCalculations():
"""Calculate descriptors for a specified list of descriptors."""
# Setup a molecule reader...
MiscUtil.PrintInfo("\nProcessing file %s..." % OptionsInfo["Infile"])
Mols = RDKitUtil.ReadMolecules(OptionsInfo["Infile"],
**OptionsInfo["InfileParams"])
# Setup a writer...
Writer = SetupMoleculeWriter()
# Process molecules...
MolCount, ValidMolCount = ProcessMolecules(Mols, Writer)
if Writer is not None:
Writer.close()
MiscUtil.PrintInfo("\nTotal number of molecules: %d" % MolCount)
MiscUtil.PrintInfo("Number of valid molecules: %d" % ValidMolCount)
MiscUtil.PrintInfo("Number of ignored molecules: %d" %
(MolCount - ValidMolCount))
def InitializeWorkerProcess(*EncodedArgs):
"""Initialize data for a worker process."""
global Options, OptionsInfo
MiscUtil.PrintInfo("Starting process (PID: %s)..." % os.getpid())
# Decode Options and OptionInfo...
Options = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[0])
OptionsInfo = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[1])
RetrieveMolecularDescriptorsInfo(PrintInfo=False)
def PerformSearch():
"""Perform search using specified SMARTS pattern."""
# Set up a pattern molecule...
PatternMol = Chem.MolFromSmarts(OptionsInfo["Pattern"])
# Setup a molecule reader...
MiscUtil.PrintInfo("\nProcessing file %s..." % OptionsInfo["Infile"])
Mols = RDKitUtil.ReadMolecules(OptionsInfo["Infile"],
**OptionsInfo["InfileParams"])
# Set up molecule writers...
Writer, WriterFiltered = SetupMoleculeWriters()
MolCount, ValidMolCount, RemainingMolCount = ProcessMolecules(
Mols, PatternMol, Writer, WriterFiltered)
if Writer is not None:
Writer.close()
if WriterFiltered is not None:
WriterFiltered.close()
MiscUtil.PrintInfo("\nTotal number of molecules: %d" % MolCount)
MiscUtil.PrintInfo("Number of valid molecules: %d" % ValidMolCount)
MiscUtil.PrintInfo("Number of ignored molecules: %d" %
(MolCount - ValidMolCount))
MiscUtil.PrintInfo("\nNumber of remaining molecules: %d" %
RemainingMolCount)
MiscUtil.PrintInfo("Number of filtered molecules: %d" %
(ValidMolCount - RemainingMolCount))
def ListSelectionResiduesInfo(MolName, ChainIDs, SelectionType):
"""List residues information for a specified selection type. """
Lines = []
TotalResCount = 0
SelectionLabel = None
if not len(ChainIDs):
SelectionInfo, SelectionLabel = GetSelectionResiduesInfo(
MolName, None, SelectionType)
MiscUtil.PrintInfo("\nNumber of %s residues: %s" %
(SelectionLabel, TotalResCount))
return
for ChainID in ChainIDs:
SelectionInfo, SelectionLabel = GetSelectionResiduesInfo(
MolName, ChainID, SelectionType)
ChainResCount = 0
LineWords = []
SortedResNames = sorted(
SelectionInfo["ResNames"],
key=lambda ResName: SelectionInfo["ResCount"][ResName],
reverse=True)
for ResName in SortedResNames:
ResCount = SelectionInfo["ResCount"][ResName]
LineWords.append("%s - %s" % (ResName, ResCount))
ChainResCount += ResCount
TotalResCount += ResCount
Line = "; ".join(LineWords) if len(LineWords) else None
Lines.append("Chain ID: %s; Count: %s; Names: %s" %
(ChainID, ChainResCount, Line))
MiscUtil.PrintInfo("\nNumber of %s residues: %s" %
(SelectionLabel, TotalResCount))
for Line in Lines:
MiscUtil.PrintInfo("%s" % Line)
def GenerateConformers():
"""Generate conformers."""
# Setup a molecule reader...
MiscUtil.PrintInfo("\nProcessing file %s..." % OptionsInfo["Infile"])
Mols = RDKitUtil.ReadMolecules(OptionsInfo["Infile"],
**OptionsInfo["InfileParams"])
# Set up a molecule writer...
Writer = RDKitUtil.MoleculesWriter(OptionsInfo["Outfile"],
**OptionsInfo["OutfileParams"])
if Writer is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " %
OptionsInfo["Outfile"])
MiscUtil.PrintInfo("Generating file %s..." % OptionsInfo["Outfile"])
MolCount, ValidMolCount, ConfGenFailedCount = ProcessMolecules(
Mols, Writer)
if Writer is not None:
Writer.close()
MiscUtil.PrintInfo("\nTotal number of molecules: %d" % MolCount)
MiscUtil.PrintInfo("Number of valid molecules: %d" % ValidMolCount)
MiscUtil.PrintInfo(
"Number of molecules failed during conformation generation or minimization: %d"
% ConfGenFailedCount)
MiscUtil.PrintInfo("Number of ignored molecules: %d" %
(MolCount - ValidMolCount + ConfGenFailedCount))
def CalculateEnergy():
"""Calculate single point energy calculation."""
# Setup a molecule reader...
MiscUtil.PrintInfo("\nProcessing file %s..." % OptionsInfo["Infile"])
Mols = RDKitUtil.ReadMolecules(OptionsInfo["Infile"],
**OptionsInfo["InfileParams"])
# Set up a molecule writer...
Writer = RDKitUtil.MoleculesWriter(OptionsInfo["Outfile"],
**OptionsInfo["OutfileParams"])
if Writer is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " %
OptionsInfo["Outfile"])
MiscUtil.PrintInfo("Generating file %s..." % OptionsInfo["Outfile"])
MolCount, ValidMolCount, EnergyFailedCount = ProcessMolecules(Mols, Writer)
if Writer is not None:
Writer.close()
MiscUtil.PrintInfo("\nTotal number of molecules: %d" % MolCount)
MiscUtil.PrintInfo("Number of valid molecules: %d" % ValidMolCount)
MiscUtil.PrintInfo(
"Number of molecules failed during energy calculation: %d" %
EnergyFailedCount)
MiscUtil.PrintInfo("Number of ignored molecules: %d" %
(MolCount - ValidMolCount + EnergyFailedCount))
def WriteAlignedInputObject(FileIndex):
"""Write out aligned input object"""
Outfile = OptionsInfo["InfilesInfo"]["OutfilesNames"][FileIndex]
InputName = OptionsInfo["InfilesInfo"]["PyMOLObjectNames"][FileIndex]
MiscUtil.PrintInfo("Generating aligned output file %s..." % Outfile)
pymol.cmd.save(Outfile, InputName)
if not os.path.exists(Outfile):
MiscUtil.PrintWarning("Failed to generate aligned output file, %s..." %
(Outfile))
def ListBoundingBoxInfo(MolName):
"""List bounding box information. """
if not (OptionsInfo["All"] or OptionsInfo["BoundingBox"]):
return
MolSelection = "(%s)" % MolName
MolExtents = pymol.cmd.get_extent(MolSelection)
XMin, YMin, ZMin = MolExtents[0]
XMax, YMax, ZMax = MolExtents[1]
XSize = abs(XMax - XMin)
YSize = abs(YMax - YMin)
ZSize = abs(ZMax - ZMin)
MiscUtil.PrintInfo(
"\nBounding box coordinates: <XMin, XMax> - <%.3f, %.3f>; <YMin, YMax> - <%.3f, %.3f>; <ZMin, ZMax> - <%.3f, %.3f>"
% (XMin, XMax, YMin, YMax, ZMin, ZMax))
MiscUtil.PrintInfo(
"Bounding box size in Angstroms: XSize - %.3f; YSize - %.3f; ZSize - %.3f"
% (XSize, YSize, ZSize))
def ListHeaderInfo(Infile):
"""List header information."""
if not (OptionsInfo["All"] or OptionsInfo["Header"]):
return
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = [
"Not Available"
] * 5
if re.match("^pdb$", FileExt, re.I):
Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = RetriveHeadAndExperimentalInfoFromPDBFile(
Infile)
elif re.match("^cif$", FileExt, re.I):
Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = RetriveHeadAndExperimentalInfoFromCIFFile(
Infile)
MiscUtil.PrintInfo("\nID: %s\nClassification: %s\nDeposition date: %s" %
(IDCode, Classification, DepositionDate))
MiscUtil.PrintInfo("\nExperimental technique: %s\nResolution: %s" %
(ExperimentalTechnique, Resolution))
def InitializeWorkerProcess(*EncodedArgs):
"""Initialize data for a worker process."""
global Options, OptionsInfo
MiscUtil.PrintInfo("Starting process (PID: %s)..." % os.getpid())
# Decode Options and OptionInfo...
Options = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[0])
OptionsInfo = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[1])
# Set up salt remover...
OptionsInfo["SaltRemover"] = SetupSaltRemover()
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Feedback"] = True if re.match("^Yes$", Options["--feedback"],
re.I) else False
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["Outfile"] = Options["--outfile"]
def InitializeWorkerProcess(*EncodedArgs):
"""Initialize data for a worker process."""
global Options, OptionsInfo
MiscUtil.PrintInfo("Starting process (PID: %s)..." % os.getpid())
# Decode Options and OptionInfo...
Options = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[0])
OptionsInfo = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[1])
# Decode ChEMBLPatternMols...
OptionsInfo["ChEMBLPatternMols"] = [RDKitUtil.MolFromBase64EncodedMolString(EncodedMol) for EncodedMol in OptionsInfo["EncodedChEMBLPatternMols"]]
def ListInterfaceChainsAndResiduesInfo(InterfaceID, InterfaceChainIDs,
ChainNames, ResiduesInfo):
"""List interface chains and residues. """
for ChainID in InterfaceChainIDs:
if not ChainID in ChainNames:
MiscUtil.PrintInfo(
"\nInterface chain IDs: %s; ChainID: %s; Number of interface residues: 0"
% (InterfaceID, ChainID))
continue
for Index in range(0, len(ChainNames)):
ChainName = ChainNames[Index]
ChainResiduesInfo = ResiduesInfo[Index]
if re.match(ChainID, ChainName, re.I):
MiscUtil.PrintInfo(
"\nInterface chain IDs: %s; ChainID: %s; Number of interface residues: %d"
% (InterfaceID, ChainName, ChainResiduesInfo[0]))
MiscUtil.PrintInfo(
"Residue distribution: %s\nResidue IDs: %s" %
(ChainResiduesInfo[1], ChainResiduesInfo[2]))
continue
def RetrieveChainsIDs():
"""Retrieve chain IDs. """
MolName = OptionsInfo["InfileRoot"]
Infile = OptionsInfo["Infile"]
MiscUtil.PrintInfo("\nRetrieving chains information for input file %s..." % Infile)
LoadMolecule(Infile, MolName)
ChainIDs = PyMOLUtil.GetChains(MolName)
DeleteMolecule(MolName)
if ChainIDs is None:
ChainIDs = []
# Print out chain and ligand IDs...
ChainInfo = ", ".join(ChainIDs) if len(ChainIDs) else "None"
MiscUtil.PrintInfo("Chain IDs: %s" % ChainInfo)
OptionsInfo["ChainIDs"] = ChainIDs
def ConvertLigandFileFormat():
"""Comvert ligand file format."""
Infile = OptionsInfo["Infile"]
Outfile = OptionsInfo["Outfile"]
MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
PyMOLUtil.ConvertFileFormat(Infile, Outfile)
if not os.path.exists(Outfile):
MiscUtil.PrintWarning("Failed to generate Outfile file, %s..." %
(Outfile))
def main():
"""Start execution of the script"""
MiscUtil.PrintInfo(
"\n%s (PyMOL v%s; %s) Starting...\n" %
(ScriptName, pymol.cmd.get_version()[1], time.asctime()))
(WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
# Retrieve command line arguments and options...
RetrieveOptions()
# Process and validate command line arguments and options...
ProcessOptions()
# Perform actions required by the script...
SplitChainsAndLigands()
MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
MiscUtil.PrintInfo(
"Total time: %s" %
MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
def InitializeWorkerProcess(*EncodedArgs):
"""Initialize data for a worker process."""
global Options, OptionsInfo
MiscUtil.PrintInfo("Starting process (PID: %s)..." % os.getpid())
# Decode Options and OptionInfo...
Options = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[0])
OptionsInfo = MiscUtil.ObjectFromBase64EncodedString(EncodedArgs[1])
# Decode RefMol...
OptionsInfo["RefMol"] = RDKitUtil.MolFromBase64EncodedMolString(OptionsInfo["EncodedRefMol"])
def RetrieveChEMBLFiltersInfo():
"""Retrieve information for ChEMBL filters."""
MayaChemToolsDataDir = MiscUtil.GetMayaChemToolsLibDataPath()
ChEMBLFiltersFilePath = os.path.join(MayaChemToolsDataDir, "ChEMBLFilters.csv")
MiscUtil.PrintInfo("\nRetrieving ChEMBL alerts SMARTS patterns from file %s" % (ChEMBLFiltersFilePath))
Delimiter = ','
QuoteChar = '"'
IgnoreHeaderLine = True
FilterLinesWords = MiscUtil.GetTextLinesWords(ChEMBLFiltersFilePath, Delimiter, QuoteChar, IgnoreHeaderLine)
ChEMBLFiltersMap = {}
ChEMBLFiltersMap["FilterTypes"] = []
ChEMBLFiltersMap["ID"] = {}
ChEMBLFiltersMap["SMARTS"] = {}
for LineWords in FilterLinesWords:
FilterType = LineWords[0]
ID = LineWords[1]
SMARTS = LineWords[2]
if not FilterType in ChEMBLFiltersMap["FilterTypes"]:
ChEMBLFiltersMap["FilterTypes"].append(FilterType)
ChEMBLFiltersMap["ID"][FilterType] = []
ChEMBLFiltersMap["SMARTS"][FilterType] = []
ChEMBLFiltersMap["ID"][FilterType].append(ID)
ChEMBLFiltersMap["SMARTS"][FilterType].append(SMARTS)
OptionsInfo["ChEMBLFiltersMap"] = ChEMBLFiltersMap
MiscUtil.PrintInfo("\nTotal number alerts: %d" % len(FilterLinesWords))
MiscUtil.PrintInfo("Number of filter family types: %d\nFilter familty types: %s\n" % (len(ChEMBLFiltersMap["FilterTypes"]), ", ".join(ChEMBLFiltersMap["FilterTypes"])))
for FilterType in ChEMBLFiltersMap["FilterTypes"]:
MiscUtil.PrintInfo("Filter family type: %s; Number of alerts: %d" % (FilterType, len(ChEMBLFiltersMap["ID"][FilterType])))
MiscUtil.PrintInfo("")
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
if re.match("^UFF$", Options["--forceField"], re.I):
ForceField = "UFF"
UseUFF = True
UseMMFF = False
elif re.match("^MMFF$", Options["--forceField"], re.I):
ForceField = "MMFF"
UseUFF = False
UseMMFF = True
else:
MiscUtil.PrintError(
"The value, %s, specified for \"--forceField\" is not supported." %
(Options["--forceField"], ))
MMFFVariant = "MMFF94" if re.match(
"^MMFF94$", Options["--forceFieldMMFFVariant"], re.I) else "MMFF94s"
OptionsInfo["ForceField"] = ForceField
OptionsInfo["MMFFVariant"] = MMFFVariant
OptionsInfo["UseMMFF"] = UseMMFF
OptionsInfo["UseUFF"] = UseUFF
if UseMMFF:
OptionsInfo["EnergyLabel"] = "%s_Energy" % MMFFVariant
else:
OptionsInfo["EnergyLabel"] = "%s_Energy" % ForceField
OptionsInfo["MPMode"] = True if re.match("^yes$", Options["--mp"],
re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters(
"--mpParams", Options["--mpParams"])
OptionsInfo["QuietMode"] = True if re.match("^yes$", Options["--quiet"],
re.I) else False
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Autocorr2DExclude"] = True
if not re.match("^Yes$", Options["--autocorr2DExclude"], re.I):
OptionsInfo["Autocorr2DExclude"] = False
OptionsInfo["FragmentCount"] = True
if not re.match("^Yes$", Options["--fragmentCount"], re.I):
OptionsInfo["FragmentCount"] = False
OptionsInfo["DescriptorNames"] = Options["--descriptorNames"]
OptionsInfo["Mode"] = Options["--mode"]
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"], Options["--infile"],
Options["--outfile"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
TextOutFileMode = False
TextOutFileDelim = ""
if MiscUtil.CheckFileExt(Options["--outfile"], "csv"):
TextOutFileMode = True
TextOutFileDelim = ","
elif MiscUtil.CheckFileExt(Options["--outfile"], "tsv txt"):
TextOutFileMode = True
TextOutFileDelim = "\t"
OptionsInfo["TextOutFileMode"] = TextOutFileMode
OptionsInfo["TextOutFileDelim"] = TextOutFileDelim
OptionsInfo["MPMode"] = True if re.match("^yes$", Options["--mp"],
re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters(
"--mpParams", Options["--mpParams"])
OptionsInfo["Precision"] = int(Options["--precision"])
OptionsInfo["SMILESOut"] = False
if re.match("^Yes$", Options["--smilesOut"], re.I):
OptionsInfo["SMILESOut"] = True
