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"], Options["--infile"], Options["--outfile"])
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Options["--outfile"])
OutfileFiltered = "%s_Filtered.%s" % (FileName, FileExt)
OptionsInfo["OutfileFiltered"] = OutfileFiltered
OptionsInfo["OutfileFilteredMode"] = True if re.match("^yes$", Options["--outfileFiltered"], re.I) else False
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["CountMode"] = True if re.match("^count$", Options["--mode"], re.I) else False
OptionsInfo["NegateMatch"] = True if re.match("^yes$", Options["--negate"], re.I) else False
OptionsInfo["MPMode"] = True if re.match("^yes$", Options["--mp"], re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters("--mpParams", Options["--mpParams"])
OptionsInfo["AlertsMode"] = Options["--alertsMode"]
ProcessChEMBLAlertsMode()
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"], Options["--infile"], Options["--outfile"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["CountMode"] = False
if re.match("^count$", Options["--mode"], re.I):
OptionsInfo["CountMode"] = True
# Setup outfile for writing out duplicates...
OptionsInfo["DuplicatesOutfile"] = ""
if not OptionsInfo["CountMode"] :
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
OptionsInfo["DuplicatesOutfile"] = "%sDuplicates.%s" % (FileName, FileExt)
OptionsInfo["UseChirality"] = False
if re.match("^yes$", Options["--useChirality"], re.I):
OptionsInfo["UseChirality"] = True
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["DiscardNonPhysical"] = True
if re.match("^no$", Options["--discardNonPhysical"], re.I):
OptionsInfo["DiscardNonPhysical"] = False
OptionsInfo["Mode"] = Options["--mode"]
UnassignedOnly = True
if re.match("^All$", Options["--mode"], re.I):
UnassignedOnly = False
OptionsInfo["UnassignedOnly"] = UnassignedOnly
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["MaxIsomers"] = int(Options["--maxIsomers"])
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"], Options["--infile"],
Options["--outfile"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["CountMode"] = False
if re.match("^count$", Options["--mode"], re.I):
OptionsInfo["CountMode"] = True
OptionsInfo["NegateMatch"] = False
if re.match("^yes$", Options["--negate"], re.I):
OptionsInfo["NegateMatch"] = True
OptionsInfo["PAINSMode"] = Options["--painsMode"]
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"], Options["--infile"],
Options["--outfile"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["CountMode"] = True if re.match("^count$", Options["--mode"],
re.I) else False
# Setup outfile for writing out molecule number for invalid molecules...
OptionsInfo["InvalidMolsOutfile"] = ""
if not OptionsInfo["CountMode"]:
FileDir, FileName, FileExt = MiscUtil.ParseFileName(
OptionsInfo["Outfile"])
OptionsInfo["InvalidMolsOutfile"] = "%sInvalidMols.csv" % (FileName)
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Mode"] = Options["--mode"]
OptionsInfo["Fingerprints"] = Options["--fingerprints"]
OptionsInfo["ClusteringMethod"] = Options["--clusteringMethod"]
ProcessClusteringMethodParameter()
OptionsInfo["NumMols"] = int(Options["--numMols"])
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["SimilarityMetric"] = Options["--similarityMetric"]
ProcessSimilarityMetricParameter()
OptionsInfo["ParamsFingerprints"] = Options["--paramsFingerprints"]
ProcessFingerprintsParameters()
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"], 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$", Options["--mp"], re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters("--mpParams", Options["--mpParams"])
SaltsByComponentsMode = False
SaltsBySMARTSFileMode = False
SaltsBySMARTSMode = False
if re.match("^ByComponent$", Options["--saltsMode"], re.I):
SaltsByComponentsMode = True
elif re.match("^BySMARTSFile$", Options["--saltsMode"], re.I):
SaltsBySMARTSFileMode = False
elif re.match("^BySMARTS$", Options["--saltsMode"], re.I):
SaltsBySMARTSMode = True
else:
MiscUtil.PrintError("The salts mode specified, %s, using \"--saltsMode\" option is not valid." % Options["--saltsMode"])
OptionsInfo["SaltsByComponentsMode"] = SaltsByComponentsMode
OptionsInfo["SaltsBySMARTSFileMode"] = SaltsBySMARTSFileMode
OptionsInfo["SaltsBySMARTSMode"] = SaltsBySMARTSMode
SaltsFile = None
if re.match("^BySMARTSFile$", Options["--saltsMode"], re.I):
if not re.match("^auto$", Options["--saltsFile"], re.I):
SaltsFile = Options["--saltsFile"]
OptionsInfo["SaltsFile"] = SaltsFile
SaltsSMARTS = None
if re.match("^BySMARTS$", Options["--saltsMode"], re.I):
if not Options["--saltsSMARTS"]:
MiscUtil.PrintError("No salts SMARTS pattern specified using \"--saltsSMARTS\" option during \"BySMARTS\" value of \"-s, --saltsMode\" option")
SaltsSMARTS = Options["--saltsSMARTS"].strip(" ")
if not len(SaltsSMARTS):
MiscUtil.PrintError("Empty SMARTS pattern specified using \"--saltsSMARTS\" option during \"BySMARTS\" value of \"-s, --saltsMode\" option")
if re.search(" ", SaltsSMARTS):
SaltsSMARTS = re.sub('[ ]+', '\n', SaltsSMARTS)
OptionsInfo["SaltsSMARTS"] = SaltsSMARTS
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["CombineMatches"] = Options["--combineMatches"]
OptionsInfo["CombineMatchResults"] = True
if re.match("^No$", 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$", Options["--useChirality"], re.I):
OptionsInfo["UseChirality"] = True
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Autocorr2DExclude"] = True
if not re.match("^Yes$", 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$", Options["--smilesOut"], re.I):
OptionsInfo["SMILESOut"] = True
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
if re.match("^UFF$", 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["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["Mode"] = Options["--mode"]
OptionsInfo["UseGraphFrameworks"] = False
if re.match("^GraphFrameworks$", OptionsInfo["Mode"], re.I):
OptionsInfo["UseGraphFrameworks"] = True
OptionsInfo["RemoveDuplicates"] = Options["--removeDuplicates"]
OptionsInfo["RemoveDuplicateFrameworks"] = False
if re.match("^Yes$", OptionsInfo["RemoveDuplicates"], re.I):
OptionsInfo["RemoveDuplicateFrameworks"] = True
# Setup outfile for writing out duplicates...
OptionsInfo["DuplicatesOutfile"] = ""
if OptionsInfo["RemoveDuplicateFrameworks"]:
FileDir, FileName, FileExt = MiscUtil.ParseFileName(
OptionsInfo["Outfile"])
OptionsInfo["DuplicatesOutfile"] = "%sDuplicates.%s" % (FileName,
FileExt)
OptionsInfo["Sort"] = Options["--sort"]
OptionsInfo["SortFrameworks"] = False
if re.match("^Yes$", OptionsInfo["Sort"], re.I):
OptionsInfo["SortFrameworks"] = True
OptionsInfo["SortOrder"] = Options["--sortOrder"]
OptionsInfo["DescendingSortOrder"] = False
if re.match("^Descending$", OptionsInfo["SortOrder"], re.I):
OptionsInfo["DescendingSortOrder"] = True
OptionsInfo["UseChirality"] = False
if re.match("^yes$", Options["--useChirality"], re.I):
OptionsInfo["UseChirality"] = True
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
# Process and setup options for RDKit functions...
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters("--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters("--outfileParams", Options["--outfileParams"], Options["--infile"], Options["--outfile"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
AllowParamFailure = True
if re.match("^No", Options["--allowParamFailure"], re.I):
AllowParamFailure = False
OptionsInfo["AllowParamFailure"] = AllowParamFailure
AtomAliasesFormatMode = True
if re.match("^DataField", Options["--chargesSDFormat"], re.I):
AtomAliasesFormatMode = False
OptionsInfo["AtomAliasesFormatMode"] = AtomAliasesFormatMode
OptionsInfo["DataFieldLabel"] = Options["--dataFieldLabel"]
MMFFChargesMode = False
if re.match("^MMFF", Options["--mode"], re.I):
MMFFChargesMode = True
OptionsInfo["Mode"] = Options["--mode"]
OptionsInfo["MMFFChargesMode"] = MMFFChargesMode
OptionsInfo["MPMode"] = True if re.match("^yes$", Options["--mp"],
re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters(
"--mpParams", Options["--mpParams"])
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["NumIters"] = int(Options["--numIters"])
OptionsInfo["Precision"] = int(Options["--precision"])
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Alignment"] = Options["--alignment"]
OptionsInfo["UseRMSD"] = False
OptionsInfo["UseBestRMSD"] = False
OptionsInfo["UseOpen3A"] = False
OptionsInfo["UseCrippenOpen3A"] = False
# Process alignment
if re.match("^RMSD$", OptionsInfo["Alignment"], re.I):
OptionsInfo["UseRMSD"] = True
elif re.match("^BestRMSD$", OptionsInfo["Alignment"], re.I):
OptionsInfo["UseBestRMSD"] = True
elif re.match("^Open3A$", OptionsInfo["Alignment"], re.I):
OptionsInfo["UseOpen3A"] = True
elif re.match("^CrippenOpen3A$", OptionsInfo["Alignment"], re.I):
OptionsInfo["UseCrippenOpen3A"] = True
OptionsInfo["MaxIters"] = int(Options["--maxIters"])
OptionsInfo["Mode"] = Options["--mode"]
OptionsInfo["RefFile"] = Options["--reffile"]
OptionsInfo["ProbeFile"] = Options["--probefile"]
# No need for any RDKit specific --outfileParams....
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
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"]
OptionsInfo["AddHydrogens"] = True
if re.match("^no$", Options["--addHydrogens"], re.I):
OptionsInfo["AddHydrogens"] = False
OptionsInfo["AlignConformers"] = True
if re.match("^no$", Options["--alignConformers"], re.I):
OptionsInfo["AlignConformers"] = False
if re.match("^ETDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "ETDG"
UseExpTorsionAnglePrefs = True
UseBasicKnowledge = False
elif re.match("^KDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "KDG"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = True
elif re.match("^ETKDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "ETKDG"
UseExpTorsionAnglePrefs = True
UseBasicKnowledge = True
elif re.match("^SDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "SDG"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = False
OptionsInfo["ConformerGenerator"] = ConformerGenerator
OptionsInfo["UseExpTorsionAnglePrefs"] = UseExpTorsionAnglePrefs
OptionsInfo["UseBasicKnowledge"] = UseBasicKnowledge
if re.match("^UFF$", Options["--forceField"], re.I):
ForceField = "UFF"
UseUFF = True
UseMMFF = False
SkipForceFieldMinimization = False
elif re.match("^MMFF$", Options["--forceField"], re.I):
ForceField = "MMFF"
UseUFF = False
UseMMFF = True
SkipForceFieldMinimization = False
else:
ForceField = "None"
UseUFF = False
UseMMFF = False
SkipForceFieldMinimization = True
MMFFVariant = "MMFF94" if re.match(
"^MMFF94$", Options["--forceFieldMMFFVariant"], re.I) else "MMFF94s"
OptionsInfo["SkipForceFieldMinimization"] = SkipForceFieldMinimization
OptionsInfo["ForceField"] = ForceField
OptionsInfo["MMFFVariant"] = MMFFVariant
OptionsInfo["UseMMFF"] = UseMMFF
OptionsInfo["UseUFF"] = UseUFF
OptionsInfo["EnergyOut"] = True if re.match(
"^yes$", Options["--energyOut"], re.I) else False
if UseUFF:
EnergyLabel = "UFF_Energy"
elif UseMMFF:
EnergyLabel = "%s_Energy" % MMFFVariant
else:
EnergyLabel = "Energy"
OptionsInfo["EnergyLabel"] = EnergyLabel
OptionsInfo["EnforceChirality"] = True
if re.match("^no$", Options["--enforceChirality"], re.I):
OptionsInfo["EnforceChirality"] = False
OptionsInfo["EnergyWindow"] = float(Options["--energyWindow"])
EmbedRMSDCutoff = -1.0
if not re.match("^none$", Options["--embedRMSDCutoff"], re.I):
EmbedRMSDCutoff = float(Options["--embedRMSDCutoff"])
OptionsInfo["EmbedRMSDCutoff"] = EmbedRMSDCutoff
EnergyRMSDCutoff = -1.0
if not re.match("^none$", Options["--energyRMSDCutoff"], re.I):
EnergyRMSDCutoff = float(Options["--energyRMSDCutoff"])
OptionsInfo["EnergyRMSDCutoff"] = EnergyRMSDCutoff
OptionsInfo["MaxIters"] = int(Options["--maxIters"])
OptionsInfo["MaxConfs"] = Options["--maxConfs"]
OptionsInfo["MPMode"] = True if re.match("^yes$", Options["--mp"],
re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters(
"--mpParams", Options["--mpParams"])
OptionsInfo["QuietMode"] = True if re.match("^yes$", Options["--quiet"],
re.I) else False
RandomSeed = -1
if not re.match("^auto$", Options["--randomSeed"], re.I):
RandomSeed = int(Options["--randomSeed"])
OptionsInfo["RandomSeed"] = RandomSeed
OptionsInfo["RemoveHydrogens"] = True
if re.match("^no$", Options["--removeHydrogens"], re.I):
OptionsInfo["RemoveHydrogens"] = False
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["AddHydrogens"] = True
if re.match("^no$", Options["--addHydrogens"], re.I):
OptionsInfo["AddHydrogens"] = False
if re.match("^ETDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "ETDG"
UseExpTorsionAnglePrefs = True
UseBasicKnowledge = False
SkipConformerGeneration = False
elif re.match("^KDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "KDG"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = True
SkipConformerGeneration = False
elif re.match("^ETKDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "ETKDG"
UseExpTorsionAnglePrefs = True
UseBasicKnowledge = True
SkipConformerGeneration = False
elif re.match("^SDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "SDG"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = False
SkipConformerGeneration = False
else:
ConformerGenerator = "None"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = False
SkipConformerGeneration = True
OptionsInfo["SkipConformerGeneration"] = SkipConformerGeneration
OptionsInfo["ConformerGenerator"] = ConformerGenerator
OptionsInfo["UseExpTorsionAnglePrefs"] = UseExpTorsionAnglePrefs
OptionsInfo["UseBasicKnowledge"] = UseBasicKnowledge
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
OptionsInfo["ForceField"] = ForceField
OptionsInfo["UseMMFF"] = UseMMFF
OptionsInfo["UseUFF"] = UseUFF
OptionsInfo["EnforceChirality"] = True
if re.match("^no$", Options["--enforceChirality"], re.I):
OptionsInfo["EnforceChirality"] = False
OptionsInfo["MaxIters"] = int(Options["--maxIters"])
OptionsInfo["MaxConfs"] = int(Options["--maxConfs"])
RandomSeed = -1
if not re.match("^auto$", Options["--randomSeed"], re.I):
RandomSeed = int(Options["--randomSeed"])
OptionsInfo["RandomSeed"] = RandomSeed
OptionsInfo["RemoveHydrogens"] = True
if re.match("^no$", Options["--removeHydrogens"], re.I):
OptionsInfo["RemoveHydrogens"] = False
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["ButinaSimilarityCutoff"] = float(Options["--butinaSimilarityCutoff"])
OptionsInfo["ButinaReordering"] = False
if re.match("^Yes$", Options["--butinaReordering"], re.I):
OptionsInfo["ButinaReordering"] = True
OptionsInfo["Fingerprints"] = Options["--fingerprints"]
OptionsInfo["FingerprintsType"] = Options["--fingerprintsType"]
OptionsInfo["ClusteringMethod"] = Options["--clusteringMethod"]
ProcessClusteringMethodParameter()
OptionsInfo["NumClusters"] = int(Options["--numClusters"])
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["OutFileMode"] = Options["--outfileMode"]
SingleOutFileMode = True
if not re.match("^SingleFile$", Options["--outfileMode"], re.I):
SingleOutFileMode = False
OptionsInfo["SingleOutFileMode"] = SingleOutFileMode
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Options["--outfile"])
OptionsInfo["OutfileBasename"] = FileName
OptionsInfo["OutfileExt"] = FileExt
TextOutFileMode = False
TextOutFileDelim = ""
TextOutFileTitleLine = True
if MiscUtil.CheckFileExt(Options["--outfile"], "csv"):
TextOutFileMode = True
TextOutFileDelim = ","
elif MiscUtil.CheckFileExt(Options["--outfile"], "tsv txt"):
TextOutFileMode = True
TextOutFileDelim = "\t"
elif MiscUtil.CheckFileExt(Options["--outfile"], "smi"):
TextOutFileMode = True
TextOutFileDelim = OptionsInfo["OutfileParams"]["SMILESDelimiter"]
TextOutFileTitleLine = OptionsInfo["OutfileParams"]["SMILESTitleLine"]
OptionsInfo["TextOutFileMode"] = TextOutFileMode
OptionsInfo["TextOutFileDelim"] = TextOutFileDelim
OptionsInfo["TextOutFileTitleLine"] = TextOutFileTitleLine
OptionsInfo["SimilarityMetric"] = Options["--similarityMetric"]
ProcessSimilarityMetricParameter()
OptionsInfo["ParamsFingerprints"] = Options["--paramsFingerprints"]
ProcessFingerprintsParameters()
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["CoreScaffold"] = Options["--coreScaffold"]
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"])
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
TextOutQuote = False
if re.match("^auto$", Options["--quote"], re.I):
if MiscUtil.CheckFileExt(Options["--outfile"], "csv"):
TextOutQuote = True
else:
if re.match("^yes$", Options["--quote"], re.I):
TextOutQuote = True
OptionsInfo["TextOutQuote"] = TextOutQuote
OptionsInfo["Overwrite"] = Options["--overwrite"]
RemoveUnmatchedMode = False
UnmatchedOutfile = None
if re.match("^yes$", Options["--removeUnmatched"], re.I):
RemoveUnmatchedMode = True
FileDir, FileName, FileExt = MiscUtil.ParseFileName(
OptionsInfo["Outfile"])
UnmatchedOutfile = "%sUnmatched.%s" % (FileName, FileExt)
OptionsInfo["RemoveUnmatchedMode"] = RemoveUnmatchedMode
OptionsInfo["UnmatchedOutfile"] = UnmatchedOutfile
OptionsInfo["SpecifiedDecompositionParams"] = Options[
"--decompositionParams"]
ProcessDecompositionParameters()
OptionsInfo["SpecifiedMCSParams"] = Options["--mcsParams"]
ProcessMCSParameters()
SMARTSOrSMILESCoreScaffold = ""
SMARTSOrSMILESCoreScaffoldList = []
if not re.match("^none$", Options["--smartsOrSmilesCoreScaffold"],
re.I) or len(Options["--smartsOrSmilesCoreScaffold"]):
if re.match("^(BySMARTS|BySMILES)$", Options["--coreScaffold"], re.I):
SMARTSOrSMILESCoreScaffold = re.sub(
" ", "", Options["--smartsOrSmilesCoreScaffold"])
if not SMARTSOrSMILESCoreScaffold:
MiscUtil.PrintError(
"A non empty value must be specified for \"-s, --smartsOrSmilesCoreScaffold\" during %s value of \"-c, --coreScaffold\" option "
% (Options["--coreScaffold"]))
SMARTSOrSMILESCoreScaffoldList = SMARTSOrSMILESCoreScaffold.split(
",")
OptionsInfo["SMARTSOrSMILESCoreScaffold"] = SMARTSOrSMILESCoreScaffold
OptionsInfo[
"SMARTSOrSMILESCoreScaffoldList"] = SMARTSOrSMILESCoreScaffoldList
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["RefFile"] = Options["--reffile"]
OptionsInfo["Scaffold"] = Options["--scaffold"]
if re.match("^auto$", Options["--scaffold"], re.I):
UseScaffoldMCS = True
UseScaffoldSMARTS = False
ScaffoldSMARTS = None
else:
UseScaffoldMCS = False
UseScaffoldSMARTS = True
ScaffoldSMARTS = OptionsInfo["Scaffold"]
OptionsInfo["UseScaffoldMCS"] = UseScaffoldMCS
OptionsInfo["UseScaffoldSMARTS"] = UseScaffoldSMARTS
OptionsInfo["ScaffoldSMARTS"] = ScaffoldSMARTS
OptionsInfo["ScaffoldPatternMol"] = None
OptionsInfo["SpecifiedMCSParams"] = Options["--mcsParams"]
ProcessMCSParameters()
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters("--outfileParams", Options["--outfileParams"])
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["AddHydrogens"] = True if re.match("^yes$", Options["--addHydrogens"], re.I) else False
if re.match("^ETDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "ETDG"
UseExpTorsionAnglePrefs = True
UseBasicKnowledge = False
elif re.match("^KDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "KDG"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = True
elif re.match("^ETKDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "ETKDG"
UseExpTorsionAnglePrefs = True
UseBasicKnowledge = True
elif re.match("^SDG$", Options["--conformerGenerator"], re.I):
ConformerGenerator = "SDG"
UseExpTorsionAnglePrefs = False
UseBasicKnowledge = False
else:
MiscUtil.PrintError("The value, %s, specified for option \"-c, --conformerGenerator\" is not supported." % (Options["--conformerGenerator"]))
OptionsInfo["ConformerGenerator"] = ConformerGenerator
OptionsInfo["UseExpTorsionAnglePrefs"] = UseExpTorsionAnglePrefs
OptionsInfo["UseBasicKnowledge"] = UseBasicKnowledge
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$", Options["--forceFieldMMFFVariant"], re.I) else "MMFF94s"
OptionsInfo["ForceField"] = ForceField
OptionsInfo["MMFFVariant"] = MMFFVariant
OptionsInfo["UseMMFF"] = UseMMFF
OptionsInfo["UseUFF"] = UseUFF
OptionsInfo["ScaffoldRMSDOut"] = True if re.match("^yes$", Options["--scaffoldRMSDOut"], re.I) else False
OptionsInfo["EnergyOut"] = True if re.match("^yes$", Options["--energyOut"], re.I) else False
if UseMMFF:
OptionsInfo["EnergyLabel"] = "%s_Energy" % MMFFVariant
else:
OptionsInfo["EnergyLabel"] = "%s_Energy" % ForceField
OptionsInfo["EnforceChirality"] = True if re.match("^yes$", Options["--enforceChirality"], re.I) else False
OptionsInfo["MaxConfs"] = int(Options["--maxConfs"])
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
OptionsInfo["RemoveHydrogens"] = True if re.match("^yes$", Options["--removeHydrogens"], re.I) else False
OptionsInfo["UseTethers"] = True if re.match("^yes$", Options["--useTethers"], re.I) else False
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
Compute2DCoords = True
if not re.match("^yes$", Options["--compute2DCoords"], re.I):
Compute2DCoords = False
OptionsInfo["Compute2DCoords"] = Compute2DCoords
OptionsInfo["Mode"] = Options["--mode"]
RxnByNameMode = True
if not re.match("^RxnByName$", Options["--mode"], re.I):
RxnByNameMode = False
OptionsInfo["RxnByNameMode"] = RxnByNameMode
OptionsInfo["ProdMolNamesMode"] = Options["--prodMolNames"]
UseReactantNames = False
if re.match("^UseReactants$", Options["--prodMolNames"], re.I):
UseReactantNames = True
OptionsInfo["UseReactantNames"] = UseReactantNames
OptionsInfo["RxnName"] = Options["--rxnName"]
OptionsInfo["RxnNameSMIRKS"] = None
if OptionsInfo["RxnByNameMode"]:
if not Options["--rxnName"]:
MiscUtil.PrintError(
"No rxn name specified using \"-r, --rxnName\" option during \"RxnByName\" value of \"-m, --mode\" option"
)
OptionsInfo["RxnNamesFile"] = None
if not re.match("^auto$", Options["--rxnNamesFile"], re.I):
OptionsInfo["RxnNamesFile"] = Options["--rxnNamesFile"]
ReactantFiles = re.sub(" ", "", Options["--infiles"])
ReactantFilesList = []
ReactantFilesList = ReactantFiles.split(",")
OptionsInfo["ReactantFiles"] = ReactantFiles
OptionsInfo["ReactantFilesList"] = ReactantFilesList
OptionsInfo["SpecifiedSMIRKS"] = Options["--smirksRxn"]
if not OptionsInfo["RxnByNameMode"]:
if not Options["--smirksRxn"]:
MiscUtil.PrintError(
"No rxn SMIRKS pattern specified using \"-r, --rxnName\" option during \"RxnByName\" value of \"-m, --mode\" option"
)
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["Overwrite"] = Options["--overwrite"]
# Use first reactant file as input file as all input files have the same format...
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters(
"--infileParams", Options["--infileParams"], ReactantFilesList[0])
# No need to pass any input or output file name due to absence of any auto parameter...
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters(
"--outfileParams", Options["--outfileParams"])
Sanitize = True
if not re.match("^yes$", Options["--sanitize"], re.I):
Sanitize = False
OptionsInfo["Sanitize"] = Sanitize
