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"] = 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["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"]) 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["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"] = True if re.match("^count$", Options["--mode"], re.I) else False # Setup outfile for writing out molecule number for invalid molecules... OptionsInfo["InvalidMolsOutfile"] = "" if not OptionsInfo["CountMode"]: FileDir, FileName, FileExt = MiscUtil.ParseFileName( OptionsInfo["Outfile"]) OptionsInfo["InvalidMolsOutfile"] = "%sInvalidMols.csv" % (FileName)
def ProcessOptions(): """Process and validate command line arguments and options""" MiscUtil.PrintInfo("Processing options...") # Validate options... ValidateOptions() OptionsInfo["CalcRMSD"] = Options["--calcRMSD"] OptionsInfo["UseBestRMSD"] = False if re.match("^BestRMSD$", OptionsInfo["CalcRMSD"], re.I): OptionsInfo["UseBestRMSD"] = 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["Overwrite"] = Options["--overwrite"] OptionsInfo["OutDelim"] = " " if MiscUtil.CheckFileExt(OptionsInfo["Outfile"], "csv"): OptionsInfo["OutDelim"] = "," elif MiscUtil.CheckFileExt(OptionsInfo["Outfile"], "tsv txt"): OptionsInfo["OutDelim"] = "\t" else: MiscUtil.PrintError("The file name specified , %s, for option \"--outfile\" is not valid. Supported file formats: csv tsv txt\n" % (OptionsInfo["Outfile"]))
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
def ProcessOptions(): """Process and validate command line arguments and options""" MiscUtil.PrintInfo("Processing options...") # Validate options... ValidateOptions() OptionsInfo["Infile"] = Options["--infile"] OptionsInfo["Outfile"] = Options["--outfile"] OptionsInfo["Overwrite"] = Options["--overwrite"] # No need for any RDKit specific --outfileParams.... OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters("--infileParams", Options["--infileParams"], OptionsInfo["Infile"]) AlignmentSMARTSPattern = None if not re.match("^None$", Options["--alignmentSMARTS"], re.I): AlignmentSMARTSPattern = Options["--alignmentSMARTS"] OptionsInfo["AlignmentSMARTSPattern"] = AlignmentSMARTSPattern OptionsInfo["AtomLabelFontSize"] = Options["--atomLabelFontSize"] OptionsInfo["BondLineWidth"] = Options["--bondLineWidth"] Compute2DCoords = True if re.match("^yes$", Options["--compute2DCoords"], re.I): Compute2DCoords = True elif re.match("^no$", Options["--compute2DCoords"], re.I): Compute2DCoords = False OptionsInfo["Compute2DCoords"] = Compute2DCoords CounterCol = True if re.match("^no$", Options["--counterCol"], re.I): CounterCol = False OptionsInfo["CounterCol"] = CounterCol ColVisibility = True if re.match("^no$", Options["--colVisibility"], re.I): ColVisibility = False OptionsInfo["ColVisibility"] = ColVisibility OptionsInfo["FontBold"] = True if re.match("^no$", Options["--fontBold"], re.I): OptionsInfo["FontBold"] = False Footer = None if not re.match("^None$", Options["--footer"], re.I): Footer = Options["--footer"] OptionsInfo["Footer"] = Footer FooterClass = Options["--footerClass"].strip() if MiscUtil.IsEmpty(FooterClass): MiscUtil.PrintError("The value specified using option \"--footerClass\" is empty.") OptionsInfo["FooterClass"] = FooterClass Header = None if not re.match("^None$", Options["--header"], re.I): Header = Options["--header"] OptionsInfo["Header"] = Header HeaderStyle = Options["--headerStyle"].strip() if MiscUtil.IsEmpty(HeaderStyle): MiscUtil.PrintError("The value specified using option \"--headerStyle\" is empty.") OptionsInfo["HeaderStyle"] = HeaderStyle HighlightSMARTSPattern = None if not re.match("^None$", Options["--highlightSMARTS"], re.I): HighlightSMARTSPattern = Options["--highlightSMARTS"] OptionsInfo["HighlightSMARTSPattern"] = HighlightSMARTSPattern OptionsInfo["Kekulize"] = True if re.match("^no$", Options["--kekulize"], re.I): OptionsInfo["Kekulize"] = False OptionsInfo["KeysNavigation"] = True if re.match("^no$", Options["--keysNavigation"], re.I): OptionsInfo["KeysNavigation"] = False SizeValues = Options["--molImageSize"].split(",") OptionsInfo["MolImageWidth"] = int(SizeValues[0]) OptionsInfo["MolImageHeight"] = int(SizeValues[1]) OptionsInfo["MolImageEncoded"] = True if re.match("^no$", Options["--molImageEncoded"], re.I): OptionsInfo["MolImageEncoded"] = False OptionsInfo["NumOfMolsPerRow"] = int(Options["--numOfMolsPerRow"]) OptionsInfo["Paging"] = True if re.match("^no$", Options["--paging"], re.I): OptionsInfo["Paging"] = False PagingType = Options["--pagingType"] if not re.match("^(numbers|simple|simple_numbers|full|full_numbers|simple_number)$", Options["--pagingType"], re.I): MiscUtil.PrintWarning("The paging type name, %s, specified using option \"--pagingType\" appears to be a unknown type..." % (PagingType)) OptionsInfo["PagingType"] = PagingType.lower() OptionsInfo["PageLength"] = int(Options["--pageLength"]) OptionsInfo["Popover"] = True if re.match("^no$", Options["--popover"], re.I): OptionsInfo["Popover"] = False OptionsInfo["PopoverDataCount"] = int(Options["--popoverDataCount"]) OptionsInfo["PopoverTextWidth"] = int(Options["--popoverTextWidth"]) OptionsInfo["ShowMolName"] = True if re.match("^no$", Options["--showMolName"], re.I): OptionsInfo["ShowMolName"] = False OptionsInfo["ScrollX"] = True if re.match("^no$", Options["--scrollX"], re.I): OptionsInfo["ScrollX"] = False OptionsInfo["ScrollY"] = True if re.match("^no$", Options["--scrollY"], re.I): OptionsInfo["ScrollY"] = False OptionsInfo["ScrollYSize"] = Options["--scrollYSize"] if re.match("vh$", Options["--scrollYSize"], re.I): ScrollYSize = int(re.sub("vh$", "", Options["--scrollYSize"])) if ScrollYSize <= 0: MiscUtil.PrintError("The value specified, %s, for option \"--scrollYSize\" is not valid. Supported value: > 0 followed by \"vh\"" % Options["--scrollYSize"]) TableStyle = None if not re.match("^None$", Options["--tableStyle"], re.I): if re.match("^All$", Options["--tableStyle"], re.I): TableStyle = "table table-striped table-bordered table-hover table-dark" else: TableStyle = re.sub(" ", "", Options["--tableStyle"]) for Style in [Style for Style in TableStyle.split(",")]: if not re.match("^(table|table-striped|table-bordered|table-hover|table-dark|table-sm)$", Style, re.I): MiscUtil.PrintWarning("The table style name, %s, specified using option \"-t, --tableStyle\" appears to be a unknown style..." % (Style)) TableStyle = re.sub(",", " ", TableStyle.lower()) OptionsInfo["TableStyle"] = TableStyle OptionsInfo["TableFooter"] = True if re.match("^no$", Options["--tableFooter"], re.I): OptionsInfo["TableFooter"] = False OptionsInfo["TableHeader"] = True if re.match("^no$", Options["--tableHeader"], re.I): OptionsInfo["TableHeader"] = False TableHeaderStyle = None if not re.match("^None$", Options["--tableHeaderStyle"], re.I): TableHeaderStyle = Options["--tableHeaderStyle"] TableHeaderStyle = TableHeaderStyle.lower() CheckOptionTableClassColorValues("--tableHeaderStyle", [TableHeaderStyle]) OptionsInfo["TableHeaderStyle"] = TableHeaderStyle