def ValidateOptions(): """Validate option values""" MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super") MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex") # Expand infiles to handle presence of multiple input files... InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",") if len(InfileNames) < 2: MiscUtil.PrintError( "Number of input files specified for \"-i, --infiles\" option, %d, must be greater than 2..." % (len(InfileNames))) # Validate file extensions... for Infile in InfileNames: MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile) MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif") Options["--infileNames"] = InfileNames if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I): AlignRefFile = Options["--alignRefFile"] MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile) MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
def ValidateOptions(): """Validate option values""" # Expand infile names.. InfilesNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",") # Validate file extensions... for Infile in InfilesNames: MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile) MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif") Options["--infilesNames"] = InfilesNames if not re.match("^auto$", Options["--interfaceResiduesCutoff"], re.I): MiscUtil.ValidateOptionFloatValue("--interfaceResiduesCutoff", Options["--interfaceResiduesCutoff"], {">": 0.0}) MiscUtil.ValidateOptionTextValue( "--interfaceResiduesMethod", Options["--interfaceResiduesMethod"], "BySASAChange ByHeavyAtomsDistance ByCAlphaAtomsDistance") MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0}) MiscUtil.ValidateOptionTextValue("--phiPsiMode", Options["--phiPsiMode"], "All Categories") MiscUtil.ValidateOptionIntegerValue("--phiPsiPrecision", Options["--phiPsiPrecision"], {">": 0}) MiscUtil.ValidateOptionFloatValue("--surfaceResiduesCutoff", Options["--surfaceResiduesCutoff"], {">": 0.0}) MiscUtil.ValidateOptionTextValue("--surfaceResiduesIDs", Options["--surfaceResiduesIDs"], "Yes No")
def ValidateOptions(): """Validate option values""" MiscUtil.ValidateOptionTextValue("-a, -addHydrogens", Options["--addHydrogens"], "yes no") MiscUtil.ValidateOptionTextValue("--keepInorganics", Options["--keepInorganics"], "yes no") MiscUtil.ValidateOptionTextValue("--keepLigands", Options["--keepLigands"], "yes no") MiscUtil.ValidateOptionTextValue("--keepSolvents", Options["--keepSolvents"], "yes no") # Expand infile names.. InfilesNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",") # Validate file extensions... for Infile in InfilesNames: MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile) MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif") Options["--infilesNames"] = InfilesNames MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "csv tsv txt") MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"]) MiscUtil.ValidateOptionIntegerValue("-p, --precision", Options["--precision"], {">": 0}) MiscUtil.ValidateOptionTextValue("--quiet", Options["--quiet"], "yes no")
def ValidateOptions(): """Validate option values""" MiscUtil.ValidateOptionTextValue("-a, --alignMethod", Options["--alignMethod"], "align cealign super") MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex") MiscUtil.ValidateOptionTextValue("-m, --mode", Options["--mode"], "OneToOne AllToAll FirstToAll") # Expand reffiles to handle presence of multiple input files... RefFilesNames = MiscUtil.ExpandFileNames(Options["--reffiles"], ",") # Validate file extensions... for RefFile in RefFilesNames: MiscUtil.ValidateOptionFilePath("-r, --reffiles", RefFile) MiscUtil.ValidateOptionFileExt("-r, --reffiles", RefFile, "pdb cif") Options["--refFilesNames"] = RefFilesNames # Expand probefiles to handle presence of multiple input files... ProbeFilesNames = MiscUtil.ExpandFileNames(Options["--probefiles"], ",") # Validate file extensions... for ProbeFile in ProbeFilesNames: MiscUtil.ValidateOptionFilePath("-p, --probefiles", ProbeFile) MiscUtil.ValidateOptionFileExt("-p, --probefiles", ProbeFile, "pdb cif") Options["--probeFilesNames"] = ProbeFilesNames MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "csv tsv txt") MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"]) MiscUtil.ValidateOptionTextValue("--outMatrix", Options["--outMatrix"], "Yes No")
def ValidateOptions(): """Validate option values""" # Expand infile names.. InfilesNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",") # Validate file extensions... for Infile in InfilesNames: MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile) MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif") Options["--infilesNames"] = InfilesNames MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})