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})
