def SetupPlotTypesOutfiles():
"""Setup output file names for plot types """
OptionsInfo["OutfilesList"] = []
OptionsInfo["OutfilesList"].append(OptionsInfo["Outfile"])
OptionsInfo["PlotTypesInfo"]["Outfiles"] = {}
for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
OptionsInfo["PlotTypesInfo"]["Outfiles"][PlotType] = None
if not OptionsInfo["MultipleOutFiles"]:
return
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
OutfileRoot = FileName
OutfileExt = FileExt
for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
PlotOutfile = "%s_%s.%s" % (OutfileRoot, PlotType, OutfileExt)
if os.path.exists(PlotOutfile):
if not OptionsInfo["Overwrite"]:
MiscUtil.PrintError(
"The plot output file, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again.\n"
% (PlotOutfile))
OptionsInfo["PlotTypesInfo"]["Outfiles"][PlotType] = PlotOutfile
OptionsInfo["OutfilesList"].append(PlotOutfile)
def SetupCategoryOutfiles():
"""Setup output file names for different categories of phi and psi angles. """
# Initialize...
OptionsInfo["OutfilesList"] = []
OptionsInfo["OutfilesList"].append(OptionsInfo["Outfile"])
OptionsInfo["Categories"] = ["General", "Glycine", "Proline", "PreProline"]
OptionsInfo["CategoriesOutfiles"] = {}
for Category in OptionsInfo["Categories"]:
OptionsInfo["CategoriesOutfiles"][Category] = None
if not OptionsInfo["MultipleOutFiles"]:
return
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
OutfileRoot = FileName
OutfileExt = FileExt
for Category in OptionsInfo["Categories"]:
CategoryOutfile = "%s_%s.%s" % (OutfileRoot, Category, OutfileExt)
if os.path.exists(CategoryOutfile):
if not OptionsInfo["Overwrite"]:
MiscUtil.PrintError("The category output file, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again.\n" % (CategoryOutfile))
OptionsInfo["CategoriesOutfiles"][Category] = CategoryOutfile
OptionsInfo["OutfilesList"].append(CategoryOutfile)
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["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$", Options["--mode"],
re.I) else False
# Setup outfile for writing out molecule number for invalid molecules...
OptionsInfo["InvalidMolsOutfile"] = ""
if not OptionsInfo["CountMode"]:
FileDir, FileName, FileExt = MiscUtil.ParseFileName(
OptionsInfo["Outfile"])
OptionsInfo["InvalidMolsOutfile"] = "%sInvalidMols.csv" % (FileName)
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters("--infileParams", Options["--infileParams"], Options["--infile"])
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["OutfileParams"] = MiscUtil.ProcessOptionOutfileParameters("--outfileParams", Options["--outfileParams"], Options["--infile"], Options["--outfile"])
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Options["--outfile"])
OutfileFiltered = "%s_Filtered.%s" % (FileName, FileExt)
OptionsInfo["OutfileFiltered"] = OutfileFiltered
OptionsInfo["OutfileFilteredMode"] = True if re.match("^yes$", 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$", Options["--mp"], re.I) else False
OptionsInfo["MPParams"] = MiscUtil.ProcessOptionMultiprocessingParameters("--mpParams", Options["--mpParams"])
OptionsInfo["AlertsMode"] = Options["--alertsMode"]
ProcessChEMBLAlertsMode()
def RetrieveRefFileInfo():
"""Retrieve information for ref file."""
RefFileInfo = {}
RefFile = OptionsInfo["RefFileName"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
RefFileRoot = FileName
if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
ChainIDs = OptionsInfo["InfilesInfo"]["ChainIDs"][0]
else:
MiscUtil.PrintInfo(
"\nRetrieving chains information for alignment reference file %s..."
% RefFile)
ChainIDs = RetrieveChainIDs(RefFile, RefFileRoot)
if not len(ChainIDs):
if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
MiscUtil.PrintError(
"The align mode, %s, can't be used for aligning chains: No non-empty chain IDs found in input file."
% (OptionsInfo["AlignMode"]))
RefFileInfo["RefFileName"] = RefFile
RefFileInfo["RefFileRoot"] = RefFileRoot
RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
RefFileInfo["ChainIDs"] = ChainIDs
OptionsInfo["RefFileInfo"] = RefFileInfo
def ListFileInfo(Infile):
"""List information for macromolecules in a file."""
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
MolName = FileName
# Load infile...
pymol.cmd.load(Infile, MolName)
ChainIDs = PyMOLUtil.GetChains(MolName)
ListHeaderInfo(Infile)
ListChainsInfo(MolName, ChainIDs)
ListChainsResiduesInfo(MolName, ChainIDs)
ListLigandsInfo(MolName, ChainIDs)
ListSolventsInfo(MolName, ChainIDs)
ListInorganicsInfo(MolName, ChainIDs)
ListPocketsInfo(MolName, ChainIDs)
ListInterfaceResiduesInfo(MolName, ChainIDs)
ListSurfaceResiduesInfo(MolName, ChainIDs)
ListPhiPsiAnglesInfo(MolName, ChainIDs)
ListBoundingBoxInfo(MolName)
# Delete infile object...
pymol.cmd.delete(MolName)
ListFileSizeAndModificationInfo(Infile)
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"])
OptionsInfo["InfileRoot"] = FileName
OptionsInfo["Outfile"] = Options["--outfile"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
OptionsInfo["OutfileRoot"] = FileName
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"]))
OptionsInfo["OutMode"] = Options["--outMode"]
OptionsInfo["MultipleOutFiles"] = True if re.match(
"^MultipleFiles$", OptionsInfo["OutMode"], re.I) else False
OptionsInfo["OutChainID"] = True if re.match(
"^Yes$", Options["--outChainID"], re.I) else False
OptionsInfo["OutCategory"] = True if re.match(
"^Yes$", Options["--outCategory"], re.I) else False
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["Precision"] = int(Options["--precision"])
RetrieveInfileInfo()
OptionsInfo["ChainIDs"] = Options["--chainIDs"]
ProcessChainIDs()
SetupCategoryOutfiles()
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["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$", Options["--useChirality"], re.I):
OptionsInfo["UseChirality"] = True
def RetrieveInfilesInfo(InfilesMode):
"""Retrieve information for input files."""
if re.match("^ProbeFiles$", InfilesMode, re.I):
MiscUtil.PrintInfo("Retrieving information for probe files...")
InfilesNames = OptionsInfo["ProbeFilesNames"]
NameSuffix = "_Probe"
elif re.match("^RefFiles$", InfilesMode, re.I):
MiscUtil.PrintInfo("Retrieving information for reference files...")
InfilesNames = OptionsInfo["RefFilesNames"]
NameSuffix = "_Ref"
else:
MiscUtil.PrintError("Internal Error: Unknown infiles mode: %s" %
InfilesMode)
InfilesInfo = {}
InfilesInfo["FilesNames"] = []
InfilesInfo["FilesRoots"] = []
InfilesInfo["ChainIDs"] = []
InfilesInfo["PyMOLObjectNames"] = []
for Infile in InfilesNames:
MiscUtil.PrintInfo(
"\nRetrieving chains information for input file %s..." % Infile)
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
InfileRoot = FileName
ChainIDs = RetrieveChainIDs(Infile, InfileRoot)
if not len(ChainIDs):
if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
MiscUtil.PrintError(
"The align mode, %s, can't be used for calculating RMSD: No non-empty chain IDs found in input file."
% (OptionsInfo["AlignMode"]))
InfilesInfo["FilesNames"].append(Infile)
InfilesInfo["FilesRoots"].append(InfileRoot)
InfilesInfo["ChainIDs"].append(ChainIDs)
Name = "%s%s" % (InfileRoot, NameSuffix)
InfilesInfo["PyMOLObjectNames"].append(Name)
if re.match("^ProbeFiles$", InfilesMode, re.I):
OptionsInfo["ProbeFilesInfo"] = InfilesInfo
elif re.match("^RefFiles$", InfilesMode, re.I):
OptionsInfo["RefFilesInfo"] = InfilesInfo
def RetrieveInfilesInfo():
"""Retrieve information for input files."""
InfilesInfo = {}
InfilesInfo["InfilesNames"] = []
InfilesInfo["InfilesRoots"] = []
InfilesInfo["ChainIDs"] = []
InfilesInfo["PyMOLObjectNames"] = []
InfilesInfo["OutfilesNames"] = []
OutSuffix = OptionsInfo["OutSuffix"]
for Infile in OptionsInfo["InfilesNames"]:
MiscUtil.PrintInfo(
"\nRetrieving chains information for input file %s..." % Infile)
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
InfileRoot = FileName
ChainIDs = RetrieveChainIDs(Infile, InfileRoot)
if not len(ChainIDs):
if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
MiscUtil.PrintError(
"The align mode, %s, can't be used for aligning chains: No non-empty chain IDs found in input file."
% (OptionsInfo["AlignMode"]))
InfilesInfo["InfilesNames"].append(Infile)
InfilesInfo["InfilesRoots"].append(InfileRoot)
InfilesInfo["ChainIDs"].append(ChainIDs)
InfilesInfo["PyMOLObjectNames"].append(InfileRoot)
# Setup outfile name...
Outfile = "%s%s.pdb" % (InfileRoot, OutSuffix)
InfilesInfo["OutfilesNames"].append(Outfile)
if os.path.exists(Outfile):
if not OptionsInfo["Overwrite"]:
MiscUtil.PrintError(
"\nThe output file, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again.\n"
% (Outfile))
OptionsInfo["InfilesInfo"] = InfilesInfo
def RetrieveInfilesInfo():
"""Retrieve information for input files."""
InfilesInfo = {}
InfilesInfo["InfilesNames"] = []
InfilesInfo["InfilesRoots"] = []
InfilesInfo["ChainsAndLigandsInfo"] = []
for Infile in OptionsInfo["InfilesNames"]:
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
InfileRoot = FileName
ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
InfilesInfo["InfilesNames"].append(Infile)
InfilesInfo["InfilesRoots"].append(InfileRoot)
InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
OptionsInfo["InfilesInfo"] = InfilesInfo
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Mode"] = Options["--mode"]
OptionsInfo["ChainsMode"] = False
if re.match("^Chains$", OptionsInfo["Mode"], re.I):
OptionsInfo["ChainsMode"] = True
OptionsInfo["LigandFileFormat"] = Options["--ligandFileFormat"]
LigandFileExt = "mol"
if re.match("^PDB$", OptionsInfo["LigandFileFormat"], re.I):
LigandFileExt = "pdb"
elif re.match("^(SD|SDF)$", OptionsInfo["LigandFileFormat"], re.I):
LigandFileExt = "sdf"
elif re.match("^MOL$", OptionsInfo["LigandFileFormat"], re.I):
LigandFileExt = "mol"
OptionsInfo["LigandFileExt"] = LigandFileExt
OptionsInfo["KeepInorganics"] = True if re.match(
"^Yes$", Options["--keepInorganics"], re.I) else False
OptionsInfo["KeepSolvents"] = True if re.match(
"^Yes$", Options["--keepSolvents"], re.I) else False
OptionsInfo["Infile"] = Options["--infile"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"])
OptionsInfo["InfileRoot"] = FileName
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["ChainIDs"] = Options["--chainIDs"]
OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
ProcessChainAndLigandIDs()
SetupChainAndLigandOutfiles()
def ListHeaderInfo(Infile):
"""List header information."""
if not (OptionsInfo["All"] or OptionsInfo["Header"]):
return
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = [
"Not Available"
] * 5
if re.match("^pdb$", FileExt, re.I):
Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = RetriveHeadAndExperimentalInfoFromPDBFile(
Infile)
elif re.match("^cif$", FileExt, re.I):
Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = RetriveHeadAndExperimentalInfoFromCIFFile(
Infile)
MiscUtil.PrintInfo("\nID: %s\nClassification: %s\nDeposition date: %s" %
(IDCode, Classification, DepositionDate))
MiscUtil.PrintInfo("\nExperimental technique: %s\nResolution: %s" %
(ExperimentalTechnique, Resolution))
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"])
OptionsInfo["InfileRoot"] = FileName
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["Outfile"] = Options["--outfile"]
RetrieveChainsIDs()
Mutations = Options["--mutations"]
if re.match("^None$", Mutations, re.I):
MiscUtil.PrintError("No mutations specified using \"-m, --mutations\" option.")
OptionsInfo["Mutations"] = Options["--mutations"]
ProcessSpecifiedMutations()
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)$", Options["--coreScaffold"], re.I):
SMARTSOrSMILESCoreScaffold = re.sub(
" ", "", Options["--smartsOrSmilesCoreScaffold"])
if not SMARTSOrSMILESCoreScaffold:
MiscUtil.PrintError(
"A non empty value must be specified for \"-s, --smartsOrSmilesCoreScaffold\" during %s value of \"-c, --coreScaffold\" option "
% (Options["--coreScaffold"]))
SMARTSOrSMILESCoreScaffoldList = SMARTSOrSMILESCoreScaffold.split(
",")
OptionsInfo["SMARTSOrSMILESCoreScaffold"] = SMARTSOrSMILESCoreScaffold
OptionsInfo[
"SMARTSOrSMILESCoreScaffoldList"] = SMARTSOrSMILESCoreScaffoldList
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["OutMode"] = Options["--outMode"]
OptionsInfo["MultipleOutFiles"] = True if re.match(
"^MultipleFiles$", OptionsInfo["OutMode"], re.I) else False
MultipleOutFiles = OptionsInfo["MultipleOutFiles"]
OptionsInfo["FigDPI"] = int(Options["--figDPI"])
FigSize = Options["--figSize"]
Width = 6.4
Height = 4.8 if MultipleOutFiles else 6.4
if not re.match("^auto$", FigSize, re.I):
FigSizeWords = FigSize.split(",")
Width = float(FigSizeWords[0])
Height = float(FigSizeWords[1])
OptionsInfo["FigSize"] = FigSize
OptionsInfo["FigWidth"] = Width
OptionsInfo["FigHeight"] = Height
OptionsInfo["FontFamily"] = Options["--fontFamily"]
OptionsInfo["FontAxesSize"] = Options["--fontAxesSize"]
OptionsInfo["FontAxesWeight"] = Options["--fontAxesWeight"]
OptionsInfo["FontTicksSize"] = Options["--fontTicksSize"]
OptionsInfo["FontTicksWeight"] = Options["--fontTicksWeight"]
OptionsInfo["FontTitleSize"] = Options["--fontTitleSize"]
OptionsInfo["FontTitleWeight"] = Options["--fontTitleWeight"]
OptionsInfo["Greek"] = True if re.match("^Yes$", Options["--greek"],
re.I) else False
OptionsInfo["Grid"] = True if re.match("^Yes$", Options["--grid"],
re.I) else False
OptionsInfo["GridLineColor"] = Options["--gridLineColor"]
OptionsInfo["GridLineStyle"] = Options["--gridLineStyle"]
OptionsInfo["GridLineWidth"] = float(Options["--gridLineWidth"])
OptionsInfo["Infile"] = Options["--infile"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"])
OptionsInfo["InfileRoot"] = FileName
OptionsInfo["LevelsAndColorsScheme"] = Options["--levelsAndColorsScheme"]
OptionsInfo["Outfile"] = Options["--outfile"]
FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
OptionsInfo["OutfileRoot"] = FileName
OptionsInfo["Overwrite"] = Options["--overwrite"]
OptionsInfo["Precision"] = int(Options["--precision"])
OptionsInfo["ScatterMarkerColor"] = Options["--scatterMarkerColor"]
OptionsInfo["ScatterMarkerSize"] = float(Options["--scatterMarkerSize"])
OptionsInfo["ScatterMarkerStyle"] = Options["--scatterMarkerStyle"]
TicksMajorInterval = 90 if MultipleOutFiles else 180
if not re.match("^auto$", Options["--ticksMajorInterval"], re.I):
TicksMajorInterval = int(Options["--ticksMajorInterval"])
OptionsInfo["TicksMajorInterval"] = TicksMajorInterval
OptionsInfo["TicksMinor"] = True if re.match(
"^Yes$", Options["--ticksMinor"], re.I) else False
TicksMinorInterval = 10 if MultipleOutFiles else 45
if not re.match("^auto$", Options["--ticksMinorInterval"], re.I):
TicksMinorInterval = int(Options["--ticksMinorInterval"])
OptionsInfo["TicksMinorInterval"] = TicksMinorInterval
RetrieveInfileInfo()
OptionsInfo["ChainIDs"] = Options["--chainIDs"]
ProcessChainIDs()
OptionsInfo["LevelsAndColors"] = Options["--levelsAndColors"]
SetupPlotsInfo()
