def RetrieveChEMBLFiltersInfo():
"""Retrieve information for ChEMBL filters."""
MayaChemToolsDataDir = MiscUtil.GetMayaChemToolsLibDataPath()
ChEMBLFiltersFilePath = os.path.join(MayaChemToolsDataDir,
"ChEMBLFilters.csv")
MiscUtil.PrintInfo(
"\nRetrieving ChEMBL alerts SMARTS patterns from file %s" %
(ChEMBLFiltersFilePath))
Delimiter = ','
QuoteChar = '"'
IgnoreHeaderLine = True
FilterLinesWords = MiscUtil.GetTextLinesWords(ChEMBLFiltersFilePath,
Delimiter, QuoteChar,
IgnoreHeaderLine)
ChEMBLFiltersMap = {}
ChEMBLFiltersMap["FilterTypes"] = []
ChEMBLFiltersMap["ID"] = {}
ChEMBLFiltersMap["SMARTS"] = {}
for LineWords in FilterLinesWords:
FilterType = LineWords[0]
ID = LineWords[1]
SMARTS = LineWords[2]
if not FilterType in ChEMBLFiltersMap["FilterTypes"]:
ChEMBLFiltersMap["FilterTypes"].append(FilterType)
ChEMBLFiltersMap["ID"][FilterType] = []
ChEMBLFiltersMap["SMARTS"][FilterType] = []
ChEMBLFiltersMap["ID"][FilterType].append(ID)
ChEMBLFiltersMap["SMARTS"][FilterType].append(SMARTS)
OptionsInfo["ChEMBLFiltersMap"] = ChEMBLFiltersMap
MiscUtil.PrintInfo("\nTotal number alerts: %d" % len(FilterLinesWords))
MiscUtil.PrintInfo(
"Number of filter family types: %d\nFilter familty types: %s\n" %
(len(ChEMBLFiltersMap["FilterTypes"]), ", ".join(
ChEMBLFiltersMap["FilterTypes"])))
for FilterType in ChEMBLFiltersMap["FilterTypes"]:
MiscUtil.PrintInfo(
"Filter family type: %s; Number of alerts: %d" %
(FilterType, len(ChEMBLFiltersMap["ID"][FilterType])))
MiscUtil.PrintInfo("")
def RetrieveReactionNamesInfo():
"""Retrieve reaction names information."""
RxnNamesFilePath = OptionsInfo["RxnNamesFile"]
if RxnNamesFilePath is None:
MayaChemToolsDataDir = MiscUtil.GetMayaChemToolsLibDataPath()
RxnNamesFilePath = os.path.join(MayaChemToolsDataDir,
"ReactionNamesAndSMIRKS.csv")
MiscUtil.PrintInfo(
"\nRetrieving reaction names and SMIRKS patterns from file %s" %
(RxnNamesFilePath))
if not os.path.exists(RxnNamesFilePath):
MiscUtil.PrintError("The reaction names file, %s, doesn't exist.\n" %
(RxnNamesFilePath))
Delimiter = ','
QuoteChar = '"'
IgnoreHeaderLine = True
RxnLinesWords = MiscUtil.GetTextLinesWords(RxnNamesFilePath, Delimiter,
QuoteChar, IgnoreHeaderLine)
RxnNamesMap['Names'] = []
RxnNamesMap['SMIRKSPattern'] = {}
for LineWords in RxnLinesWords:
Name = LineWords[0]
SMIRKSPattern = LineWords[1]
if Name in RxnNamesMap['SMIRKSPattern']:
MiscUtil.PrintWarning("Ignoring duplicate reaction name: %s..." %
Name)
else:
RxnNamesMap['Names'].append(Name)
RxnNamesMap['SMIRKSPattern'][Name] = SMIRKSPattern
if not len(RxnNamesMap['Names']):
MiscUtil.PrintError(
"Failed to retrieve any reaction names and SMIRKS patterns...")
MiscUtil.PrintInfo(
"Total number of reactions present in reaction names and SMIRKS file: %d"
% (len(RxnNamesMap['Names'])))
