def RetrievePAINSPatterns(PAINSFilterMode):
"""Retrieve PAINS patterns for specified PAINS mode"""
MayaChemToolsDataDir = MiscUtil.GetMayaChemToolsLibDataPath()
PAINSFiltersFilePath = os.path.join(MayaChemToolsDataDir,
"PAINSFilters.csv")
MiscUtil.PrintInfo(
"\nRetrieving PAINS SMARTS patterns for PAINS filter type, %s, from file %s"
% (PAINSFilterMode, PAINSFiltersFilePath))
if not os.path.exists(PAINSFiltersFilePath):
MiscUtil.PrintError("The PAINS filters file, %s, doesn't exist.\n" %
(PAINSFiltersFilePath))
FilterFile = open(PAINSFiltersFilePath, "r")
if FilterFile is None:
MiscUtil.PrintError("Couldn't open PAINS filter file: %s.\n" %
(PAINSFiltersFilePath))
# Collect all PAINS filter lines...
HeaderLine = True
FiltersLines = []
for Line in FilterFile:
Line = Line.rstrip()
# Ignore comments...
if re.match("^#", Line, re.I):
continue
# Ignore header line...
if HeaderLine:
HeaderLine = False
continue
FiltersLines.append(Line)
# Process PAINS filter lines using csv reader...
SMARTSPatterns = []
FiltersReader = csv.reader(FiltersLines, delimiter=',', quotechar='"')
for LineWords in FiltersReader:
FilterType = LineWords[0]
ID = LineWords[1]
SMARTS = LineWords[2]
if re.match("^All$", PAINSFilterMode,
re.I) or FilterType.lower() == PAINSFilterMode.lower():
SMARTSPatterns.append(SMARTS)
FilterFile.close()
MiscUtil.PrintInfo("Total number of PAINS SMARTS patterns: %d" %
(len(SMARTSPatterns)))
return SMARTSPatterns
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'])))
def InitializePlotTypesInfo():
"""Initialize information for generating plots. """
PlotTypesInfo = {}
PlotTypesInfo["Types"] = []
PlotTypesInfo["PhiPsiDensityFiles"] = {}
PlotTypesInfo["PhiPsiDensityInfo"] = {}
PlotTypesInfo["PhiPsiContourInfo"] = {}
PlotTypesInfo["Titles"] = {}
PlotTypesInfo["DrawXLabel"] = {}
PlotTypesInfo["DrawYLabel"] = {}
PlotTypesInfo["Limits"] = {}
PlotTypesInfo["MajorTickPositions"] = {}
PlotTypesInfo["MajorTickLabels"] = {}
PlotTypesInfo["MinorTickPositions"] = {}
PlotTypesInfo["Levels"] = {}
PlotTypesInfo["Colors"] = {}
PlotTypesInfo["Outfiles"] = {}
PlotTypesInfo["PhiAngles"] = {}
PlotTypesInfo["PsiAngles"] = {}
MayaChemToolsDataDir = MiscUtil.GetMayaChemToolsLibDataPath()
# Setup contour colors for supported default schemes...
ContourColorSchemes = {}
ContourColorSchemes["General"] = {
"MuttedColorShades1": ["#FFFFFF", "#EBF1DE", "#C3D69B"],
"MuttedColorShades2": ["#FFFFFF", "#EBF1DE", "#D7E4BD"],
"BrightColorShades": ["#FFFFFF", "#B3E8FF", "#7FD9FF"]
}
ContourColorSchemes["Glycine"] = {
"MuttedColorShades1": ["#FFFFFF", "#FDEADA", "#FAC090"],
"MuttedColorShades2": ["#FFFFFF", "#FDEADA", "#FCD5B5"],
"BrightColorShades": ["#FFFFFF", "#FFE8C5", "#FFCC7F"]
}
ContourColorSchemes["Proline"] = {
"MuttedColorShades1": ["#FFFFFF", "#E6E0EC", "#B3A2C7"],
"MuttedColorShades2": ["#FFFFFF", "#E6E0EC", "#CCC1DA"],
"BrightColorShades": ["#FFFFFF", "#D0FFC5", "#7FFF8C"]
}
ContourColorSchemes["PreProline"] = {
"MuttedColorShades1": ["#FFFFFF", "#DCE6F2", "#95B3D7"],
"MuttedColorShades2": ["#FFFFFF", "#DCE6F2", "#B9CDE5"],
"BrightColorShades": ["#FFFFFF", "#B3E8FF", "#7FD9FF"]
}
if re.match("^MuttedColorShades1$", OptionsInfo["LevelsAndColorsScheme"],
re.I):
DefaultColorScheme = "MuttedColorShades1"
elif re.match("^MuttedColorShades2$", OptionsInfo["LevelsAndColorsScheme"],
re.I):
DefaultColorScheme = "MuttedColorShades2"
elif re.match("^BrightColorShades$", OptionsInfo["LevelsAndColorsScheme"],
re.I):
DefaultColorScheme = "BrightColorShades"
else:
MiscUtil.PrintError(
"The color scheme, %s, specified using \"--levelsAndColorsScheme\" option is not supported."
% (OptionsInfo["LevelsAndColorsScheme"]))
for Type in ["General", "Glycine", "Proline", "PreProline"]:
PlotTypesInfo["Types"].append(Type)
# Setup phi and psi density file...
DensityFile = os.path.join(MayaChemToolsDataDir,
"PhiPsiDensity%s.csv" % (Type))
if not os.path.exists(DensityFile):
MiscUtil.PrintError(
"The phi and psi density file file, %s, doesn't exist. This is required for generating contour plots.\n"
% (DensityFile))
PlotTypesInfo["PhiPsiDensityFiles"][Type] = DensityFile
# Setup plot title...
Title = Type
if re.match("^PreProline$", Type, re.I):
Title = "pre-Proline"
PlotTypesInfo["Titles"][Type] = Title
# Setup flags for drawing axis labels...
DrawXLabel, DrawYLabel = [True] * 2
if not OptionsInfo["MultipleOutFiles"]:
# Turn off XLabel for plots in first row...
DrawXLabel = False if re.match("^(General|Glycine)$", Type,
re.I) else True
# Turn off YLabel for plots in second column...
DrawYLabel = False if re.match("^(Glycine|PreProline)$", Type,
re.I) else True
PlotTypesInfo["DrawXLabel"][Type] = DrawXLabel
PlotTypesInfo["DrawYLabel"][Type] = DrawYLabel
# Setup limits...
(MinLimit, MaxLimit) = [-180, 180]
PlotTypesInfo["Limits"][Type] = [MinLimit, MaxLimit]
# Setup major tick labels and positions...
MajorTickPositions = list(
range(MinLimit, MaxLimit, OptionsInfo["TicksMajorInterval"]))
MajorTickPositions.append(MaxLimit)
MajorTickLabels = ["%s" % Position for Position in MajorTickPositions]
PlotTypesInfo["MajorTickPositions"][Type] = MajorTickPositions
PlotTypesInfo["MajorTickLabels"][Type] = MajorTickLabels
# Setup minor tick positions without any labels...
MinorTickPositions = list(
range(MinLimit, MaxLimit, OptionsInfo["TicksMinorInterval"]))
MinorTickPositions.append(MaxLimit)
PlotTypesInfo["MinorTickPositions"][Type] = MinorTickPositions
# Setup contour levels and colors...
Levels = []
Colors = []
if re.match("^General$", Type, re.I):
Levels = [0.0, 0.0005, 0.02, 1.0]
Colors = ContourColorSchemes[Type][DefaultColorScheme]
elif re.match("^Glycine$", Type, re.I):
Levels = [0.0, 0.002, 0.02, 1.0]
Colors = ContourColorSchemes[Type][DefaultColorScheme]
elif re.match("^Proline$", Type, re.I):
Levels = [0.0, 0.002, 0.02, 1.0]
Colors = ContourColorSchemes[Type][DefaultColorScheme]
elif re.match("^PreProline$", Type, re.I):
Levels = [0.0, 0.002, 0.02, 1.0]
Colors = ContourColorSchemes[Type][DefaultColorScheme]
PlotTypesInfo["Levels"][Type] = Levels
PlotTypesInfo["Colors"][Type] = Colors
OptionsInfo["PlotTypesInfo"] = PlotTypesInfo
