def GetMolPopoverTag(Mol):
"""Set up a popover window containing any additional information about molecule."""
if not OptionsInfo["Popover"]:
return None
# Set up data label and values...
AvailableDataLabels = Mol.GetPropNames(includePrivate=False,
includeComputed=False)
DataContentLines = []
MaxDataCharWidth = OptionsInfo["PopoverTextWidth"]
MaxDataDisplayCount = OptionsInfo["PopoverDataCount"]
DataDisplayCount = 0
SkippedDataDisplay = False
for DataLabel in AvailableDataLabels:
DataDisplayCount += 1
if DataDisplayCount > MaxDataDisplayCount:
SkippedDataDisplay = True
break
DataValue = "%s" % Mol.GetProp(DataLabel)
DataValue = DataValue.strip()
if MiscUtil.IsEmpty(DataValue):
continue
# Change any new lines to ;
if re.search("(\r\n|\r|\n)", DataValue):
DataValue = re.sub("(\r\n|\r|\n)", "; ", DataValue)
DataValue = MiscUtil.TruncateText(DataValue, MaxDataCharWidth, "...")
DataValue = MiscUtil.ReplaceHTMLEntitiesInText(DataValue)
DataContent = "<b>%s</b>: %s" % (DataLabel, DataValue)
DataContentLines.append(DataContent)
if not len(DataContentLines):
return None
if SkippedDataDisplay:
DataContent = "<b>... ... ...</b>"
DataContentLines.append(DataContent)
DataContent = "Showing 1 to %s of %s" % (MaxDataDisplayCount,
len(AvailableDataLabels))
DataContentLines.append(DataContent)
else:
DataContent = "Showing 1 to %s of %s" % (DataDisplayCount,
len(AvailableDataLabels))
DataContentLines.append(DataContent)
DataContent = MiscUtil.JoinWords(DataContentLines, "<br/>")
PopoverTag = """class="MolPopover" data-toggle="popover" data-html="true" data-trigger="click" data-placement="right" title="<span class='small'><b>Additional Information</b></span>" data-content="<span class='small'>%s</span>" """ % DataContent
return PopoverTag
def ProcessOptions():
"""Process and validate command line arguments and options"""
MiscUtil.PrintInfo("Processing options...")
# Validate options...
ValidateOptions()
OptionsInfo["Infile"] = Options["--infile"]
OptionsInfo["Outfile"] = Options["--outfile"]
OptionsInfo["Overwrite"] = Options["--overwrite"]
# No need for any RDKit specific --outfileParams....
OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters("--infileParams", Options["--infileParams"], OptionsInfo["Infile"])
AlignmentSMARTSPattern = None
if not re.match("^None$", Options["--alignmentSMARTS"], re.I):
AlignmentSMARTSPattern = Options["--alignmentSMARTS"]
OptionsInfo["AlignmentSMARTSPattern"] = AlignmentSMARTSPattern
OptionsInfo["AtomLabelFontSize"] = Options["--atomLabelFontSize"]
OptionsInfo["BondLineWidth"] = Options["--bondLineWidth"]
Compute2DCoords = True
if re.match("^yes$", Options["--compute2DCoords"], re.I):
Compute2DCoords = True
elif re.match("^no$", Options["--compute2DCoords"], re.I):
Compute2DCoords = False
OptionsInfo["Compute2DCoords"] = Compute2DCoords
CounterCol = True
if re.match("^no$", Options["--counterCol"], re.I):
CounterCol = False
OptionsInfo["CounterCol"] = CounterCol
ColVisibility = True
if re.match("^no$", Options["--colVisibility"], re.I):
ColVisibility = False
OptionsInfo["ColVisibility"] = ColVisibility
OptionsInfo["FontBold"] = True
if re.match("^no$", Options["--fontBold"], re.I):
OptionsInfo["FontBold"] = False
Footer = None
if not re.match("^None$", Options["--footer"], re.I):
Footer = Options["--footer"]
OptionsInfo["Footer"] = Footer
FooterClass = Options["--footerClass"].strip()
if MiscUtil.IsEmpty(FooterClass):
MiscUtil.PrintError("The value specified using option \"--footerClass\" is empty.")
OptionsInfo["FooterClass"] = FooterClass
Header = None
if not re.match("^None$", Options["--header"], re.I):
Header = Options["--header"]
OptionsInfo["Header"] = Header
HeaderStyle = Options["--headerStyle"].strip()
if MiscUtil.IsEmpty(HeaderStyle):
MiscUtil.PrintError("The value specified using option \"--headerStyle\" is empty.")
OptionsInfo["HeaderStyle"] = HeaderStyle
HighlightSMARTSPattern = None
if not re.match("^None$", Options["--highlightSMARTS"], re.I):
HighlightSMARTSPattern = Options["--highlightSMARTS"]
OptionsInfo["HighlightSMARTSPattern"] = HighlightSMARTSPattern
OptionsInfo["Kekulize"] = True
if re.match("^no$", Options["--kekulize"], re.I):
OptionsInfo["Kekulize"] = False
OptionsInfo["KeysNavigation"] = True
if re.match("^no$", Options["--keysNavigation"], re.I):
OptionsInfo["KeysNavigation"] = False
SizeValues = Options["--molImageSize"].split(",")
OptionsInfo["MolImageWidth"] = int(SizeValues[0])
OptionsInfo["MolImageHeight"] = int(SizeValues[1])
OptionsInfo["MolImageEncoded"] = True
if re.match("^no$", Options["--molImageEncoded"], re.I):
OptionsInfo["MolImageEncoded"] = False
OptionsInfo["NumOfMolsPerRow"] = int(Options["--numOfMolsPerRow"])
OptionsInfo["Paging"] = True
if re.match("^no$", Options["--paging"], re.I):
OptionsInfo["Paging"] = False
PagingType = Options["--pagingType"]
if not re.match("^(numbers|simple|simple_numbers|full|full_numbers|simple_number)$", Options["--pagingType"], re.I):
MiscUtil.PrintWarning("The paging type name, %s, specified using option \"--pagingType\" appears to be a unknown type..." % (PagingType))
OptionsInfo["PagingType"] = PagingType.lower()
OptionsInfo["PageLength"] = int(Options["--pageLength"])
OptionsInfo["Popover"] = True
if re.match("^no$", Options["--popover"], re.I):
OptionsInfo["Popover"] = False
OptionsInfo["PopoverDataCount"] = int(Options["--popoverDataCount"])
OptionsInfo["PopoverTextWidth"] = int(Options["--popoverTextWidth"])
OptionsInfo["ShowMolName"] = True
if re.match("^no$", Options["--showMolName"], re.I):
OptionsInfo["ShowMolName"] = False
OptionsInfo["ScrollX"] = True
if re.match("^no$", Options["--scrollX"], re.I):
OptionsInfo["ScrollX"] = False
OptionsInfo["ScrollY"] = True
if re.match("^no$", Options["--scrollY"], re.I):
OptionsInfo["ScrollY"] = False
OptionsInfo["ScrollYSize"] = Options["--scrollYSize"]
if re.match("vh$", Options["--scrollYSize"], re.I):
ScrollYSize = int(re.sub("vh$", "", Options["--scrollYSize"]))
if ScrollYSize <= 0:
MiscUtil.PrintError("The value specified, %s, for option \"--scrollYSize\" is not valid. Supported value: > 0 followed by \"vh\"" % Options["--scrollYSize"])
TableStyle = None
if not re.match("^None$", Options["--tableStyle"], re.I):
if re.match("^All$", Options["--tableStyle"], re.I):
TableStyle = "table table-striped table-bordered table-hover table-dark"
else:
TableStyle = re.sub(" ", "", Options["--tableStyle"])
for Style in [Style for Style in TableStyle.split(",")]:
if not re.match("^(table|table-striped|table-bordered|table-hover|table-dark|table-sm)$", Style, re.I):
MiscUtil.PrintWarning("The table style name, %s, specified using option \"-t, --tableStyle\" appears to be a unknown style..." % (Style))
TableStyle = re.sub(",", " ", TableStyle.lower())
OptionsInfo["TableStyle"] = TableStyle
OptionsInfo["TableFooter"] = True
if re.match("^no$", Options["--tableFooter"], re.I):
OptionsInfo["TableFooter"] = False
OptionsInfo["TableHeader"] = True
if re.match("^no$", Options["--tableHeader"], re.I):
OptionsInfo["TableHeader"] = False
TableHeaderStyle = None
if not re.match("^None$", Options["--tableHeaderStyle"], re.I):
TableHeaderStyle = Options["--tableHeaderStyle"]
TableHeaderStyle = TableHeaderStyle.lower()
CheckOptionTableClassColorValues("--tableHeaderStyle", [TableHeaderStyle])
OptionsInfo["TableHeaderStyle"] = TableHeaderStyle
