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 WriteRGroups(Mols, RGroups, UnmatchedMolIndices):
"""Write out R groups"""
Outfile = OptionsInfo["Outfile"]
UnmatchedOutfile = OptionsInfo["UnmatchedOutfile"]
RemoveUnmatchedMode = OptionsInfo["RemoveUnmatchedMode"]
Compute2DCoords = OptionsInfo["OutfileParams"]["Compute2DCoords"]
TextOutFileMode = OptionsInfo["TextOutFileMode"]
TextOutFileDelim = OptionsInfo["TextOutFileDelim"]
Quote = OptionsInfo["TextOutQuote"]
SMILESIsomeric = OptionsInfo["OutfileParams"]["SMILESIsomeric"]
SMILESKekulize = OptionsInfo["OutfileParams"]["Kekulize"]
# Setup writers...
Writer = None
UnmatchedWriter = None
if TextOutFileMode:
Writer = open(Outfile, "w")
if RemoveUnmatchedMode:
UnmatchedWriter = open(UnmatchedOutfile, "w")
else:
Writer = RDKitUtil.MoleculesWriter(Outfile,
**OptionsInfo["OutfileParams"])
if RemoveUnmatchedMode:
UnmatchedWriter = RDKitUtil.MoleculesWriter(
UnmatchedOutfile, **OptionsInfo["OutfileParams"])
if Writer is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " %
Outfile)
if RemoveUnmatchedMode:
if UnmatchedWriter is None:
MiscUtil.PrintError("Failed to setup a writer for output fie %s " %
UnmatchedOutfile)
if RemoveUnmatchedMode:
MiscUtil.PrintInfo("\nGenerating files: %s %s..." %
(Outfile, UnmatchedOutfile))
else:
MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
# Set up data keys and labels for core and R groups...
RGroupsDataKeys = []
RGroupsDataLabels = []
CoreDataLabelPresent = False
for DataLabel in sorted(RGroups):
if re.match("^Core", DataLabel, re.I):
CoreDataLabelPresent = True
RGroupsDataKeys.append(DataLabel)
RGroupsDataLabels.append("SMILES%s" % DataLabel)
elif re.match("^R", DataLabel, re.I):
RGroupsDataKeys.append(DataLabel)
RGroupsDataLabels.append("SMILES%s" % DataLabel)
else:
MiscUtil.PrintWarning(
"Ignoring unknown R group data label, %s, found during R group decomposition..."
% DataLabel)
if CoreDataLabelPresent:
RGroupsCategoriesCount = len(RGroupsDataLabels) - 1
else:
RGroupsCategoriesCount = len(RGroupsDataLabels)
RGroupsMolUnmatchedCount = len(UnmatchedMolIndices)
RGroupsMolMatchedCount = len(Mols) - RGroupsMolUnmatchedCount
# Wite out headers for a text file...
if TextOutFileMode:
LineWords = ["SMILES", "Name"]
if RemoveUnmatchedMode:
Line = MiscUtil.JoinWords(LineWords, TextOutFileDelim, Quote)
UnmatchedWriter.write("%s\n" % Line)
LineWords.extend(RGroupsDataLabels)
Line = MiscUtil.JoinWords(LineWords, TextOutFileDelim, Quote)
Writer.write("%s\n" % Line)
MolCount = 0
RGroupsResultIndex = -1
for MolIndex, Mol in enumerate(Mols):
MolCount += 1
UnmatchedMol = False
if MolIndex in UnmatchedMolIndices:
UnmatchedMol = True
if UnmatchedMol:
RGroupsDataSMILES = [""] * len(RGroupsDataKeys)
else:
RGroupsResultIndex += 1
RGroupsDataSMILES = [
RGroups[RGroupsDataKey][RGroupsResultIndex]
for RGroupsDataKey in RGroupsDataKeys
]
if TextOutFileMode:
# Write out text file including SMILES file...
MolSMILES = Chem.MolToSmiles(Mol,
isomericSmiles=SMILESIsomeric,
kekuleSmiles=SMILESKekulize)
MolName = RDKitUtil.GetMolName(Mol, MolCount)
LineWords = [MolSMILES, MolName]
if UnmatchedMol and RemoveUnmatchedMode:
Line = MiscUtil.JoinWords(LineWords, TextOutFileDelim, Quote)
UnmatchedWriter.write("%s\n" % Line)
else:
LineWords.extend(RGroupsDataSMILES)
Line = MiscUtil.JoinWords(LineWords, TextOutFileDelim, Quote)
Writer.write("%s\n" % Line)
else:
# Write out SD file...
if Compute2DCoords:
AllChem.Compute2DCoords(Mol)
if UnmatchedMol and RemoveUnmatchedMode:
UnmatchedWriter.write(Mol)
else:
for (Name, Value) in zip(RGroupsDataLabels, RGroupsDataSMILES):
Mol.SetProp(Name, Value)
Writer.write(Mol)
if Writer is not None:
Writer.close()
if UnmatchedWriter is not None:
UnmatchedWriter.close()
MiscUtil.PrintInfo("\nTotal number of molecules: %d" % MolCount)
MiscUtil.PrintInfo("Number of R group categories: %d" %
RGroupsCategoriesCount)
MiscUtil.PrintInfo(
"Number of matched molecules containing core scaffold(s): %d" %
RGroupsMolMatchedCount)
MiscUtil.PrintInfo(
"Number of unmatched molecules containing no core scaffold(s): %d" %
RGroupsMolUnmatchedCount)
def WriteHTMLPageHeader(Writer, MolCount):
"""Write out HTML page header."""
ColCount = GetColCount(MolCount)
# Exclude counter and structure columns from sorting and searching...
if OptionsInfo["CounterCol"]:
ColIndicesList = ["0"]
ColVisibilityExcludeColIndicesList = ["0"]
ColIndexOffset = 1
FreezeLeftColumns = "1"
else:
ColIndicesList = []
ColVisibilityExcludeColIndicesList = []
ColIndexOffset = 0
MaxDataColVisColCount = 25
for Index in range(0, ColCount):
ColIndex = Index + ColIndexOffset
ColIndicesList.append("%s" % ColIndex)
if OptionsInfo["ColVisibility"]:
if Index >= MaxDataColVisColCount:
ColVisibilityExcludeColIndicesList.append("%s" %ColIndex)
ColIndices = MiscUtil.JoinWords(ColIndicesList, ", ") if len(ColIndicesList) else ""
ColVisibilityExcludeColIndices = MiscUtil.JoinWords(ColVisibilityExcludeColIndicesList, ", ") if len(ColVisibilityExcludeColIndicesList) else ""
DataColVisibilityExclude = False
if OptionsInfo["ColVisibility"]:
if ColCount > MaxDataColVisColCount:
DataColVisibilityExclude = True
MiscUtil.PrintWarning("The number of data columns, %d, is quite large. Only first %d data columns will be available in column visibility pulldown." % (ColCount, MaxDataColVisColCount))
DisplayButtons = False
if OptionsInfo["ColVisibility"]:
if ColCount > 0:
DisplayButtons = True
FreezeCols = False
if (OptionsInfo["CounterCol"] and OptionsInfo["ScrollX"]):
FreezeCols = True
Paging = "true" if OptionsInfo["Paging"] else "false"
PageLength = "%d" % OptionsInfo["PageLength"]
PagingType = "\"%s\"" % OptionsInfo["PagingType"]
ScrollX = "true" if OptionsInfo["ScrollX"] else "false"
ScrollY = ""
if OptionsInfo["ScrollY"]:
if re.search("vh$", OptionsInfo["ScrollYSize"]):
ScrollY = "\"%s\"" % OptionsInfo["ScrollYSize"]
else:
ScrollY = "%s" % OptionsInfo["ScrollYSize"]
# Start HTML header...
Title = "Molecules table" if OptionsInfo["Header"] is None else OptionsInfo["Header"]
Writer.write("""\
<!doctype html>
<html lang="en">
<head>
<title>%s</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.16/css/dataTables.bootstrap4.min.css">
""" % (Title))
if (FreezeCols):
Writer.write("""\
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/fixedcolumns/3.2.4/css/fixedColumns.bootstrap4.min.css">
""")
if (OptionsInfo["KeysNavigation"]):
Writer.write("""\
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/keytable/2.3.2/css/keyTable.bootstrap4.min.css">
""")
Writer.write("""\
<script type="text/javascript" language="javascript" src="https://code.jquery.com/jquery-1.12.4.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.16/js/dataTables.bootstrap4.min.js"></script>
""")
if (OptionsInfo["Popover"]):
Writer.write("""\
<script type="text/javascript" language="javascript" src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js"></script>
<script type="text/javascript" language="javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"></script>
""")
if DisplayButtons:
Writer.write("""\
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.1/js/dataTables.buttons.min.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.1/js/buttons.bootstrap4.min.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.1/js/buttons.colVis.min.js"></script>
""")
if (FreezeCols):
Writer.write("""\
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/fixedcolumns/3.2.4/js/dataTables.fixedColumns.min.js"></script>
""")
if (OptionsInfo["KeysNavigation"]):
Writer.write("""\
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/keytable/2.3.2/js/dataTables.keyTable.min.js"></script>
""")
# Intialize table using Bootstrap, DataTables and JQuery frameworks...
Writer.write("""\
<script type="text/javascript" class="init">
$(document).ready(function() {
""")
if (OptionsInfo["Popover"]):
Writer.write("""\
$('.MolPopover').popover();
""")
Writer.write("""\
var MolsTable = $('#MolsTable').DataTable( {
"columnDefs": [
{
"orderable": false,
"searchable": false,
"targets": [%s]
},
""" % (ColIndices))
if OptionsInfo["ColVisibility"]:
Writer.write("""\
{
"className": "noColVisCtrl",
"targets": [%s]
}
""" % (ColVisibilityExcludeColIndices))
Writer.write("""\
],
""")
# Set up dom for displaying button and other options...
if OptionsInfo["ColVisibility"]:
if OptionsInfo["Paging"]:
Writer.write("""\
"dom": "<'row'<'col-sm-6'l><'col-sm-6'<'float-right'B>>>" +
"<'row'<'col-sm-12'tr>>" +
"<'row'<'col-sm-5'i><'col-sm-7'p>>",
""")
else:
Writer.write("""\
"dom": "<'row'<'col'<'float-right'B>>>" +
"<'row'<'col-sm-12'tr>>" +
"<'row'<'col-sm-5'i><'col-sm-7'p>>",
""")
else:
Writer.write("""\
"dom": "<'row'<'col'l>>" +
"<'row'<'col-sm-12'tr>>" +
"<'row'<'col-sm-5'i><'col-sm-7'p>>",
""")
#
if OptionsInfo["ColVisibility"]:
# Set up buttons...
Writer.write("""\
"buttons": [
{
"extend": "colvis",
"text": "Column visibility",
"className": "btn btn-outline-light text-dark",
"columns": ":not(.noColVisCtrl)",
""")
if not DataColVisibilityExclude:
Writer.write("""\
"prefixButtons": [ "colvisRestore" ],
""")
Writer.write("""\
"columnText": function ( dt, colIndex, colLabel ) {
return "Column " + (colIndex + 1);
},
}
],
""")
# Write out rest of the variables for DataTables...
if FreezeCols:
Writer.write("""\
"fixedColumns": {
"leftColumns": %s
},
""" % (FreezeLeftColumns))
if (OptionsInfo["KeysNavigation"]):
Writer.write("""\
"keys": true,
""")
Writer.write("""\
"pageLength": %s,
"lengthMenu": [ [5, 10, 15, 25, 50, 100, 500, 1000, -1], [5, 10, 15, 25, 50, 100, 500, 1000, "All"] ],
"paging": %s,
"pagingType": %s,
"scrollX": %s,
"scrollY": %s,
"scrollCollapse": true,
"order": [],
} );
""" % (PageLength, Paging, PagingType, ScrollX, ScrollY))
if OptionsInfo["CounterCol"]:
Writer.write("""\
MolsTable.on( 'order.dt search.dt', function () {
MolsTable.column(0, {search:'applied', order:'applied'}).nodes().each( function (cell, rowIndex) {
cell.innerHTML = rowIndex + 1;
} );
} ).draw();
""")
# End of Javacscript code...
Writer.write("""\
} );
</script>
""")
# Finish up HTML header...
Writer.write("""\
</head>
<body>
<div class="container-fluid">
<br/>
""")
