def ToPdf(mol, oname, frags):#, fragcombs):
"""
Parameters
----------
mol: charged OEMolGraph
oname: str
Output file name
Returns
-------
"""
itf = oechem.OEInterface()
oedepict.OEPrepareDepiction(mol)
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
ropts.SetHeaderHeight(ropts.GetPageHeight() / 4.0)
report = oedepict.OEReport(ropts)
# setup decpiction options
opts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(opts, itf)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
opts.SetAtomLabelFontScale(1.2)
DepictMoleculeWithFragmentCombinations(report, mol, frags, opts)
return oedepict.OEWriteReport(oname, report)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
ifs.SetConfTest(oechem.OEAbsoluteConfTest()) # VTL
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if ext != "pdf":
oechem.OEThrow.Fatal("Output must be PDF format.")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(),
oedepict.OEScale_AutoScale)
for mol in ifs.GetOEMols(): # VTL ignore confs; dont use GetOEGraphMols
print(mol.GetTitle()) # VTL
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(cell, disp)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, 12,
oedepict.OEAlignment_Center, oechem.OEBlack)
for pagenum, footer in enumerate(report.GetFooters()):
text = "Page %d of %d" % (pagenum + 1, report.NumPages())
oedepict.OEDrawTextToCenter(footer, text, font)
oedepict.OEWriteReport(ofs, ext, report)
return 0
def prep_pdf_writer():
itf = oechem.OEInterface()
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(), oedepict.OEScale_AutoScale)
return popts, dopts, report
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ifname = itf.GetString("-ringdict")
ofname = itf.GetString("-out")
if not oechem.OEIsValid2DRingDictionary(ifname):
oechem.OEThrow.Fatal("Invalid ring dictionary file!")
ringdict = oechem.OE2DRingDictionary(ifname)
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
oedepict.OEWrite2DRingDictionaryReport(ofname, ringdict, ropts)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
oedepict.OEConfigureHighlightParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
qname = itf.GetString("-query")
tname = itf.GetString("-target")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredMultiPageImageFile(ext):
oechem.OEThrow.Fatal("Unknown multipage image type!")
qfile = oechem.oemolistream()
if not qfile.open(qname):
oechem.OEThrow.Fatal("Cannot open mdl query file!")
if qfile.GetFormat() != oechem.OEFormat_MDL and qfile.GetFormat(
) != oechem.OEFormat_SDF:
oechem.OEThrow.Fatal("Query file has to be an MDL file!")
ifs = oechem.oemolistream()
if not ifs.open(tname):
oechem.OEThrow.Fatal("Cannot open target input file!")
depictquery = oechem.OEGraphMol()
if not oechem.OEReadMDLQueryFile(qfile, depictquery):
oechem.OEThrow.Fatal("Cannot read query molecule!")
oedepict.OEPrepareDepiction(depictquery)
queryopts = oechem.OEMDLQueryOpts_Default | oechem.OEMDLQueryOpts_SuppressExplicitH
qmol = oechem.OEQMol()
oechem.OEBuildMDLQueryExpressions(qmol, depictquery, queryopts)
ss = oechem.OESubSearch()
if not ss.Init(qmol):
oechem.OEThrow.Fatal("Cannot initialize substructure search!")
hstyle = oedepict.OEGetHighlightStyle(itf)
hcolor = oedepict.OEGetHighlightColor(itf)
align = itf.GetBool("-align")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetHeaderHeight(140.0)
report = oedepict.OEReport(ropts)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
dopts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
unique = True
for mol in ifs.GetOEGraphMols():
oechem.OEPrepareSearch(mol, ss)
miter = ss.Match(mol, unique)
if not miter.IsValid():
continue # no match
alignres = oedepict.OEAlignmentResult(miter.Target())
if align:
alignres = oedepict.OEPrepareAlignedDepiction(mol, ss)
else:
oedepict.OEPrepareDepiction(mol)
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, dopts)
if alignres.IsValid():
oedepict.OEAddHighlighting(disp, hcolor, hstyle, alignres)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawBorder(cell, oedepict.OELightGreyPen)
# render query structure in each header
headwidth, headheight = report.GetHeaderWidth(), report.GetHeaderHeight()
dopts.SetDimensions(headwidth, headheight, oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(depictquery, dopts)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, oedepict.OELightGreyPen)
oedepict.OEWriteReport(oname, report)
return 0