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 main(argv=[__name__]): # import configuration file itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) # add configuration for image size and display options oedepict.OEConfigureImageOptions(itf) oedepict.OEConfigure2DMolDisplayOptions(itf) if not oechem.OEParseCommandLine(itf, argv): oechem.OEThrow.Fatal("Unable to interpret command line!") ifname = itf.GetString("-in") ofname = itf.GetString("-out") ifs = oechem.oemolistream(ifname) mol = oechem.OEGraphMol() oechem.OEReadMolecule(ifs, mol) oedepict.OEPrepareDepiction(mol) width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf) opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) # set up display options from command line parameters oedepict.OESetup2DMolDisplayOptions(opts, itf) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule(ofname, disp)
def main(argv=[__name__]): itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) oedepict.OEConfigureImageWidth(itf, 400.0) oedepict.OEConfigureImageHeight(itf, 400.0) oedepict.OEConfigureImageGridParams(itf) oedepict.OEConfigurePrepareDepictionOptions(itf) oedepict.OEConfigure2DMolDisplayOptions(itf) if not oechem.OEParseCommandLine(itf, argv): oechem.OEThrow.Fatal("Unable to interpret command line!") oname = itf.GetString("-out") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight( itf) image = oedepict.OEImage(width, height) rows = oedepict.OEGetImageGridNumRows(itf) cols = oedepict.OEGetImageGridNumColumns(itf) grid = oedepict.OEImageGrid(image, rows, cols) popts = oedepict.OEPrepareDepictionOptions() oedepict.OESetupPrepareDepictionOptions(popts, itf) dopts = oedepict.OE2DMolDisplayOptions() oedepict.OESetup2DMolDisplayOptions(dopts, itf) dopts.SetDimensions(grid.GetCellWidth(), grid.GetCellHeight(), oedepict.OEScale_AutoScale) celliter = grid.GetCells() for iname in itf.GetStringList("-in"): ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Warning("Cannot open %s input file!" % iname) continue for mol in ifs.GetOEGraphMols(): if not celliter.IsValid(): break oedepict.OEPrepareDepiction(mol, popts) disp = oedepict.OE2DMolDisplay(mol, dopts) oedepict.OERenderMolecule(celliter.Target(), disp) celliter.Next() oedepict.OEWriteImage(ofs, ext, image) return 0
def main(argv=[__name__]): itf = oechem.OEInterface(InterfaceData) oedepict.OEConfigureImageOptions(itf) oedepict.OEConfigurePrepareDepictionOptions(itf) oedepict.OEConfigure2DMolDisplayOptions(itf) if not oechem.OEParseCommandLine(itf, argv): oechem.OEThrow.Fatal("Unable to interpret command line!") iname = itf.GetString("-in") oname = itf.GetString("-out") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") mol = oechem.OEGraphMol() if not oechem.OEReadMolecule(ifs, mol): oechem.OEThrow.Fatal("Cannot read input file!") if itf.HasString("-ringdict"): rdfname = itf.GetString("-ringdict") if not oechem.OEInit2DRingDictionary(rdfname): oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!") popts = oedepict.OEPrepareDepictionOptions() oedepict.OESetupPrepareDepictionOptions(popts, itf) oedepict.OEPrepareDepiction(mol, popts) width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight( itf) dopts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(dopts, itf) disp = oedepict.OE2DMolDisplay(mol, dopts) oedepict.OERenderMolecule(ofs, ext, disp) return 0
def main(argv=[__name__]): itf = oechem.OEInterface(InterfaceData) oedepict.OEConfigureImageOptions(itf) oedepict.OEConfigure2DMolDisplayOptions(itf) if not oechem.OEParseCommandLine(itf, argv): oechem.OEThrow.Fatal("Unable to interpret command line!") iname = itf.GetString("-in") oname = itf.GetString("-out") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") if ifs.GetFormat() != oechem.OEFormat_MDL: oechem.OEThrow.Fatal("Input file is not an MDL query file") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") mol = oechem.OEGraphMol() if not oechem.OEReadMDLQueryFile(ifs, mol): oechem.OEThrow.Fatal("Cannot read mdl query input file!") clearcoords, suppressH = False, False oedepict.OEPrepareDepiction(mol, clearcoords, suppressH) width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight( itf) opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(opts, itf) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule(ofs, ext, disp) return 0
def render_atom_mapping(filename, molecule1, molecule2, new_to_old_atom_map, width=1200, height=600): """ Render the atom mapping to a PDF file. Parameters ---------- filename : str The PDF filename to write to. molecule1 : openeye.oechem.OEMol Initial molecule molecule2 : openeye.oechem.OEMol Final molecule new_to_old_atom_map : dict of int new_to_old_atom_map[molecule2_atom_index] is the corresponding molecule1 atom index width : int, optional, default=1200 Width in pixels height : int, optional, default=1200 Height in pixels """ from openeye import oechem, oedepict # Make copies of the input molecules molecule1, molecule2 = oechem.OEGraphMol(molecule1), oechem.OEGraphMol(molecule2) oechem.OEGenerate2DCoordinates(molecule1) oechem.OEGenerate2DCoordinates(molecule2) # Add both to an OEGraphMol reaction rmol = oechem.OEGraphMol() rmol.SetRxn(True) def add_molecule(mol): # Add atoms new_atoms = list() old_to_new_atoms = dict() for old_atom in mol.GetAtoms(): new_atom = rmol.NewAtom(old_atom.GetAtomicNum()) new_atoms.append(new_atom) old_to_new_atoms[old_atom] = new_atom # Add bonds for old_bond in mol.GetBonds(): rmol.NewBond(old_to_new_atoms[old_bond.GetBgn()], old_to_new_atoms[old_bond.GetEnd()], old_bond.GetOrder()) return new_atoms, old_to_new_atoms [new_atoms_1, old_to_new_atoms_1] = add_molecule(molecule1) [new_atoms_2, old_to_new_atoms_2] = add_molecule(molecule2) # Label reactant and product for atom in new_atoms_1: atom.SetRxnRole(oechem.OERxnRole_Reactant) for atom in new_atoms_2: atom.SetRxnRole(oechem.OERxnRole_Product) core1 = oechem.OEAtomBondSet() core2 = oechem.OEAtomBondSet() # add all atoms to the set core1.AddAtoms(new_atoms_1) core2.AddAtoms(new_atoms_2) # Label mapped atoms core_change = oechem.OEAtomBondSet() index =1 for (index2, index1) in new_to_old_atom_map.items(): new_atoms_1[index1].SetMapIdx(index) new_atoms_2[index2].SetMapIdx(index) # now remove the atoms that are core, so only uniques are highlighted core1.RemoveAtom(new_atoms_1[index1]) core2.RemoveAtom(new_atoms_2[index2]) if new_atoms_1[index1].GetAtomicNum() != new_atoms_2[index2].GetAtomicNum(): # this means the element type is changing core_change.AddAtom(new_atoms_1[index1]) core_change.AddAtom(new_atoms_2[index2]) index += 1 # Set up image options itf = oechem.OEInterface() oedepict.OEConfigureImageOptions(itf) ext = oechem.OEGetFileExtension(filename) if not oedepict.OEIsRegisteredImageFile(ext): raise Exception('Unknown image type for filename %s' % filename) ofs = oechem.oeofstream() if not ofs.open(filename): raise Exception('Cannot open output file %s' % filename) # Setup depiction options oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle) opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(opts, itf) opts.SetBondWidthScaling(True) opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx()) opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome) # Depict reaction with component highlights oechem.OEGenerate2DCoordinates(rmol) rdisp = oedepict.OE2DMolDisplay(rmol, opts) oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPink),oedepict.OEHighlightStyle_Stick, core1) oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPurple),oedepict.OEHighlightStyle_Stick, core2) oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEGreen),oedepict.OEHighlightStyle_Stick, core_change) oedepict.OERenderMolecule(ofs, ext, rdisp) ofs.close()
def main(argv=[__name__]): itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) oedepict.OEConfigureImageWidth(itf, 900.0) oedepict.OEConfigureImageHeight(itf, 600.0) oedepict.OEConfigure2DMolDisplayOptions( itf, oedepict.OE2DMolDisplaySetup_AromaticStyle) oechem.OEConfigureSplitMolComplexOptions( itf, oechem.OESplitMolComplexSetup_LigName) if not oechem.OEParseCommandLine(itf, argv): return 1 iname = itf.GetString("-complex") oname = itf.GetString("-out") ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") complexmol = oechem.OEGraphMol() if not oechem.OEReadMolecule(ifs, complexmol): oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname) if not oechem.OEHasResidues(complexmol): oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All) # Separate ligand and protein sopts = oechem.OESplitMolComplexOptions() oechem.OESetupSplitMolComplexOptions(sopts, itf) ligand = oechem.OEGraphMol() protein = oechem.OEGraphMol() water = oechem.OEGraphMol() other = oechem.OEGraphMol() pfilter = sopts.GetProteinFilter() wfilter = sopts.GetWaterFilter() sopts.SetProteinFilter(oechem.OEOrRoleSet(pfilter, wfilter)) sopts.SetWaterFilter( oechem.OEMolComplexFilterFactory( oechem.OEMolComplexFilterCategory_Nothing)) oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts) if ligand.NumAtoms() == 0: oechem.OEThrow.Fatal("Cannot separate complex!") # Perceive interactions asite = oechem.OEInteractionHintContainer(protein, ligand) if not asite.IsValid(): oechem.OEThrow.Fatal("Cannot initialize active site!") asite.SetTitle(ligand.GetTitle()) oechem.OEPerceiveInteractionHints(asite) oegrapheme.OEPrepareActiveSiteDepiction(asite) # Depict active site with interactions width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight( itf) image = oedepict.OEImage(width, height) cframe = oedepict.OEImageFrame(image, width * 0.80, height, oedepict.OE2DPoint(0.0, 0.0)) lframe = oedepict.OEImageFrame(image, width * 0.20, height, oedepict.OE2DPoint(width * 0.80, 0.0)) opts = oegrapheme.OE2DActiveSiteDisplayOptions(cframe.GetWidth(), cframe.GetHeight()) oedepict.OESetup2DMolDisplayOptions(opts, itf) adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts) oegrapheme.OERenderActiveSite(cframe, adisp) lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(10, 1) oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts) oedepict.OEWriteImage(oname, image) return 0
def main(argv=[__name__]): itf = oechem.OEInterface(InterfaceData) oedepict.OEConfigureImageOptions(itf) oedepict.OEConfigurePrepareDepictionOptions(itf) oedepict.OEConfigure2DMolDisplayOptions(itf) oedepict.OEConfigureHighlightParams(itf) if not oechem.OEParseCommandLine(itf, argv): oechem.OEThrow.Fatal("Unable to interpret command line!") iname = itf.GetString("-in") oname = itf.GetString("-out") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") mol = oechem.OEGraphMol() if not oechem.OEReadMolecule(ifs, mol): oechem.OEThrow.Fatal("Cannot read input file!") smarts = itf.GetString("-smarts") ss = oechem.OESubSearch() if not ss.Init(smarts): oechem.OEThrow.Fatal("Cannot parse smarts: %s" % smarts) popts = oedepict.OEPrepareDepictionOptions() oedepict.OESetupPrepareDepictionOptions(popts, itf) oedepict.OEPrepareDepiction(mol, popts) width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight( itf) dopts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(dopts, itf) dopts.SetMargins(10.0) disp = oedepict.OE2DMolDisplay(mol, dopts) hstyle = oedepict.OEGetHighlightStyle(itf) hcolor = oedepict.OEGetHighlightColor(itf) oechem.OEPrepareSearch(mol, ss) unique = True for match in ss.Match(mol, unique): oedepict.OEAddHighlighting(disp, hcolor, hstyle, match) oedepict.OERenderMolecule(ofs, ext, disp) 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
def main(argv=[__name__]): itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) oedepict.OEConfigureImageWidth(itf, 600.0) oedepict.OEConfigureImageHeight(itf, 600.0) oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle) oechem.OEConfigureSplitMolComplexOptions(itf, oechem.OESplitMolComplexSetup_LigName) if not oechem.OEParseCommandLine(itf, argv): return 1 iname = itf.GetString("-complex") oname = itf.GetString("-out") ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") complexmol = oechem.OEGraphMol() if not oechem.OEReadMolecule(ifs, complexmol): oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname) if not oechem.OEHasResidues(complexmol): oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All) # Separate ligand and protein sopts = oechem.OESplitMolComplexOptions() oechem.OESetupSplitMolComplexOptions(sopts, itf) ligand = oechem.OEGraphMol() protein = oechem.OEGraphMol() water = oechem.OEGraphMol() other = oechem.OEGraphMol() oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts) if ligand.NumAtoms() == 0: oechem.OEThrow.Fatal("Cannot separate complex!") # Calculate average BFactor of the whole complex avgbfactor = GetAverageBFactor(complexmol) # Calculate minimum and maximum BFactor of the ligand and its environment minbfactor, maxbfactor = GetMinAndMaxBFactor(ligand, protein) # Attach to each ligand atom the average BFactor of the nearby protein atoms stag = "avg residue BFfactor" itag = oechem.OEGetTag(stag) SetAverageBFactorOfNearbyProteinAtoms(ligand, protein, itag) oechem.OEThrow.Info("Average BFactor of the complex = %+.3f" % avgbfactor) oechem.OEThrow.Info("Minimum BFactor of the ligand and its environment = %+.3f" % minbfactor) oechem.OEThrow.Info("Maximum BFactor of the ligand and its environment = %+.3f" % maxbfactor) # Create image imagewidth, imageheight = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf) image = oedepict.OEImage(imagewidth, imageheight) mframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.90, oedepict.OE2DPoint(0.0, 0.0)) lframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.10, oedepict.OE2DPoint(0.0, imageheight * 0.90)) opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(), mframe.GetHeight(), oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(opts, itf) opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome) # Create BFactor color gradient colorg = oechem.OELinearColorGradient() colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEDarkBlue)) colorg.AddStop(oechem.OEColorStop(10.0, oechem.OELightBlue)) colorg.AddStop(oechem.OEColorStop(25.0, oechem.OEYellowTint)) colorg.AddStop(oechem.OEColorStop(50.0, oechem.OERed)) colorg.AddStop(oechem.OEColorStop(100.0, oechem.OEDarkRose)) # Prepare ligand for depiction oegrapheme.OEPrepareDepictionFrom3D(ligand) arcfxn = BFactorArcFxn(colorg, itag) for atom in ligand.GetAtoms(): oegrapheme.OESetSurfaceArcFxn(ligand, atom, arcfxn) opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(ligand, opts)) # Render ligand and visualize BFactor disp = oedepict.OE2DMolDisplay(ligand, opts) colorbfactor = ColorLigandAtomByBFactor(colorg) oegrapheme.OEAddGlyph(disp, colorbfactor, oechem.OEIsTrueAtom()) oegrapheme.OEDraw2DSurface(disp) oedepict.OERenderMolecule(mframe, disp) # Draw color gradient opts = oegrapheme.OEColorGradientDisplayOptions() opts.SetColorStopPrecision(1) opts.AddMarkedValue(avgbfactor) opts.SetBoxRange(minbfactor, maxbfactor) oegrapheme.OEDrawColorGradient(lframe, colorg, opts) oedepict.OEWriteImage(oname, image) return 0
def main(argv=[__name__]): itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) oedepict.OEConfigureImageWidth(itf, 900.0) oedepict.OEConfigureImageHeight(itf, 600.0) oedepict.OEConfigure2DMolDisplayOptions( itf, oedepict.OE2DMolDisplaySetup_AromaticStyle) oechem.OEConfigureSplitMolComplexOptions( itf, oechem.OESplitMolComplexSetup_LigName | oechem.OESplitMolComplexSetup_CovLig) if not oechem.OEParseCommandLine(itf, argv): return 1 if itf.HasString("-complex") and (itf.HasString("-protein") or itf.HasString("-ligand")): oechem.OEThrow.Warning("Only complex in %s file fill be used!" % itf.GetString("-complex")) if not (itf.HasString("-complex")) ^ (itf.HasString("-protein") and itf.HasString("-ligand")): oechem.OEThrow.Fatal( "Please specify either complex or ligand and protein input files!") oname = itf.GetString("-out") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") # initialize protein and ligand protein = oechem.OEGraphMol() ligand = oechem.OEGraphMol() if not get_protein_and_ligands(protein, ligand, itf): oechem.OEThrow.Fatal("Cannot initialize protein and/or ligand!") # depict active site with interactions width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight( itf) image = oedepict.OEImage(width, height) interactive_legend = False magnify_residue = 1.0 if ext == 'svg': interactive_legend = itf.GetBool("-interactive-legend") magnify_residue = itf.GetFloat("-magnify-residue") cwidth, cheight = width, height if not interactive_legend: cwidth = cwidth * 0.8 opts = oegrapheme.OE2DActiveSiteDisplayOptions(cwidth, cheight) oedepict.OESetup2DMolDisplayOptions(opts, itf) opts.SetRenderInteractiveLegend(interactive_legend) opts.SetSVGMagnifyResidueInHover(magnify_residue) if interactive_legend: depict_complex(image, protein, ligand, opts) else: main_frame = oedepict.OEImageFrame( image, width * 0.80, height, oedepict.OE2DPoint(width * 0.2, 0.0)) legend_frame = oedepict.OEImageFrame( image, width * 0.20, height, oedepict.OE2DPoint(width * 0.0, 0.0)) depict_complex(main_frame, protein, ligand, opts, legend_frame) if ext == 'svg' and (interactive_legend or magnify_residue > 1.0): iconscale = 0.5 oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight, iconscale) oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0) oedepict.OEWriteImage(oname, image) return 0