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(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(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