def make_restraints_from_mmcif_dict(cif_file_name_in, comp_id, mogul_dir, output_dir, output_postfix, quartet_planes, quartet_hydrogen_planes, use_mmff, pdb_out_file_name, mmcif_restraints_out_file_name): if not test_for_mogul(): return [(None, None)] if comp_id == "TRY_ALL_COMP_IDS": types = pysw.types_from_mmcif_dictionary(cif_file_name_in) l = [] for r_type in types: file_name_stub = r_type + "-" + output_postfix if options.output_dir != ".": file_name_stub = os.path.join(options.output_dir, file_name_stub) pdb_out_file_name_local = file_name_stub + ".pdb" mmcif_restraints_out_file_name_local = file_name_stub + ".cif" # t_mol = make_restraints_from_mmcif_dict_single(cif_file_name_in, r_type, mogul_dir, output_postfix, quartet_planes, quartet_hydrogen_planes, use_mmff, pdb_out_file_name_local, mmcif_restraints_out_file_name_local) l.append((t_mol, r_type)) return l else: # just the one m = make_restraints_from_mmcif_dict_single(cif_file_name_in, comp_id, mogul_dir, output_postfix, quartet_planes, quartet_hydrogen_planes, use_mmff, pdb_out_file_name, mmcif_restraints_out_file_name) return [(m, comp_id)]
def make_restraints_from_mmcif_dict(cif_file_name_in, comp_id, mogul_dir, output_dir, output_postfix, quartet_planes, quartet_hydrogen_planes, use_mmff, pdb_out_file_name, mmcif_restraints_out_file_name): if not test_for_mogul(): return [(None, None)] if comp_id == "TRY_ALL_COMP_IDS": types = pysw.types_from_mmcif_dictionary(cif_file_name_in) l = [] for r_type in types: file_name_stub = r_type + "-" + output_postfix if options.output_dir != ".": file_name_stub = os.path.join(options.output_dir, file_name_stub) pdb_out_file_name_local = file_name_stub + ".pdb" mmcif_restraints_out_file_name_local = file_name_stub + ".cif" # t_mol = make_restraints_from_mmcif_dict_single(cif_file_name_in, r_type, mogul_dir, output_postfix, quartet_planes, quartet_hydrogen_planes, use_mmff, pdb_out_file_name_local, mmcif_restraints_out_file_name_local) l.append((t_mol, r_type)) return l else: # just the one m = make_restraints_from_mmcif_dict_single(cif_file_name_in, comp_id, mogul_dir, output_postfix, quartet_planes, quartet_hydrogen_planes, use_mmff, pdb_out_file_name, mmcif_restraints_out_file_name) return [(m, comp_id)]
if options.show_tautomers or options.show_smiles: # ------------------------ Tautomers and SMILES --------------------------------------------- mol = False if len(args) > 0: smi_raw = args[0] smiles,compound_name = smiles_and_name_from(smi_raw) mol = Chem.MolFromSmiles(smiles) else: if options.sdf_file != None: mol = Chem.MolFromMolFile(options.sdf_file) else: if options.mmcif_file_name != None: types = pysw.types_from_mmcif_dictionary(options.mmcif_file_name) print '-- tautomer mode: mmcif file types:', types for type in types: mol_local = pyrogen_boost.rdkit_mol_chem_comp_pdbx(options.mmcif_file_name, type) score_and_print_tautomers(mol_local, type, options.output_postfix, options.drawing) if mol: if options.show_tautomers: score_and_print_tautomers(mol, comp_id, options.output_postfix, options.drawing) if options.show_smiles: s = Chem.MolToSmiles(mol); print s else: # ------------------------ dict-build-mode ---------------------------------------------------
if options.show_tautomers or options.show_smiles: # ------------------------ Tautomers and SMILES --------------------------------------------- mol = False if len(args) > 0: smi_raw = args[0] smiles,compound_name = smiles_and_name_from(smi_raw) mol = Chem.MolFromSmiles(smiles) else: if options.sdf_file != None: mol = Chem.MolFromMolFile(options.sdf_file) else: if options.mmcif_file_name != None: types = pysw.types_from_mmcif_dictionary(options.mmcif_file_name) print '-- tautomer mode: mmcif file types:', types for type in types: mol_local = pyrogen_boost.rdkit_mol_chem_comp_pdbx(options.mmcif_file_name, type) score_and_print_tautomers(mol_local, type, options.output_postfix, options.drawing) if mol: if options.show_tautomers: score_and_print_tautomers(mol, comp_id, options.output_postfix, options.drawing) if options.show_smiles: s = Chem.MolToSmiles(mol); print s else: # ------------------------ dict-build-mode ---------------------------------------------------