def get_cmpd_information(molec): """Get information from CHEBI Database of a compound from CHEBI ID. Online using libChEBIpy (https://github.com/libChEBI/libChEBIpy) """ if molec.chebiID is None and molec.iupac_name is not None: # try one more time for chebi ID chebiID = get_chebiID(mol_name=molec.name, iupac_name=molec.iupac_name) if chebiID is None: print('cannot get structure from chebi') return None molec.chebiID = [chebiID] # at this point, molec.chebiID will be a list - iterarte over it # the iteration stops if any CHEBI ID produces a structure for CID in molec.chebiID: if CID == '' or ' ' in CID or 'null' in CID: print(CID, '- not a real CHEBI ID') continue # get entity with chebiID entity = ChebiEntity(CID) # check for parent ID entity, CID = convert_entity_to_parent(entity, ID=CID, CID=CID) # attemp to get structure # SMILES smile = entity.get_smiles() print('libchebipy result:', smile) if smile is not None: rdkitmol = Chem.MolFromSmiles(smile) if rdkitmol is None: print('structure could not be deciphered') molec.SMILES = smile molec.mol = None continue else: rdkitmol.Compute2DCoords() molec.SMILES = smile # remove molecules with generalised atoms if '*' in smile: molec.mol = None else: molec.mol = rdkitmol elif smile is None: print('molecule does not have recorded structure in CHEBI DB') print('probably a generic structure - skipping.') molec.SMILES = smile molec.mol = None continue # set passed = True if this chebi ID produced a structure # would not get up to this point if it didnt # if not CIDs pass then the chebiIDs remain a list and will # fail the # next step passed = True # set molecule properties if passed: molec.chebiID = CID molec.DB_ID = CID # save InChiKey iKEY = entity.get_inchi_key() if iKEY is not None: molec.InChiKey = iKEY # save inchi inchi = entity.get_inchi() if inchi is not None: molec.InChi = inchi # set name if name is only a code at this point try: if molec.change_name is True: molec.name = entity.get_name() molec.change_name = False except AttributeError: molec.change_name = False return None
class TestChebiEntity(unittest.TestCase): '''COMMENT''' def setUp(self): '''COMMENT''' self.__existing = ChebiEntity('4167') self.__secondary = ChebiEntity('CHEBI:5585') def test_get_non_existing(self): '''COMMENT''' self.assertRaises(ChebiException, ChebiEntity, '-1') def test_get_id_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_id() == 'CHEBI:4167') def test_get_id_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_id() == 'CHEBI:5585') def test_get_formulae_existing(self): '''COMMENT''' this_formula = Formula('C6H12O6', 'KEGG COMPOUND') self.assertTrue(this_formula in self.__existing.get_formulae()) def test_get_formulae_secondary(self): '''COMMENT''' this_formula = Formula('H2O', 'ChEBI') self.assertTrue(this_formula in self.__secondary.get_formulae()) def test_get_formula_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_formula() == 'C6H12O6') def test_get_formula_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_formula() == 'H2O') def test_get_mass_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_mass(), 180.15588) def test_get_mass_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mass(), 18.01530) def test_get_charge_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_charge(), 0) def test_get_charge_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_charge(), 0) def test_get_charge_secondary2(self): '''COMMENT''' self.assertEquals(-2, ChebiEntity('43474').get_charge()) def test_get_comments_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('29044') this_comment = Comment('General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_comments_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('11505') this_comment = Comment('General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_source_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_source(), 'KEGG COMPOUND') def test_get_source_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_source(), 'KEGG COMPOUND') def test_get_prnt_id_existing(self): '''COMMENT''' self.assertIsNone(self.__existing.get_parent_id()) def test_get_prnt_id_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_parent_id(), 'CHEBI:15377') def test_get_name_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_name(), 'D-glucopyranose') def test_get_name_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_name(), 'water') def test_get_definition_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_definition(), 'A glucopyranose having D-configuration.') def test_get_definition_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('41140') self.assertEqual(this_chebi_entity.get_definition(), 'D-Glucopyranose with beta configuration at the ' 'anomeric centre.') def test_get_mod_on_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_modified_on() > datetime.datetime.strptime('2014-01-01', '%Y-%M-%d')) def test_get_mod_on_secondary(self): '''COMMENT''' self.assertIsNotNone(self.__secondary.get_modified_on()) def test_get_created_by_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_created_by(), 'CHEBI') def test_get_created_by_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_created_by(), 'ops$mennis') def test_get_star_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_star(), 3) def test_get_star_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_star(), 3) def test_get_db_acc_existing(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'D-Glucose', 'MetaCyc') self.assertTrue(dat_acc in self.__existing.get_database_accessions()) def test_get_db_acc_secondary(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'WATER', 'MetaCyc') self.assertTrue(dat_acc in self.__secondary.get_database_accessions()) def test_get_inchi_existing(self): '''COMMENT''' inchi = 'InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/' + \ 'h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1' self.assertEqual(self.__existing.get_inchi(), inchi) def test_get_inchi_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi(), 'InChI=1S/H2O/h1H2') def test_get_inchi_key_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_inchi_key(), 'WQZGKKKJIJFFOK-GASJEMHNSA-N') def test_get_inchi_key_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi_key(), 'XLYOFNOQVPJJNP-UHFFFAOYSA-N') def test_get_smiles_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_smiles(), 'OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O') def test_get_smiles_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_smiles(), '[H]O[H]') def test_get_mol_existing(self): '''COMMENT''' chebi_id = 73938 this_chebi_entity = ChebiEntity(str(chebi_id)) self.assertEqual(this_chebi_entity.get_mol(), _read_mol_file(chebi_id)) def test_get_mol_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mol(), _read_mol_file(15377)) def test_get_mol_file_existing(self): '''COMMENT''' chebi_id = 73938 self.__get_mol_file(chebi_id, chebi_id) def test_get_mol_file_secondary(self): '''COMMENT''' read_id = 15377 retrieved_id = 42857 self.__get_mol_file(read_id, retrieved_id) def test_get_names_existing(self): '''COMMENT''' this_name = Name('Grape sugar', 'SYNONYM', 'KEGG COMPOUND', False, 'en') self.assertTrue(this_name in self.__existing.get_names()) def test_get_names_secondary(self): '''COMMENT''' this_name = Name('eau', 'SYNONYM', 'ChEBI', False, 'fr') self.assertTrue(this_name in self.__secondary.get_names()) def test_get_references_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('15347') this_reference = Reference('WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_references_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('22182') this_reference = Reference('WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_cmp_orig_existing(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue(this_compound_origin in self.__existing.get_compound_origins()) def test_get_cmp_orig_secondary(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue(this_compound_origin in self.__secondary.get_compound_origins()) def test_get_out_existing(self): '''COMMENT''' this_relation = Relation('is_a', '17634', 'C') self.assertTrue(this_relation in self.__existing.get_outgoings()) def test_get_out_secondary(self): '''COMMENT''' this_relation = Relation('has_role', 'CHEBI:48360', 'C') self.assertTrue(this_relation in self.__secondary.get_outgoings()) def test_get_in_existing(self): '''COMMENT''' this_relation = Relation('has_functional_parent', 'CHEBI:15866', 'C') self.assertTrue(this_relation in self.__existing.get_incomings()) def test_get_in_secondary(self): '''COMMENT''' this_relation = Relation('is_conjugate_acid_of', '29412', 'C') self.assertTrue(this_relation in self.__secondary.get_incomings()) def __get_mol_file(self, read_id, retrieved_id): '''COMMENT''' mol_read = _read_mol_file(read_id) this_chebi_entity = ChebiEntity(str(retrieved_id)) textfile_retrieved = open(this_chebi_entity.get_mol_filename(), 'r') mol_retrieved = textfile_retrieved.read() textfile_retrieved.close() self.assertEquals(mol_read, mol_retrieved)
class TestChebiEntity(unittest.TestCase): '''COMMENT''' def setUp(self): '''COMMENT''' self.__existing = ChebiEntity('4167') self.__secondary = ChebiEntity('CHEBI:5585') def test_get_non_existing(self): '''COMMENT''' self.assertRaises(ChebiException, ChebiEntity, '-1') def test_get_id_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_id() == 'CHEBI:4167') def test_get_id_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_id() == 'CHEBI:5585') def test_get_formulae_existing(self): '''COMMENT''' this_formula = Formula('C6H12O6', 'KEGG COMPOUND') self.assertTrue(this_formula in self.__existing.get_formulae()) def test_get_formulae_secondary(self): '''COMMENT''' this_formula = Formula('H2O', 'ChEBI') self.assertTrue(this_formula in self.__secondary.get_formulae()) def test_get_formula_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_formula() == 'C6H12O6') def test_get_formula_secondary(self): '''COMMENT''' self.assertTrue(self.__secondary.get_formula() == 'H2O') def test_get_mass_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_mass(), 180.15588) def test_get_mass_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mass(), 18.01530) def test_get_charge_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_charge(), 0) def test_get_charge_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_charge(), 0) def test_get_charge_secondary2(self): '''COMMENT''' self.assertEquals(-2, ChebiEntity('43474').get_charge()) def test_get_comments_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('29044') this_comment = Comment( 'General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_comments_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('11505') this_comment = Comment( 'General', 'General', 'The substituent name \'3-oxoprop-2-enyl\' is ' 'incorrect but is used in various databases.', datetime.datetime.strptime('2005-03-18', '%Y-%M-%d')) self.assertTrue(this_comment in this_chebi_entity.get_comments()) def test_get_source_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_source(), 'KEGG COMPOUND') def test_get_source_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_source(), 'KEGG COMPOUND') def test_get_prnt_id_existing(self): '''COMMENT''' self.assertIsNone(self.__existing.get_parent_id()) def test_get_prnt_id_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_parent_id(), 'CHEBI:15377') def test_get_name_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_name(), 'D-glucopyranose') def test_get_name_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_name(), 'water') def test_get_definition_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_definition(), 'A glucopyranose having D-configuration.') def test_get_definition_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('41140') self.assertEqual( this_chebi_entity.get_definition(), 'D-Glucopyranose with beta configuration at the ' 'anomeric centre.') def test_get_mod_on_existing(self): '''COMMENT''' self.assertTrue(self.__existing.get_modified_on() > datetime.datetime.strptime('2014-01-01', '%Y-%M-%d')) def test_get_mod_on_secondary(self): '''COMMENT''' self.assertIsNotNone(self.__secondary.get_modified_on()) def test_get_created_by_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_created_by(), 'CHEBI') def test_get_created_by_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_created_by(), 'ops$mennis') def test_get_star_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_star(), 3) def test_get_star_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_star(), 3) def test_get_db_acc_existing(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'D-Glucose', 'MetaCyc') self.assertTrue(dat_acc in self.__existing.get_database_accessions()) def test_get_db_acc_secondary(self): '''COMMENT''' dat_acc = DatabaseAccession('MetaCyc accession', 'WATER', 'MetaCyc') self.assertTrue(dat_acc in self.__secondary.get_database_accessions()) def test_get_inchi_existing(self): '''COMMENT''' inchi = 'InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/' + \ 'h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1' self.assertEqual(self.__existing.get_inchi(), inchi) def test_get_inchi_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi(), 'InChI=1S/H2O/h1H2') def test_get_inchi_key_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_inchi_key(), 'WQZGKKKJIJFFOK-GASJEMHNSA-N') def test_get_inchi_key_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_inchi_key(), 'XLYOFNOQVPJJNP-UHFFFAOYSA-N') def test_get_smiles_existing(self): '''COMMENT''' self.assertEqual(self.__existing.get_smiles(), 'OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O') def test_get_smiles_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_smiles(), '[H]O[H]') def test_get_mol_existing(self): '''COMMENT''' chebi_id = 73938 this_chebi_entity = ChebiEntity(str(chebi_id)) self.assertEqual(this_chebi_entity.get_mol(), _read_mol_file(chebi_id)) def test_get_mol_secondary(self): '''COMMENT''' self.assertEqual(self.__secondary.get_mol(), _read_mol_file(15377)) def test_get_mol_file_existing(self): '''COMMENT''' chebi_id = 73938 self.__get_mol_file(chebi_id, chebi_id) def test_get_mol_file_secondary(self): '''COMMENT''' read_id = 15377 retrieved_id = 42857 self.__get_mol_file(read_id, retrieved_id) def test_get_names_existing(self): '''COMMENT''' this_name = Name('Grape sugar', 'SYNONYM', 'KEGG COMPOUND', False, 'en') self.assertTrue(this_name in self.__existing.get_names()) def test_get_names_secondary(self): '''COMMENT''' this_name = Name('eau', 'SYNONYM', 'ChEBI', False, 'fr') self.assertTrue(this_name in self.__secondary.get_names()) def test_get_references_existing(self): '''COMMENT''' this_chebi_entity = ChebiEntity('15347') this_reference = Reference( 'WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_references_secondary(self): '''COMMENT''' this_chebi_entity = ChebiEntity('22182') this_reference = Reference( 'WO2006008754', 'Patent', '', 'NOVEL INTERMEDIATES FOR LINEZOLID ' 'AND RELATED COMPOUNDS') self.assertTrue(this_reference in this_chebi_entity.get_references()) def test_get_cmp_orig_existing(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue( this_compound_origin in self.__existing.get_compound_origins()) def test_get_cmp_orig_secondary(self): '''COMMENT''' this_compound_origin = CompoundOrigin('H**o sapiens', 'NCBI:9606', None, None, None, None, 'DOI', '10.1038/nbt.2488', None) self.assertTrue( this_compound_origin in self.__secondary.get_compound_origins()) def test_get_out_existing(self): '''COMMENT''' this_relation = Relation('is_a', '17634', 'C') self.assertTrue(this_relation in self.__existing.get_outgoings()) def test_get_out_secondary(self): '''COMMENT''' this_relation = Relation('has_role', 'CHEBI:48360', 'C') self.assertTrue(this_relation in self.__secondary.get_outgoings()) def test_get_in_existing(self): '''COMMENT''' this_relation = Relation('has_functional_parent', 'CHEBI:15866', 'C') self.assertTrue(this_relation in self.__existing.get_incomings()) def test_get_in_secondary(self): '''COMMENT''' this_relation = Relation('is_conjugate_acid_of', '29412', 'C') self.assertTrue(this_relation in self.__secondary.get_incomings()) def __get_mol_file(self, read_id, retrieved_id): '''COMMENT''' mol_read = _read_mol_file(read_id) this_chebi_entity = ChebiEntity(str(retrieved_id)) textfile_retrieved = open(this_chebi_entity.get_mol_filename(), 'r') mol_retrieved = textfile_retrieved.read() textfile_retrieved.close() self.assertEquals(mol_read, mol_retrieved)