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)