def test_chebi_mass(): ch = ChEBI() mass1 = ch.getCompleteEntity("CHEBI:27732").mass assert float(mass1) == 194.19076 res = ch.getLiteEntity("194.19076", "MASS", 5, 2) assert res[0]["chebiId"] == "CHEBI:27732" # should return nothing res = ch.getLiteEntity("194.19076", "SMILES", 5, 2)
def chebi2name(self, name): """Return the ASCII name of a CHEBI identifier""" from bioservices import ChEBI c = ChEBI() name = dict(c.getLiteEntity(name)[0])["chebiAsciiName"] return name
def kegg_to_chebi(compound_ids): results = {} ch = ChEBI() for compound_id in compound_ids: try: if compound_id.startswith('C'): res = ch.getLiteEntity(compound_id) assert len(res) > 0 # we should always be able to convert from KEGG -> ChEBI ids le = res[0] chebi_number = le.chebiId.split(':')[1] print('KEGG %s --> ChEBI %s' % (compound_id, chebi_number)) results[compound_id] = chebi_number else: print('ChEBI %s --> ChEBI %s' % (compound_id, compound_id)) results[compound_id] = compound_id except Exception: print('KEGG %s --> KEGG %s' % (compound_id, compound_id)) results[compound_id] = compound_id return results
def chebi2name(self, name): """Return the ASCII name of a CHEBI identifier""" from bioservices import ChEBI c = ChEBI() name = dict(c.getLiteEntity(name)[0])['chebiAsciiName'] return name