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 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
