def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "ChEMBL COMPOUND")
assert res == ["521332"]
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "ChEMBL COMPOUND")
assert res == ["521332"]
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "KEGG COMPOUND accession")
assert res == ['C07484']
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "KEGG COMPOUND accession")
assert res == ['C07484']
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def _lookup_chebi_id(self):
chebi_web = ChEBI()
lookup_id = str(self.external_id)
if not lookup_id.startswith("CHEBI:"):
lookup_id = "CHEBI:{}".format(self.external_id)
chebi = chebi_web.getCompleteEntity(lookup_id)
if not chebi:
self.error = "No results found when querying ChEBI for {}".format(
self.external_id)
return self
# Synonyms
# We get duplicates so filter these.
if self.get_synonyms:
try:
seen_it = {}
for item in chebi.Synonyms:
if item.data not in seen_it:
self.synonyms.append(item.data)
seen_it[item.data] = 1
except AttributeError:
pass # Some may not have synonyms apparently
# Name
self.name = chebi.chebiAsciiName
# inchikey
try:
self.inchikey = chebi.inchiKey
except AttributeError:
self.error = 'No InChIKey found for entry: {}'.format(
self.external_id)
return self
def get_single_compound_metadata_online(compound_id):
if compound_id.upper().startswith('C'):
s = KEGG()
res = s.get(compound_id)
return s.parse(res)
else:
ch = ChEBI()
res = ch.getCompleteEntity('CHEBI:'+compound_id)
return res
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 get_compound_id(smiles):
""" returns kegg id for compund with given smiles """
indigo = Indigo()
# convert smiles to standard format
mol = indigo.loadMolecule(smiles)
mol.aromatize()
moi_smiles = mol.canonicalSmiles()
# Get list of possible kegg IDs
url = "http://rest.genome.jp/subcomp/?smiles=%s&cutoff=1.0" % smiles
http_client = HTTPClient()
try:
response = http_client.fetch(url).body
except HTTPError as e:
raise RuntimeError("Error:", str(e))
http_client.close()
subcomp_results = response.split("\n")
subcomp_results.pop()
subcomp_results = ([i.split('\t')[0] for i in subcomp_results])
# get smiles for all compound IDs found
all_smiles = []
uni = UniChem()
mapping = uni.get_mapping("kegg_ligand", "chebi")
ch = ChEBI()
all_smiles = [ch.getCompleteEntity(mapping[x]).smiles
for x in subcomp_results]
# convert smiles to a standard format
for pos, mol in enumerate(all_smiles):
m = indigo.loadMolecule(mol)
m.aromatize()
all_smiles[pos] = m.canonicalSmiles()
# check if smiles matches given and, if so, use that compound ID
# if not, errors out
try:
index = all_smiles.index(moi_smiles)
except:
raise RuntimeError("SMILES unmatchable to: %s" % str(all_smiles))
return subcomp_results[index]
def test_structure():
ch = ChEBI()
smiles = ch.getCompleteEntity("CHEBI:27732").smiles
ch.getStructureSearch(smiles, "SMILES", "SIMILARITY", 3, 0.25)
def test_chebi_mass():
ch = ChEBI()
mass1 = ch.getCompleteEntity("CHEBI:27732").mass
assert float(mass1) == 194.19076
def test_structure():
ch = ChEBI()
smiles = ch.getCompleteEntity("CHEBI:27732").smiles
ch.getStructureSearch(smiles, "SMILES", "SIMILARITY", 3, 0.25)
def test_chebi_mass():
ch = ChEBI()
mass1 = ch.getCompleteEntity("CHEBI:27732").mass
assert float(mass1) == 194.19076
