def test_lipid_xreflist():
t = 'DAG 16:0;0_22:4;0'
lipid = Lipid.parse(t)
lipid.add_xref(
Xref('TargetDB', 'targetid')
)
assert len(lipid.xreflist) == 1
def test_swisslipids_xref():
lipid = Lipid.parse('CE(20:2)')
lipid = SwissLipids.get_xrefs(lipid)
for xref in lipid.xreflist:
assert xref.target_db == SwissLipids.NAME
assert any(x.target_id == 'SLM:000500283' for x in lipid.xreflist)
def test_parse(self):
t = 'CE 16:2;0'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'CE'
assert lipid.residueslist[0].carbon_atoms == 16
assert lipid.residueslist[0].double_bonds == 2
assert lipid.residueslist[0].oxidation == 0
t = 'CE(16:2;0)'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'CE'
assert lipid.residueslist[0].carbon_atoms == 16
assert lipid.residueslist[0].double_bonds == 2
assert lipid.residueslist[0].oxidation == 0
t = 'DAG 16:0;0_22:4;0'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'DG'
assert len(lipid.residueslist) == 2
assert lipid.residueslist[0].carbon_atoms == 16
assert lipid.residueslist[0].double_bonds == 0
assert lipid.residueslist[0].oxidation == 0
t = 'PC(28:5(13Z,16Z,19Z,22Z,25Z)/0:0)'
lipid = Lipid.parse(t)
assert lipid.lipidclass.name == 'PC'
assert len(lipid.residueslist) == 2
assert lipid.residueslist[0].carbon_atoms == 28
assert lipid.residueslist[0].double_bonds == 5
assert lipid.residueslist[0].oxidation == None
assert len(lipid.residueslist[0].zstatelist) == 5
assert str(lipid.residueslist[0].zstatelist[1]) == '16Z'
t = 'chol'
lipid = Lipid.parse(t)
assert str(lipid.lipidclass) == 'chol'
def lipid_from_id(cls, swisslipidsid: str) -> Lipid:
"""
Call API to get details for a SwissLipids ID.
:param swisslipidsid: The SwissLipids ID.
:return: Return a Lipid.
"""
request_url = cls.BASE_URL + f'/entity/{swisslipidsid.strip()}'
log.debug(f'Call: {request_url}')
result = requests.get(request_url).json()
# get abbreviation
for synonym in result['synonyms']:
if synonym['type'] == 'abbreviation':
abbreviation = synonym['name']
lipid = Lipid.parse(abbreviation)
lipid.add_xref(Xref(cls.NAME, swisslipidsid))
return lipid
def test_errors(self):
with pytest.raises(TypeError):
# string not ending with bracket
Lipid.parse("CE(14:9(9Z)/8:0")