def test_lipid_abbreviation():
l = Lipid(LipidClass('CE'), ResidueList([Residue(16, 2)]))
assert l.abbreviation() == 'CE(16:2)'
l = Lipid(LipidClass('CE'), ResidueList([Residue(16, 2), Residue(18, 1)]))
assert l.abbreviation() == 'CE(16:2/18:1)'
assert l.abbreviation(summed=True) == 'CE(34:3)'
l = Lipid(
LipidClass('CE'),
ResidueList([
Residue(16, 2, modification=ResidueModification('O-')),
Residue(18, 1)
]))
assert l.abbreviation() == 'CE(O-16:2/18:1)'
assert l.abbreviation(summed=True) == 'CE(O-34:3)'
# no residues, assure that abbreviation/summed fails with AttributeError
l = Lipid(LipidClass('CE'))
assert l.abbreviation() == 'CE'
assert l.abbreviation(summed=True) == 'CE'
def get_xrefs(cls, lipid: Lipid, summed: bool = False) -> XrefList:
xreflist = XrefList()
try:
search_term = lipid.abbreviation(summed)
except Exception as e:
log.debug(
f"No abbreviation for lipid: {lipid.lipidclass}, {lipid.residueslist}."
)
log.error(f"Failed with {e}")
search_term = lipid.abbreviation()
search_result = cls.run_search(search_term)
# search result can be empyt
if search_result:
for entity in cls.run_search(lipid.abbreviation(summed)):
xreflist.append(Xref(cls.NAME, entity['entity_id']))
return xreflist