def parse(cls, string: str) -> Lipid:
"""
Parse a string represntation of a lipid and create Lipid class.
:param string: The input string.
:return: An instance of Lipid
"""
# TODO refactor, too much code repeated in the two if blocks
# identify abbreviation type
if '(' in string and ')' in string:
string = string.strip()
if not string.endswith(')'):
raise TypeError(f"Cannot parse abbreviation {string}")
lipid_class_name = string.split('(', 1)[0]
# second part of split at first ( is residue string, add leading ( again!
residue_string = '(' + string.split('(', 1)[1]
lipidclass = LipidClass.parse(lipid_class_name)
residuelist = ResidueList.parse(residue_string)
lipid = cls(lipidclass, residuelist)
lipid._input = string
return lipid
# CE 22:4;0
elif ' ' in string:
lipid_class_name, residue_string = string.split(' ', 1)
lipidclass = LipidClass.parse(lipid_class_name)
residuelist = ResidueList.parse(residue_string)
lipid = cls(lipidclass, residuelist)
lipid._input = string
return lipid
else:
lipid = Lipid(LipidClass(string))
lipid._input = string
return lipid
def test_residuelist_parse():
test_string = '18:1;0_19:1;0'
residuelist = ResidueList.parse(test_string)
assert len(residuelist) == 2
assert residuelist[0].carbon_atoms == 18
assert residuelist[0].double_bonds == 1
assert residuelist[0].oxidation == 0
assert residuelist[1].carbon_atoms == 19
assert residuelist[1].double_bonds == 1
assert residuelist[1].oxidation == 0
test_string = '18:1_19:1'
residuelist = ResidueList.parse(test_string)
assert len(residuelist) == 2
assert residuelist[0].carbon_atoms == 18
assert residuelist[0].double_bonds == 1
assert residuelist[0].oxidation == None
assert residuelist[1].carbon_atoms == 19
assert residuelist[1].double_bonds == 1
assert residuelist[1].oxidation == None
test_string = 'O-16:0;0/18:1;0'
residuelist = ResidueList.parse(test_string)
assert len(residuelist) == 2
assert residuelist[0].carbon_atoms == 16
assert residuelist[0].double_bonds == 0
assert residuelist[0].oxidation == 0
assert residuelist[0].modification.name == 'O-'
assert residuelist[1].carbon_atoms == 18
assert residuelist[1].double_bonds == 1
assert residuelist[1].oxidation == 0