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 some_lipids_plain_list():
"""
A handful of well formatted lipids, using all annotation elements.
Return as Python list, not as LipidList Object
"""
# lists of names to draw from
lipidclass_names = ['CE', 'Cer', 'TG']
modifications = ['d', 'O-', None, None]
lipidlist = []
for i in range(10):
lipidclass = LipidClass(random.choice(lipidclass_names))
num_of_residues = random.choice([1, 2, 3])
residuelist = ResidueList()
for i in range(0, num_of_residues):
residuelist.residues.append(
Residue(random.randint(6, 50),
random.randint(0, 10),
modification=ResidueModification(
random.choice(modifications))))
lipidlist.append(Lipid(lipidclass, residuelist))
return lipidlist
def test_residuelist_sum():
r1 = Residue(18, 2)
r2 = Residue(12, 3)
residuelist = ResidueList([r1, r2])
assert residuelist.total_double_bonds == 5
assert residuelist.total_carbon_atoms == 30
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_lipid_check_consistency():
l = Lipid(LipidClass('Cer'), ResidueList([Residue(16, 2), Residue(18, 1)]))
# check inconsistent state
assert l.residueslist[0].modification == None
l.check_consistency()
# check consistent state
assert l.residueslist[0].modification == CLASS_DEFAULT_MODIFICATION['Cer']
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
def __init__(self, lipidclass: LipidClass = None, residuelist: ResidueList = None, xreflist: XrefList = None):
if residuelist:
self.residueslist = residuelist
else:
self.residueslist = ResidueList()
self.lipidclass = lipidclass
if xreflist:
self.xreflist = xreflist
else:
self.xreflist = XrefList()
self._input = None
def test_residuelist_string():
r1 = Residue(18, 2)
r2 = Residue(12, 3)
residuelist = ResidueList([r1, r2])
assert residuelist.residuelist_string == '18:2/12:3'
def test_residuelist():
residuelist = ResidueList()
assert len(residuelist) == 0