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 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 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_residue_parse():
r = Residue.parse("15:3")
assert r.carbon_atoms == 15
r = Residue.parse("d15:3")
assert r.carbon_atoms == 15
assert str(r.modification) == 'd'
r = Residue.parse("15:3(6Z)")
assert r.carbon_atoms == 15
assert len(r.zstatelist) == 1
assert str(r.zstatelist[0]) == '6Z'
def test_residue_string():
r = Residue(15, 3)
assert r.residue_string == "15:3"
r = Residue(15, 3, 2)
assert r.residue_string == '15:3;2'
r = Residue(15, 3, 2, ResidueModification('O-'))
assert r.residue_string == 'O-15:3;2'
r = Residue(15, 3, 2, ResidueModification('d'))
assert r.residue_string == 'd15:3;2'
def parse(cls, string: str) -> ResidueList:
"""
Parse a string and return a list of Residues.
:param string: Input string.
:return: ResidueList instance.
"""
string = string.strip()
# remove brackets
log.debug(f'Parse input: {string}')
# if string.count('(') > 1 or string.count(')') > 1:
# raise NotImplementedError('alternative chains not implemented')
string = remove_outside_brackets(string)
# check for residue splitter
splittable = False
split_char = None
if '/' in string:
splittable = True
split_char = '/'
elif '_' in string:
splittable = True
split_char = '_'
residues = []
residue_string_list = string.split(split_char)
for residue_string in residue_string_list:
residues.append(Residue.parse(residue_string))
return cls(residues)
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_string():
r1 = Residue(18, 2)
r2 = Residue(12, 3)
residuelist = ResidueList([r1, r2])
assert residuelist.residuelist_string == '18:2/12:3'
def sum(self):
"""
Return sum of carbon atoms and double bonds of all Residues in this ResidueList as a Residue.
"""
return Residue(self.total_carbon_atoms, self.total_double_bonds)