def test_aggregator_adduct_lookup(self):
""" """
result = self.mda.adduct_lookup(728.605042778354,
ionmode='pos')['[M+H]+'][1]
assert 'SLM:000391523' in [i.lab.db_id for i in result]
swl_cer1p = [i for i in result if i.lab.db_id == 'SLM:000391523'][0]
assert 'Ceramide phosphate (d42:2)' in swl_cer1p.lab.names
assert '' not in swl_cer1p.lab.names
assert '1P' in swl_cer1p.hg.sub
lyp_cer1p = lipproc.LipidRecord(
lab=lipproc.LipidLabel(
db_id=None,
db='lipyd.lipid',
names=('Cer-1P(DH42:2)', ),
formula='C42H82N1O6P1',
),
hg=lipproc.Headgroup(main='Cer', sub=('1P', )),
chainsum=lipproc.ChainSummary(
c=42,
u=2,
typ=('Sph', 'FA'),
attr=(lipproc.ChainAttr(sph='DH', ether=False, oh=()),
lipproc.ChainAttr(sph='', ether=False, oh=())),
),
chains=(),
)
assert lyp_cer1p in list(result)
def iterlines(self):
"""Iterates standard lines."""
for subs, inst in self.subsproduct():
full_name = inst.getname()
chains = tuple(
s.attrs.chain for s in subs if hasattr(s.attrs, 'chain')
)
chainsum = lipproc.sum_chains(chains)
name = (
(lipproc.summary_str(self.hg, chainsum),)
if self.hg and self.sum_only else
(lipproc.full_str(self.hg, chains),)
if self.hg and not self.sum_only else
()
)
lab = lipproc.LipidLabel(
db_id = None,
db = 'lipyd.lipid',
names = name,
formula = inst.formula,
)
rec = lipproc.LipidRecord(
lab = lab,
hg = self.hg,
chainsum = chainsum if chainsum.c else None,
chains = () if self.sum_only else chains,
)
yield inst.mass, rec
def test_is_subset_of(self):
empty_lab = lipproc.LipidLabel(None, None, None, None)
lnp = name.LipidNameProcessor()
pe = lnp.process('Phosphatidylethanolamine')
pe_361 = lnp.process('Phosphatidylethanolamine(36:1)')
pe_180181 = lnp.process('Phosphatidylethanolamine(18:0/18:1)')
pe = lipproc.LipidRecord(
lab=empty_lab,
hg=pe[0],
chainsum=None,
chains=(),
)
pe_361 = lipproc.LipidRecord(
lab=empty_lab,
hg=pe_361[0],
chainsum=pe_361[1],
chains=(),
)
pe_180181 = lipproc.LipidRecord(
lab=empty_lab,
hg=pe_180181[0],
chainsum=pe_180181[1],
chains=pe_180181[2],
)
assert pe_361 in pe
assert pe_180181 in pe_361
assert pe_180181 in pe
cer_d_361 = lnp.process('Ceramide(d36:1)')
cer_dh_361 = lnp.process('Ceramide(DH36:1)')
cer_d_361 = lipproc.LipidRecord(
lab=empty_lab,
hg=cer_d_361[0],
chainsum=cer_d_361[1],
chains=(),
)
cer_dh_361 = lipproc.LipidRecord(
lab=empty_lab,
hg=cer_dh_361[0],
chainsum=cer_dh_361[1],
chains=(),
)
assert cer_d_361 not in cer_dh_361
assert cer_dh_361 not in cer_d_361
def __iter__(self):
for rec in sdf.SdfReader.__iter__(self):
if ('EXACT_MASS' not in rec['annot']
or float(rec['annot']['EXACT_MASS']) == 0):
try:
exmass = formula.Formula(rec['annot']['FORMULA']).mass
except KeyError:
# if no exact mass it means
# this is a higher level category
continue
else:
exmass = float(rec['annot']['EXACT_MASS'])
names = [
rec['name'][nametype].strip()
for nametype in ('COMMON_NAME', 'SYSTEMATIC_NAME')
if nametype in rec['name']
]
if 'SYNONYMS' in rec['name']:
names.extend(n.strip()
for n in rec['name']['SYNONYMS'].split(';'))
names = [n.strip() for n in names if n.strip()]
hg, chainsum, chains = self.nameproc.process(names)
liprec = lipproc.LipidRecord(
lab=lipproc.LipidLabel(
db_id=rec['id'],
db='LipidMaps',
names=tuple(names),
formula=rec['annot']['FORMULA'],
),
hg=hg,
chainsum=chainsum,
chains=chains,
)
yield exmass, liprec
def __iter__(self):
for mol in self.itermol(obmol=False):
if not mol.swl_exact_mass:
continue
hg, chainsum, chains = self.nameproc.process(mol.title)
rec = lipproc.LipidRecord(lab=lipproc.LipidLabel(
db_id=mol.db_id,
db='SwissLipids',
names=mol.title,
formula=mol.swl_formula,
),
hg=hg,
chainsum=chainsum,
chains=chains)
# yielding mass and record
yield mol.swl_exact_mass or np.nan, rec