def __init__(self,
c=None,
u=None,
fa_counts=None,
getname=None,
sub=(),
**kwargs):
def _getname(parent, subs):
"""
Parameters
----------
parent :
subs :
Returns
-------
"""
return '%s(%u:%u)' % (parent.name, subs[0].c, subs[0].u)
metabolite.AbstractMetabolite.__init__(
self,
core='OH',
subs=[substituent.FattyAcyl(c=c, u=u, counts=fa_counts)],
name='FA',
hg=lipproc.Headgroup(main='FA', sub=()),
getname=getname or _getname,
**kwargs)
def __init__(self,
c=None,
u=None,
fa_counts=None,
getname=None,
sub=(),
**kwargs):
def _getname(parent, subs):
return '%s(%u:%u)' % (parent.name, subs[0].c, subs[0].u)
metabolite.AbstractMetabolite.__init__(
self,
core='C19OH31',
subs=[substituent.FattyAcyl(c=c, u=u, counts=fa_counts)],
name='SE',
hg=lipproc.Headgroup(main='SE', sub=()),
getname=getname or _getname,
**kwargs,
)
def __init__(self,
core='',
sph_args=None,
fa_args=None,
o='H',
lyso=False,
fa_hydroxy=False,
lcb_type='d',
name='Cer',
hg=None,
getname=None,
**kwargs):
sph_args = sph_args or {}
fa_args = fa_args or {}
if lyso:
fa = 'H'
elif fa_hydroxy:
fa = substituent.HydroxyFattyAcyl(**fa_args)
else:
fa = substituent.FattyAcyl(**fa_args)
self.fa_hydroxy = fa_hydroxy
hg = hg or lipproc.Headgroup(main='Cer')
AbstractSphingolipid.__init__(self,
o=o,
n=fa,
sph_args=sph_args,
name=name,
getname=getname,
lcb_type=lcb_type,
hg=hg,
**kwargs)
def _get_substituent(self, sub, args=None):
args = args or {}
return (substituent.FattyAcyl(
**args) if not sub else self.get_substituent(sub))
[(m.formula, m.mass) for m in halo_methanes][:3]
# Do the same with all alcohols up to 1-8 carbon count with 0-2 unsaturated bonds:
# In[34]:
chain = metabolite.AbstractSubstituent(c=(1, 8), u=(0, 2))
alcohols = metabolite.AbstractMetabolite(subs=(chain, ('OH', )))
[(m.formula, m.mass) for m in alcohols][:3]
# Make some ceramides:
# In[9]:
# fatty acyls of length 16, 18 or 20 and one or no unsaturation:
fattyacyl = substituent.FattyAcyl(c=(16, 18, 20), u=(0, 1))
lcb = substituent.Sphingosine(c=18, u=1)
ceramides = metabolite.AbstractMetabolite(core='H',
subs=(lcb, fattyacyl),
name='Cer')
# name, formula, mass, [M+H]+, [M+NH4]+
[(cer.name, cer.formula, cer.mass, cer.add_nh4()) for cer in ceramides]
# ## 4: Lipid definitions
# In the `lipyd.lipid` module more than 150 lipid varieties are predefined.
# In[11]:
from lipyd import lipid