def __init__(self, glydb):
self.glydb = glydb
mf = MonoFactory()
self.GlcNAc = mf['GlcNAc']
self.GlcNAc.set_anomer(Anomer.missing)
self.Man = mf['adMan']
self.Man.set_anomer(Anomer.missing)
self.Fuc = mf['Fuc']
self.Fuc.set_anomer(Anomer.missing)
def __init__(self, glydb):
self.glydb = glydb
gf = GlycanFactory()
mf = MonoFactory()
self.GlcNAc = mf['GlcNAc']
self.GlcNAc.set_anomer(Anomer.missing)
self.Man = mf['adMan']
self.Man.set_anomer(Anomer.missing)
self.lac = gf['Lactosamine N-glycans']
self.ngc = gf['N-Linked Core']
self.cmp = linearcodeSubtreeContainedIn()
from Glycan import Glycan
from MonoFactory import MonoFactory
import re
mf = MonoFactory()
class Glycosidase:
pass
class LeafCleaver(Glycosidase):
def cleave(self, gly):
ncleaved = 0
newcleaved = True
while newcleaved:
newcleaved = False
for l in gly.all_links():
m = l.child()
if m.compatible(self.monosaccharide) and not m.has_children():
l.parent().del_link(l)
ncleaved += 1
newcleaved = True
return ncleaved
class Serial(Glycosidase):
def __init__(self, *glycosidases):
self._glycosidases = glycosidases
def number(self):
from Monosaccharide import Monosaccharide, Linkage, Mod
from MonoFormatter import IUPACSym, LinCodeSym
iupacSym = IUPACSym()
lcSym = LinCodeSym()
from CompositionTable import Composition,ResidueCompositionTable,PermethylCompositionTable
from ElementMass import MonoisotopicElementMass
from MonoFactory import MonoFactory
from MonoFormatter import MassSym
ctable = ResidueCompositionTable()
pctable = PermethylCompositionTable()
elmt = MonoisotopicElementMass()
mfactory = MonoFactory()
msym = MassSym()
class Glycan:
iupacSym = IUPACSym()
lcSym = LinCodeSym()
glycoctformat = None
glycamformat = None
def __init__(self,root=None):
self.set_root(root)
self._undetermined = None
self._bions = None
self._yions = None
def __init__(self):
self.fmt = GlycoCTFormat()
self.mf = MonoFactory()
super(GlycanFactory, self).__init__()
class GlycanFactory(ReferenceTable):
def __init__(self):
self.fmt = GlycoCTFormat()
self.mf = MonoFactory()
super(GlycanFactory, self).__init__()
def new(self, key):
return self[key].clone()
def parseSection(self, name, kv):
aliases = [name]
g = self.fmt.toGlycan('\n'.join(kv['GlycoCT'].split()))
aliases.extend(map(str.strip, kv.get('Aliases', '').split(';')))
return [(a, g) for a in aliases]
def add_mono(self,
parent,
name,
parent_pos,
child_pos=1,
anomer=Anomer.beta,
parent_type=Linkage.oxygenPreserved,
child_type=Linkage.oxygenLost):
m = self.mf.new(name)
m.set_anomer(anomer)
parent.add_child(m,
parent_pos=parent_pos,
child_pos=child_pos,
parent_type=parent_type,
child_type=child_type)
return m
def oxford2Glycan(self, name):
if name in self:
return self.new(name)
p = 0
if name[p] == 'F':
g = self.new('FM3')
p += 1
else:
g = self.new('M3')
# print repr(g)
# print self.fmt.toStr(g)
# print self
r = g.root()
glcnac2 = filter(lambda m: m.compatible(self.mf['GlcNAc']),
r.children())[0]
man1 = glcnac2.children()[0]
man16 = [l.child() for l in man1.links() if l.parent_pos() == 6][0]
man13 = [l.child() for l in man1.links() if l.parent_pos() == 3][0]
assert name[p] == 'A'
nant = int(name[p + 1])
ant = [None]
if nant in (1, 2, 3, 4):
ant.append(self.add_mono(man13, 'GlcNAc', parent_pos=2))
if nant in (2, 3, 4):
ant.append(self.add_mono(man16, 'GlcNAc', parent_pos=2))
if nant in (3, 4):
ant.append(self.add_mono(man13, 'GlcNAc', parent_pos=4))
if nant in (4, ):
ant.append(self.add_mono(man16, 'GlcNAc', parent_pos=6))
p += 2
if p >= len(name):
return g
if name[p] == 'B':
b = self.add_mono(man1, 'GlcNAc', 4)
name[p] += 1
if p >= len(name):
return g
if name[p] == 'F':
nfuc = int(name[p + 1])
assert (nfuc <= nant)
for fi in range(1, nfuc + 1):
self.add_mono(ant[fi],
'Fuc',
parent_pos=6,
anomer=Anomer.alpha)
p += 2
if p >= len(name):
return g
assert (name[p] == 'G')
ngal = int(name[p + 1])
gal = [None]
assert (ngal <= nant)
for gi in range(1, ngal + 1):
gal.append(self.add_mono(ant[gi], 'Gal', parent_pos=4))
p += 2
if p >= len(name):
return g
assert (name[p] == 'S')
nsia = int(name[p + 1])
sia = [None]
assert (nsia <= ngal)
for si in range(1, nsia + 1):
sia.append(
self.add_mono(gal[si],
'Neu5Ac',
parent_pos=6,
child_pos=2,
anomer=Anomer.alpha))
return g