class ElementalCompositionVisit:
def __init__(self,comp):
self.table = comp
self.eltcomp = Composition()
def visit(self,m):
self.eltcomp.add(m.composition(self.table))
def fragments(self, r=None, force=False):
atroot = False
if r == None:
r = self.root()
atroot = True
if force or (not hasattr(r, '_symbol_composition')
or not hasattr(r, '_elemental_composition')):
self.subtree_composition(r,
sym_table=iupacSym,
comp_table=ctable)
links = r.links()
nlink = len(links)
if nlink == 0:
# self
fr = (copy.copy(r._symbol_composition),\
copy.copy(r._elemental_composition),True,0)
yield fr
return
fragstore0 = []
fragstore1 = []
for l in links:
fragstore0.append([])
fragstore1.append([])
for fr in self.fragments(l.child()):
if fr[2]:
fragstore0[-1].append(fr)
else:
fragstore1[-1].append(fr)
fragstore0[-1].append((Composition(), Composition(), True, 1))
for i, prd in enumerate(product(*fragstore0)):
symcomp = copy.copy(r._symbol_composition)
eltcomp = copy.copy(r._elemental_composition)
cl = 0
for l, fr in zip(links, prd):
# determine the amount to substract
symcomp1 = copy.copy(l.child()._symbol_composition)
symcomp1.sub(fr[0])
symcomp.sub(symcomp1)
eltcomp1 = copy.copy(l.child()._elemental_composition)
eltcomp1.sub(fr[1])
eltcomp.sub(eltcomp1)
cl += fr[3]
fr = (symcomp, eltcomp, True, cl)
yield fr
for i in range(nlink):
for fr in fragstore0[i][:-1]:
fr1 = (fr[0], fr[1], False, fr[3] + 1)
yield fr1
for fr in fragstore1[i]:
fr1 = (fr[0], fr[1], False, fr[3])
yield fr1
def next(self):
for gr in self.glydb:
comp = Composition()
for m in gr.glycan.all_nodes():
try:
sym = self.syms.toStr(m)
except KeyError:
if m.noring():
if m.count_mod() == 1 and \
m.count_mod(Mod.aldi) == 1:
aglycon = 'aldi?'
m1 = m.clone()
m1.clear_mods()
try:
sym = self.syms.toStr(m1)
except KeyError:
sym = 'Xxx'
else:
sym = 'Xxx'
else:
sym = 'Xxx'
comp[sym] += 1
gr['composition'] = comp
gr['compstr'] = comp2str1(comp)
yield gr
def iupac_composition(self,
floating_substituents=True,
aggregate_basecomposition=True):
c = Composition()
for sym in (self.iupac_composition_syms + self.subst_composition_syms +
['Xxx', 'X']):
c[sym] = 0
for m in self.all_nodes(undet_subst=True):
try:
sym = iupacSym.toStr(m)
except KeyError:
if isinstance(m, Monosaccharide):
c['Xxx'] += 1
else:
c['X'] += 1
continue
if floating_substituents:
syms = map(str.strip, sym.split('+'))
else:
syms = [sym]
if syms[0] not in (self.iupac_composition_syms +
self.subst_composition_syms):
if isinstance(m, Monosaccharide):
syms[0] = 'Xxx'
else:
syms[0] = 'X'
for i in range(1, len(syms)):
if syms[i] not in self.subst_composition_syms:
syms[i] = 'X'
if syms[0] == 'Xxx' or 'X' in syms:
c['Xxx'] += 1
continue
if syms[0] == 'X':
c['X'] += 1
continue
for sym in syms:
c[sym] += 1
c['Count'] = sum(
map(c.__getitem__, self.iupac_composition_syms + ['Xxx']))
if aggregate_basecomposition:
c['Hex'] = sum(map(c.__getitem__, ('Man', 'Gal', 'Glc', 'Hex')))
c['HexNAc'] = sum(
map(c.__getitem__, ('GalNAc', 'GlcNAc', 'ManNAc', 'HexNAc')))
c['dHex'] = sum(map(c.__getitem__, ('Fuc', 'dHex')))
c['Pent'] = sum(map(c.__getitem__, ('Xyl', 'Pent')))
c['Sia'] = sum(map(c.__getitem__, ('NeuAc', 'NeuGc', 'Sia')))
c['HexA'] = sum(
map(c.__getitem__, ('GlcA', 'GalA', 'IdoA', 'ManA', 'HexA')))
c['HexN'] = sum(
map(c.__getitem__, ('GlcN', 'GalN', 'ManN', 'HexN')))
return c
def visit(self,m):
if self.comp:
eltcomp = m.composition(self.comp)
for c in m.children():
eltcomp.add(c._elemental_composition)
m._elemental_composition = eltcomp
if self.sym:
symcomp = Composition()
symcomp[self.sym.toStr(m)] = 1
for c in m.children():
symcomp.add(c._symbol_composition)
m._symbol_composition = symcomp
from IsoShape import IsoShape
class MonoisotopicElementMass(dict):
def __init__(self):
elts = ElementTable()
for e in elts.values():
self[e.symbol] = e.mono
class AverageElementMass(dict):
def __init__(self):
elts = ElementTable()
for e in elts.values():
self[e.symbol] = e.ave
class ElementIsotopes(dict):
def __init__(self):
elts = ElementTable()
for e in elts.values():
self[e.symbol] = e.isotopes
def cluster(self,comp,maxpos=5):
sh = IsoShape(self,comp,maxpos)
return sh.clusterIntensities()
if __name__ == '__main__':
import sys
from CompositionTable import Composition
mt = MonoisotopicElementMass()
comp = Composition()
comp.parse(" ".join(sys.argv[1:]))
print comp.mass(mt)
def iupac_composition(self, floating_substituents=True,
aggregate_basecomposition=True,
redend_only=False):
validsyms = self.iupac_composition_syms + self.subst_composition_syms
if not floating_substituents:
validsyms += self.iupac_aldi_composition_syms
c = Composition()
for sym in (validsyms + ['Xxx','X']):
c[sym] = 0
if not redend_only:
nodeiterable = self.all_nodes(undet_subst=True)
else:
if self.has_root():
nodeiterable = [ self.root() ]
else:
nodeiterable = []
for m in nodeiterable:
try:
sym = iupacSym.toStr(m)
except KeyError:
if isinstance(m,Monosaccharide):
c['Xxx'] += 1
else:
c['X'] += 1
continue
if floating_substituents:
syms = [ s.strip() for s in sym.split('+') ]
else:
syms = [sym]
if syms[0] not in validsyms:
if isinstance(m,Monosaccharide):
syms[0] = 'Xxx'
else:
syms[0] = 'X'
for i in range(1,len(syms)):
if syms[i] not in self.subst_composition_syms:
syms[i] = 'X'
if syms[0] == 'Xxx' or 'X' in syms:
c['Xxx'] += 1
continue
if syms[0] == 'X':
c['X'] += 1
continue
for sym in syms:
c[sym] += 1
c['Count'] = sum(map(c.__getitem__,self.iupac_composition_syms + ['Xxx']))
if aggregate_basecomposition:
c['Hex'] = sum(map(c.__getitem__,('Man','Gal','Glc','Hex')))
c['Hex+aldi'] = sum(map(c.__getitem__,('Man+aldi','Gal+aldi','Glc+aldi','Hex+aldi')))
c['HexNAc'] = sum(map(c.__getitem__,('GalNAc','GlcNAc','ManNAc','HexNAc')))
c['HexNAc+aldi'] = sum(map(c.__getitem__,('GalNAc+aldi','GlcNAc+aldi','ManNAc+aldi','HexNAc+aldi')))
c['dHex'] = sum(map(c.__getitem__,('Fuc','dHex')))
c['dHex+aldi'] = sum(map(c.__getitem__,('Fuc+aldi','dHex+aldi')))
c['Pent'] = sum(map(c.__getitem__,('Xyl','Pent')))
c['Sia'] = sum(map(c.__getitem__,('NeuAc','NeuGc','Sia')))
c['HexA'] = sum(map(c.__getitem__,('GlcA','GalA','IdoA','ManA','HexA')))
c['HexN'] = sum(map(c.__getitem__,('GlcN','GalN','ManN','HexN')))
return c
def permethylated_molecular_weight(self,adduct='C2H6O'):
return self.permethylated_elemental_composition().mass(elmt) + \
Composition.fromstr(adduct).mass(elmt)
def underivitized_molecular_weight(self,adduct='H2O'):
return self.native_elemental_composition().mass(elmt) + \
Composition.fromstr(adduct).mass(elmt)
def elemental_composition(self,comp_table):
eltcomp = Composition()
for m in self.all_nodes(undet_subst=True):
ec = m.composition(comp_table)
eltcomp.add(ec)
return eltcomp
def __init__(self,comp):
self.table = comp
self.eltcomp = Composition()