def get_precursors(seq, min_mz=400, max_mz=2000, min_charge=1, max_charge=5):
m = mass_from_sequence(seq)
prec = [{
'charge_state': c,
'mz': (m + c * Formula('H').mass) / c
} for c in xrange(min_charge, max_charge + 1)]
return filter(lambda x: min_mz <= x['mz'] <= max_mz, prec)
def __init__(self, name, formula):
self.display_name = name
self.formula = formula
self.mass = Formula(formula).isotope.mass
LOSSES.add(self)
def __str__(self):
return self.formula
def predict_fragments_from_sequence(sequence=[],
nterm='N-term',
cterm='C-term'):
verify_sequence(sequence)
out = []
# b-ions
nterm_mass = AMINO_ACIDS[nterm].mass
out += append_residue(mass=nterm_mass,
pos=1,
ion_type='b_',
seq=sequence,
term=cterm,
loss=[])
for l in AMINO_ACIDS[nterm].losses:
out += append_residue(mass=nterm_mass - l.mass,
pos=1,
ion_type='b_',
seq=sequence,
term=cterm,
loss=update_loss([], l.formula))
# a-ions
nterm_mass = AMINO_ACIDS[nterm].mass - Formula('CO').isotope.mass
out += append_residue(mass=nterm_mass,
pos=1,
ion_type='a_',
seq=sequence,
term=cterm,
loss=[])
for l in AMINO_ACIDS[nterm].losses:
out += append_residue(mass=nterm_mass - l.mass,
pos=1,
ion_type='a_',
seq=sequence,
term=cterm,
loss=update_loss([], l.formula))
# y-ions
cterm_mass = AMINO_ACIDS[cterm].mass
out += append_residue(mass=cterm_mass,
pos=1,
ion_type='y_',
seq=sequence[::-1],
term=nterm,
loss=[])
for l in AMINO_ACIDS[cterm].losses:
out += append_residue(mass=cterm_mass - l.mass,
pos=1,
ion_type='y_',
seq=sequence[::-1],
term=nterm,
loss=update_loss([], l.formula))
out = sorted(list(set(out)), key=lambda x: x[0])
return out
def __init__(self, residue='', mod='', formula='', losses=[]):
self.residue = residue
self.mod = mod
self.formula = formula
if formula:
self.mass = Formula(formula).isotope.mass
else:
self.mass = 0.0
self.losses = losses
AMINO_ACIDS.add(self)
def predict_positive_fragments_from_sequence(sequence=[],
nterm='N-term',
cterm='C-term',
max_charge_state=1):
out = []
fragments = predict_fragments_from_sequence(sequence=sequence,
nterm=nterm,
cterm=cterm)
for item in fragments:
out.append((round(item[0] + Formula('H').isotope.mass,
5), item[1] + ' (+1)'))
for cs in range(2, max_charge_state + 1):
if item[0] > 200 * cs:
out.append(
(round((item[0] + cs * Formula('H').isotope.mass) / cs,
5), item[1] + ' (+' + str(cs) + ')'))
out = sorted(list(set(out)), key=lambda x: x[0])
return out