def score(candidate, target): import collections c_spectrum = peptide.cyclic_spectrum(candidate) c_counter = collections.Counter(c_spectrum) t_counter = collections.Counter(target) s = 0 for mass in c_counter: if mass in t_counter: s = s + min(c_counter[mass],t_counter[mass]) return s
for mass in c_counter:
if mass not in t_counter:
return False
if c_counter[mass] > t_counter[mass]:
return False
return True
def output_format(pep):
masses = []
for amino_acid in pep:
masses.append(peptide.mass_table[amino_acid])
return '-'.join(map(str, masses))
candidates = peptide.amino_acids
winners = []
while candidates:
candidates = branch(candidates)
new_candidates = []
for candidate in candidates:
c_spectrum = peptide.cyclic_spectrum(candidate)
l_spectrum = peptide.linear_spectrum(candidate)
if c_spectrum == spectrum:
winners.append(candidate)
elif consistent(l_spectrum, spectrum):
new_candidates.append(candidate)
candidates = new_candidates
inout.output(' '.join(set(map(output_format, winners))))
for mass in c_counter:
if mass not in t_counter:
return False
if c_counter[mass] > t_counter[mass]:
return False
return True
def output_format(pep):
masses = []
for amino_acid in pep:
masses.append(peptide.mass_table[amino_acid])
return "-".join(map(str, masses))
candidates = peptide.amino_acids
winners = []
while candidates:
candidates = branch(candidates)
new_candidates = []
for candidate in candidates:
c_spectrum = peptide.cyclic_spectrum(candidate)
l_spectrum = peptide.linear_spectrum(candidate)
if c_spectrum == spectrum:
winners.append(candidate)
elif consistent(l_spectrum, spectrum):
new_candidates.append(candidate)
candidates = new_candidates
inout.output(" ".join(set(map(output_format, winners))))
