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from IsoSpecPy import IsoThreshold, Iso, ParseFormula, Advanced
def check_estimates(formula, est_fun, thr):
it = IsoThreshold(thr, formula, absolute = False)
min_m = min(it.masses)
max_m = max(it.masses)
min_e_m, max_e_m = est_fun(formula, thr)
# assert min_e_m < min_m
# assert max_e_m > max_e
return max_e_m, max_m, min_m, min_e_m, max_e_m > max_m >= min_m > min_e_m, (max_e_m - min_e_m) / (max_m - min_m + 0.0001), (max_e_m - min_e_m), (max_m - min_m)
def est_fun_trivial(formula, _):
i = Iso(formula)
return i.getLightestPeakMass()-1.0, i.getHeaviestPeakMass()+1.0
def est_fun_margs(formula, threshold):
PC = ParseFormula(formula)
it = IsoThreshold(threshold, formula, get_confs = True)
PC = list(PC.items())
marginals = [Iso(elem, cnt) for elem, cnt in PC]
mconfs = [set() for _ in marginals]
for conf in it.confs:
for marg_conf, marg_set in zip(conf, mconfs):
marg_set.add(marg_conf)
mins = [min(marginal.conf_mass((conf,)) for conf in cset) for cset, marginal in zip(mconfs, marginals)]
maxes = [max(marginal.conf_mass((conf,)) for conf in cset) for cset, marginal in zip(mconfs, marginals)]
return sum(mins) - 1.0, sum(maxes) + 1.0
from IsoSpecPy.Formulas import *
formulas = [bovine_insulin, horse_myoglobin, sucrose, water, ubiquitin, caffeine, averagine(100.0), averagine(1000.0), "Hg7Sn3", "H1000N1000"]
def check_mass_predict(formula):
for thr in [0.1, 0.01, 0.001, 0.00001]:
for ef in [est_fun_margs, est_fun_trivial]:
ce = check_estimates(formula, ef, thr)
print(formula, thr, ce)
assert ce[4], "Estimates do not bound the actual masses for formula %s at threshold %e" % (formula, thr)
try:
import pytest
test_mass_predict = pytest.mark.parametrize("formula", formulas)(check_mass_predict)
except ImportError:
test_mass_predict = check_mass_predict
if __name__ == "__main__":
for formula in formulas:
test_mass_predict(formula)
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