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dtargets[i].extend(t)
else:
dtargets[i].extend(t[::-1])
else:
if i % 2 == 0:
dtargets[i] = [t]
else:
dtargets[i] = [t[::-1]]
elif tableau:
numby = 0
numall = 0
explainedby = 0
explainedall = 0
ts = []
ps = []
predictions = ms2pip_pyx.get_predictions(
peptide, modpeptide, charge, model_id, peaks_version, colen
)
for m, p in zip(msms, peaks):
ft.write("%s;%f;%f;;;0\n" % (title, m, 2 ** p))
# get targets
mzs, targets = ms2pip_pyx.get_targets_all(
modpeptide, msms, peaks, float(fragerror), "all"
)
# get mean by intensity values to normalize!; WRONG !!!
maxt = 0.0
maxp = 0.0
it = 0
for cion in [1, 2]:
for ionnumber in range(len(modpeptide) - 3):
for lion in ["a", "b-h2o", "b-nh3", "b", "c"]:
if (lion == "b") & (cion == 1):
ch = charges[pepid]
charge_buf.append(ch)
model_id = MODELS[model]["id"]
peaks_version = MODELS[model]["peaks_version"]
# get ion mzs
mzs = ms2pip_pyx.get_mzs(modpeptide, peaks_version)
mz_buf.append([np.array(m, dtype=np.float32) for m in mzs])
# Predict the b- and y-ion intensities from the peptide
# For C-term ion types (y, y++, z), flip the order of predictions,
# because get_predictions follows order from vector file
# enumerate works for variable number (and all) ion types
predictions = ms2pip_pyx.get_predictions(
peptide, modpeptide, ch, model_id, peaks_version, colen
) # SD: added colen
prediction_buf.append([np.array(p, dtype=np.float32) for p in predictions])
pcount += 1
if (pcount % 500) == 0:
sys.stdout.write("(%i)%i " % (worker_num, pcount))
sys.stdout.flush()
return mz_buf, prediction_buf, peplen_buf, charge_buf, pepid_buf