def getMZ(self, charge, agentFormula='H', agentCharge=1):
"""Get m/z of current sequence. Charge, agent formula and agent charge can be set."""
# get current mass and calculate mz
return basics.mz(self.getMass(), charge, agentFormula=agentFormula, agentCharge=agentCharge)
def getCharges(peaklist, maxCharge, massTolerance, intTolerance):
"""Calculate charges for peaks of given peaklist by isotopes differences and averagine distribution.
maxCharge: (int) maximu charge searched
massTolerance: (float) m/z tolerance for the next isotope
intTolerance: (float) intensity tolerance for the next isotope in %/100
"""
# check peaklist
if not isinstance(peaklist, objects.peaklist):
peaklist = objects.peaklist(peaklist)
# get averagine distribution
averagineKeys = averagine.averagineDist.keys()
averagineKeys.sort()
# clear previous results
peaklist = deepcopy(peaklist)
for x in range(len(peaklist)):
peaklist[x].charge = None
peaklist[x].isotope = None
# precalc delta mass for each charge
delta = {}
for x in range(abs(maxCharge)):
delta[x+1] = 1.00287/(x+1)
charges = delta.keys()
charges.reverse()
# set polarity
polarity = 1
if maxCharge < 0:
polarity = -1
# walk in peaklist
for x in range(len(peaklist)):
# skip identified peaks
if peaklist[x].isotope != None:
continue
else:
cluster = [peaklist[x]]
# try all charges
for z in charges:
y = 1
isotope = 0
# get isotopic pattern
pattern = None
mass = basics.mz(peaklist[x].mz, 0, z*polarity)
for key in averagineKeys:
if key >= mass:
pattern = averagine.averagineDist[key]
break
if not pattern:
pattern = averagine.makeAveragineDist(config.averagineFormula, massRange=mass)
# search for next isotope within tolerance
while x+y < len(peaklist) and ((peaklist[x+y].mz - cluster[-1].mz) - delta[z]) <= massTolerance:
if abs((peaklist[x+y].mz - cluster[-1].mz) - delta[z]) <= massTolerance:
# add peak to cluster
cluster.append(peaklist[x+y])
peaklist[x+y].charge = z*polarity
isotope += 1
# check number if isotopes
if not pattern or len(pattern)<=isotope:
break
# check isotope intensity to avoid skiping of overlaped peaks
calcIntens = ((cluster[-2].intensity-cluster[-2].baseline) / pattern[isotope-1][1]) * pattern[isotope][1]
if abs(peaklist[x+y].intensity - peaklist[x+y].baseline - calcIntens) < (calcIntens * intTolerance):
peaklist[x+y].isotope = isotope
y += 1
# skip other charges if one isotope at least was found
if len(cluster) > 1:
peaklist[x].charge = z*polarity
peaklist[x].isotope = 0
break
return peaklist
