def mz(mass,
charge,
currentCharge=0,
agentFormula='H',
agentCharge=1,
massType='Mo'):
"""Calculate m/z value for given mass and charge.
mass: (tuple of (Mo,Av) or float)
charge: (int) desired charge of ion
currentCharge: (int) if mass is charged already
agentFormula: (str) charging agent formula
agentCharge: (int) charging agent charge
massType: ('Mo' or 'Av') used mass type if mass value is float
"""
# set mass type
if massType == 'Mo':
massType = 0
else:
massType = 1
# get agent mass
agentFormula = objects.formula(agentFormula)
agentMass = agentFormula.getMass()
agentMass = (agentMass[0] - agentCharge * 0.000549,
agentMass[1] - agentCharge * 0.000549)
# recalculate zero charge
agentCount = currentCharge / agentCharge
if currentCharge != 0:
if type(mass) in (tuple, list):
massMo = mass[0] * abs(currentCharge) - agentMass[0] * agentCount
massAv = mass[1] * abs(currentCharge) - agentMass[1] * agentCount
mass = (massMo, massAv)
else:
mass = mass * abs(currentCharge) - agentMass[massType] * agentCount
if charge == 0:
return mass
# calculate final charge
agentCount = charge / agentCharge
if type(mass) in (tuple, list):
massMo = (mass[0] + agentMass[0] * agentCount) / abs(charge)
massAv = (mass[1] + agentMass[1] * agentCount) / abs(charge)
return (massMo, massAv)
else:
return (mass + agentMass[massType] * agentCount) / abs(charge)
def mz(mass, charge, currentCharge=0, agentFormula='H', agentCharge=1, massType='Mo'):
"""Calculate m/z value for given mass and charge.
mass: (tuple of (Mo,Av) or float)
charge: (int) desired charge of ion
currentCharge: (int) if mass is charged already
agentFormula: (str) charging agent formula
agentCharge: (int) charging agent charge
massType: ('Mo' or 'Av') used mass type if mass value is float
"""
# set mass type
if massType == 'Mo':
massType = 0
else:
massType = 1
# get agent mass
agentFormula = objects.formula(agentFormula)
agentMass = agentFormula.getMass()
agentMass = (agentMass[0]-agentCharge*0.000549, agentMass[1]-agentCharge*0.000549)
# recalculate zero charge
agentCount = currentCharge/agentCharge
if currentCharge != 0:
if type(mass) in (tuple, list):
massMo = mass[0]*abs(currentCharge) - agentMass[0]*agentCount
massAv = mass[1]*abs(currentCharge) - agentMass[1]*agentCount
mass = (massMo, massAv)
else:
mass = mass*abs(currentCharge) - agentMass[massType]*agentCount
if charge == 0:
return mass
# calculate final charge
agentCount = charge/agentCharge
if type(mass) in (tuple, list):
massMo = (mass[0] + agentMass[0]*agentCount)/abs(charge)
massAv = (mass[1] + agentMass[1]*agentCount)/abs(charge)
return (massMo, massAv)
else:
return (mass + agentMass[massType]*agentCount)/abs(charge)
def initMasses(self):
"""Initialize masses."""
self.mass = objects.formula(self.formula).getMass()
def initMasses(self):
"""Initialize masses."""
self.nTermMass = objects.formula(self.nTermFormula).getMass()
self.cTermMass = objects.formula(self.cTermFormula).getMass()
self.lossMass = objects.formula(self.lossFormula).getMass()
def initMasses(self):
"""Initialize masses."""
gain = objects.formula(self.gainFormula).getMass()
loss = objects.formula(self.lossFormula).getMass()
self.mass = (gain[0]-loss[0], gain[1]-loss[1])
def isoPattern(compound, fwhm=0.1, relIntTreshold=0.01, charge=1, agentFormula='H', agentCharge=1, rounding=7):
"""Calculate isotopic pattern for given compound (formula or sequence object).
Set appropriate relative intensity treshold and resolution in fwhm.
To charge isotopes set charge value. Charge agent can be changed from H
to any formula."""
finalPattern = []
# set internal treshold
internalTreshold = relIntTreshold/100.
# add charging agent to formula and get composition
composition = compound.getComposition()
if charge:
formula = compound.getFormula()
formula += '%s%d' % (agentFormula, (charge/agentCharge))
composition = objects.formula(formula).getComposition()
# check composition
for atom in composition:
if composition[atom] < 0:
return False
# calculate pattern
for atom in composition:
atomCount = composition[atom]
# get isotopic profile for current atom or specified isotope only
atomPattern = []
match = objects.elementPattern.match(atom)
symbol, massNumber, tmp = match.groups()
if massNumber:
isotope = blocks.elements[atom].isotopes[massNumber]
atomPattern.append([isotope[0], 1.])
else:
for massNumber, isotope in blocks.elements[atom].isotopes.items():
if isotope[1] > 0.:
atomPattern.append(list(isotope))
# add atoms
for i in range(atomCount):
currentPattern = {}
# if pattern in empty (first atom) add current atom pattern
if not finalPattern:
finalPattern = atomPattern
finalPattern.sort()
continue
# add atom to each peak of final pattern
for peak in finalPattern:
# skip peak under relevant abundance treshold
if peak[1] < internalTreshold:
continue
# add each isotope of current atom to peak
for isotope in atomPattern:
mass = peak[0] + isotope[0]
abundance = peak[1] * isotope[1]
# add abundance to stored peak or add new peak
mass = round(mass, rounding)
if mass in currentPattern:
currentPattern[mass] += abundance
else:
currentPattern[mass] = abundance
# replace final pattern by current
finalPattern = []
for mass, abundance in currentPattern.items():
finalPattern.append([mass, abundance])
finalPattern.sort()
# noramlize pattern
finalPattern = _normalize(finalPattern)
# check pattern
if not finalPattern:
return None
# correct charge
if charge:
for i in range(len(finalPattern)):
finalPattern[i][0] = (finalPattern[i][0]-0.000549*charge)/abs(charge)
# collect isotopes according to resolution (FWHM)
tol = fwhm/2
if charge:
tol /= abs(charge)
collectedPeaks = [finalPattern[0]]
lastPeak = finalPattern[0]
for currentPeak in finalPattern[1:]:
if (lastPeak[0] + tol) > currentPeak[0]:
abundance = lastPeak[1] + currentPeak[1]
mass = (lastPeak[0]*lastPeak[1] + currentPeak[0]*currentPeak[1]) / abundance
collectedPeaks[-1] = [mass, abundance]
lastPeak = [mass, abundance]
else:
collectedPeaks.append(currentPeak)
lastPeak = currentPeak
finalPattern = _normalize(collectedPeaks)
# discard peaks below treshold
filteredPeaks = []
for peak in finalPattern:
if peak[1] >= relIntTreshold:
filteredPeaks.append(peak)
finalPattern = filteredPeaks
return finalPattern
def initMasses(self):
"""Initialize masses."""
self.mass = objects.formula(self.formula).getMass()
def initMasses(self):
"""Initialize masses."""
self.nTermMass = objects.formula(self.nTermFormula).getMass()
self.cTermMass = objects.formula(self.cTermFormula).getMass()
self.lossMass = objects.formula(self.lossFormula).getMass()
def initMasses(self):
"""Initialize masses."""
gain = objects.formula(self.gainFormula).getMass()
loss = objects.formula(self.lossFormula).getMass()
self.mass = (gain[0] - loss[0], gain[1] - loss[1])
def isoPattern(compound,
fwhm=0.1,
relIntTreshold=0.01,
charge=1,
agentFormula='H',
agentCharge=1,
rounding=7):
"""Calculate isotopic pattern for given compound (formula or sequence object).
Set appropriate relative intensity treshold and resolution in fwhm.
To charge isotopes set charge value. Charge agent can be changed from H
to any formula."""
finalPattern = []
# set internal treshold
internalTreshold = relIntTreshold / 100.
# add charging agent to formula and get composition
composition = compound.getComposition()
if charge:
formula = compound.getFormula()
formula += '%s%d' % (agentFormula, (charge / agentCharge))
composition = objects.formula(formula).getComposition()
# check composition
for atom in composition:
if composition[atom] < 0:
return False
# calculate pattern
for atom in composition:
atomCount = composition[atom]
# get isotopic profile for current atom or specified isotope only
atomPattern = []
match = objects.elementPattern.match(atom)
symbol, massNumber, tmp = match.groups()
if massNumber:
isotope = blocks.elements[atom].isotopes[massNumber]
atomPattern.append([isotope[0], 1.])
else:
for massNumber, isotope in blocks.elements[atom].isotopes.items():
if isotope[1] > 0.:
atomPattern.append(list(isotope))
# add atoms
for i in range(atomCount):
currentPattern = {}
# if pattern in empty (first atom) add current atom pattern
if not finalPattern:
finalPattern = atomPattern
finalPattern.sort()
continue
# add atom to each peak of final pattern
for peak in finalPattern:
# skip peak under relevant abundance treshold
if peak[1] < internalTreshold:
continue
# add each isotope of current atom to peak
for isotope in atomPattern:
mass = peak[0] + isotope[0]
abundance = peak[1] * isotope[1]
# add abundance to stored peak or add new peak
mass = round(mass, rounding)
if mass in currentPattern:
currentPattern[mass] += abundance
else:
currentPattern[mass] = abundance
# replace final pattern by current
finalPattern = []
for mass, abundance in currentPattern.items():
finalPattern.append([mass, abundance])
finalPattern.sort()
# noramlize pattern
finalPattern = _normalize(finalPattern)
# check pattern
if not finalPattern:
return None
# correct charge
if charge:
for i in range(len(finalPattern)):
finalPattern[i][0] = (finalPattern[i][0] -
0.000549 * charge) / abs(charge)
# collect isotopes according to resolution (FWHM)
tol = fwhm / 2
if charge:
tol /= abs(charge)
collectedPeaks = [finalPattern[0]]
lastPeak = finalPattern[0]
for currentPeak in finalPattern[1:]:
if (lastPeak[0] + tol) > currentPeak[0]:
abundance = lastPeak[1] + currentPeak[1]
mass = (lastPeak[0] * lastPeak[1] +
currentPeak[0] * currentPeak[1]) / abundance
collectedPeaks[-1] = [mass, abundance]
lastPeak = [mass, abundance]
else:
collectedPeaks.append(currentPeak)
lastPeak = currentPeak
finalPattern = _normalize(collectedPeaks)
# discard peaks below treshold
filteredPeaks = []
for peak in finalPattern:
if peak[1] >= relIntTreshold:
filteredPeaks.append(peak)
finalPattern = filteredPeaks
return finalPattern