Exemple #1
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def md(mass, mdType='standard', kendrickFormula='CH2', rounding='floor'):
    """Calculate mass defect for given monoisotopic mass.
        mass (float) - monoisotopic mass
        mdType (fraction | standard | relative | kendrick) - mass defect type
        kendrickFormula (str) - kendrick group formula
        rounding (floor | ceil | round) - nominal mass rounding function
    """
    
    # return fractional part
    if mdType == 'fraction':
        return mass - math.floor(mass)
    
    # return standard mass defect
    elif mdType == 'standard':
        return mass - nominalmass(mass, rounding)
    
    # return relative mass defect
    elif mdType == 'relative':
        return 1e6 * (mass - nominalmass(mass, rounding)) / mass
    
    # return Kendrick mass defect
    elif mdType == 'kendrick':
        
        if not isinstance(kendrickFormula, obj_compound.compound):
            kendrickFormula = obj_compound.compound(kendrickFormula)
        
        kendrickF = kendrickFormula.nominalmass()/kendrickFormula.mass(0)
        
        return  nominalmass(mass * kendrickF, rounding) - (mass * kendrickF)
    
    # unknown mass defect type
    else: raise ValueError, 'Unknown mass defect type! --> ' + mdType
Exemple #2
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    def __init__(self,
                 formula,
                 charge,
                 scales,
                 loss='H',
                 gain='H{2}',
                 peakShape='gaussian'):

        loss = obj_compound.compound(loss)
        loss.negate()
        self._lossFormula = loss.formula()
        self._gainFormula = gain

        self.formula = formula
        self.charge = charge
        self.fwhm = 0.1
        self.peakShape = peakShape
        self.mzrange = [0.0, float('inf')]

        self.spectrum = []
        self.data = []
        self.model = []
        self.models = {}

        self.composition = None
        self.ncomposition = None
        self.average = None

        self._initModels(scales)
        self._initRange()
def averagine(mz, charge=0, composition=AVERAGE_AMINO):
    """Calculate average formula for given mass and building block composition.
        mz (float) - peak m/z
        charge (int) - peak charge
        composition (dict) - building block composition
    """

    # get average mass of block
    blockMass = 0.
    for element in composition:
        blockMass += blocks.elements[element].mass[1] * composition[element]

    # get block count
    neutralMass = mod_basics.mz(mz, charge=0, currentCharge=charge, massType=1)
    count = max(1, neutralMass / blockMass)

    # make formula
    formula = ''
    for element in composition:
        formula += '%s%d' % (element, int(composition[element]*count))
    formula = obj_compound.compound(formula)

    # add some hydrogens to reach the mass
    hydrogens = int(round((neutralMass - formula.mass(1)) / blocks.elements['H'].mass[1]))
    hydrogens = max(hydrogens, -1*formula.count('H'))
    formula += 'H%d' % hydrogens

    return formula
Exemple #4
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def averagine(mz, charge=0, composition=AVERAGE_AMINO):
    """Calculate average formula for given mass and building block composition.
        mz (float) - peak m/z
        charge (int) - peak charge
        composition (dict) - building block composition
    """
    
    # get average mass of block
    blockMass = 0.
    for element in composition:
        blockMass += blocks.elements[element].mass[1] * composition[element]
    
    # get block count
    neutralMass = mod_basics.mz(mz, charge=0, currentCharge=charge, massType=1)
    count = max(1, neutralMass / blockMass)
    
    # make formula
    formula = ''
    for element in composition:
        formula += '%s%d' % (element, int(composition[element]*count))
    formula = obj_compound.compound(formula)
    
    # add some hydrogens to reach the mass
    hydrogens = int(round((neutralMass - formula.mass(1)) / blocks.elements['H'].mass[1]))
    hydrogens = max(hydrogens, -1*formula.count('H'))
    formula += 'H%d' % hydrogens
    
    return formula
def md(mass, mdType='standard', kendrickFormula='CH2', rounding='floor'):
    """Calculate mass defect for given monoisotopic mass.
        mass (float) - monoisotopic mass
        mdType (fraction | standard | relative | kendrick) - mass defect type
        kendrickFormula (str) - kendrick group formula
        rounding (floor | ceil | round) - nominal mass rounding function
    """

    # return fractional part
    if mdType == 'fraction':
        return mass - math.floor(mass)

    # return standard mass defect
    elif mdType == 'standard':
        return mass - nominalmass(mass, rounding)

    # return relative mass defect
    elif mdType == 'relative':
        return 1e6 * (mass - nominalmass(mass, rounding)) / mass

    # return Kendrick mass defect
    elif mdType == 'kendrick':

        if not isinstance(kendrickFormula, obj_compound.compound):
            kendrickFormula = obj_compound.compound(kendrickFormula)

        kendrickF = kendrickFormula.nominalmass() / kendrickFormula.mass(0)

        return nominalmass(mass * kendrickF, rounding) - (mass * kendrickF)

    # unknown mass defect type
    else:
        raise ValueError, 'Unknown mass defect type! --> ' + mdType
def rdbe(compound):
    """Get RDBE (Range or Double Bonds Equivalents) of a given compound.
        compound (str or mspy.compound) - compound
    """

    # check compound
    if not isinstance(compound, obj_compound.compound):
        compound = obj_compound.compound(compound)

    # get composition
    comp = compound.composition()

    # get atoms from composition
    atoms = []
    for item in comp:
        match = ELEMENT_PATTERN.match(item)
        if match and not match.group(1) in atoms:
            atoms.append(match.group(1))

    # get rdbe
    rdbeValue = 0.
    for a in atoms:
        valence = blocks.elements[a].valence
        if valence:
            rdbeValue += (valence - 2) * compound.count(a, groupIsotopes=True)
    rdbeValue /= 2.
    rdbeValue += 1.

    return rdbeValue
Exemple #7
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def rdbe(compound):
    """Get RDBE (Range or Double Bonds Equivalents) of a given compound.
        compound (str or mspy.compound) - compound
    """
    
    # check compound
    if not isinstance(compound, obj_compound.compound):
        compound = obj_compound.compound(compound)
    
    # get composition
    comp = compound.composition()
    
    # get atoms from composition
    atoms = []
    for item in comp:
        match = ELEMENT_PATTERN.match(item)
        if match and not match.group(1) in atoms:
            atoms.append(match.group(1))
    
    # get rdbe
    rdbeValue = 0.
    for a in atoms:
        valence = blocks.elements[a].valence
        if valence:
            rdbeValue += (valence - 2) * compound.count(a, groupIsotopes=True)
    rdbeValue /= 2.
    rdbeValue += 1.
    
    return rdbeValue
Exemple #8
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    def __init__(self, formula, charge, scales, loss='H', gain='H{2}', peakShape='gaussian'):

        loss = obj_compound.compound(loss)
        loss.negate()
        self._lossFormula = loss.formula()
        self._gainFormula = gain

        self.formula = formula
        self.charge = charge
        self.fwhm = 0.1
        self.peakShape = peakShape
        self.mzrange = [0.0, float('inf')]

        self.spectrum = []
        self.data = []
        self.model = []
        self.models = {}

        self.composition = None
        self.ncomposition = None
        self.average = None
        self.intensity = None

        self._initModels(scales)
        self._initRange()
Exemple #9
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    def isvalid(self, charge=0, agentFormula='H', agentCharge=1):
        """Utility to check ion composition."""

        # make compound
        formula = obj_compound.compound(self.formula())

        # check ion composition
        return formula.isvalid(charge=charge,
                               agentFormula=agentFormula,
                               agentCharge=agentCharge)
Exemple #10
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 def isvalid(self, charge=0, agentFormula='H', agentCharge=1):
     """Utility to check ion composition."""
     
     # make compound
     formula = obj_compound.compound(self.formula())
     
     # check ion composition
     return formula.isvalid(
         charge = charge,
         agentFormula = agentFormula,
         agentCharge = agentCharge
     )
Exemple #11
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 def mass(self, massType=None):
     """Get mass."""
     
     # get mass
     if self._mass == None:
         self._mass = obj_compound.compound(self.formula()).mass()
     
     # return mass
     if massType == 0:
         return self._mass[0]
     elif massType ==  1:
         return self._mass[1]
     else:
         return self._mass
Exemple #12
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    def mass(self, massType=None):
        """Get mass."""

        # get mass
        if self._mass == None:
            self._mass = obj_compound.compound(self.formula()).mass()

        # return mass
        if massType == 0:
            return self._mass[0]
        elif massType == 1:
            return self._mass[1]
        else:
            return self._mass
Exemple #13
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def mz(mass,
       charge,
       currentCharge=0,
       agentFormula='H',
       agentCharge=1,
       massType=0):
    """Calculate m/z value for given mass and charge.
        mass (tuple of (Mo, Av) or float) - current mass
        charge (int) - final charge of ion
        currentCharge (int) - current mass charge
        agentFormula (str or mspy.compound) - charging agent formula
        agentCharge (int) - charging agent unit charge
        massType (0 or 1) - used mass type if mass value is float, 0 = monoisotopic, 1 = average
    """

    # check agent formula
    if agentFormula != 'e' and not isinstance(agentFormula,
                                              obj_compound.compound):
        agentFormula = obj_compound.compound(agentFormula)

    # get agent mass
    if agentFormula == 'e':
        agentMass = [ELECTRON_MASS, ELECTRON_MASS]
    else:
        agentMass = agentFormula.mass()
        agentMass = (agentMass[0] - agentCharge * ELECTRON_MASS,
                     agentMass[1] - agentCharge * ELECTRON_MASS)

    # 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)
Exemple #14
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 def _initModels(self, scales):
     """Init theoretical envelope models."""
     
     self.models = {}
     
     # generate possible models to fit
     for x in scales:
         
         CHECK_FORCE_QUIT()
         
         # make compound
         item = "%s(%s)%d(%s)%d" % (self.formula, self._lossFormula, x, self._gainFormula, x)
         compound = obj_compound.compound(item)
         
         # check compound
         if not compound.isvalid(charge=self.charge):
             continue
         
         # append model [0-compound, 1-pattern, 2-abs abundance, 3-rel abundance]
         self.models[x] = [compound, [], 0.0, 0.0]
Exemple #15
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def mz(mass, charge, currentCharge=0, agentFormula='H', agentCharge=1, massType=0):
    """Calculate m/z value for given mass and charge.
        mass (tuple of (Mo, Av) or float) - current mass
        charge (int) - final charge of ion
        currentCharge (int) - current mass charge
        agentFormula (str or mspy.compound) - charging agent formula
        agentCharge (int) - charging agent unit charge
        massType (0 or 1) - used mass type if mass value is float, 0 = monoisotopic, 1 = average
    """
    
    # check agent formula
    if agentFormula != 'e' and not isinstance(agentFormula, obj_compound.compound):
        agentFormula = obj_compound.compound(agentFormula)
    
    # get agent mass
    if agentFormula == 'e':
        agentMass = [ELECTRON_MASS, ELECTRON_MASS]
    else:
        agentMass = agentFormula.mass()
        agentMass = (agentMass[0]-agentCharge*ELECTRON_MASS, agentMass[1]-agentCharge*ELECTRON_MASS)
    
    # 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)
Exemple #16
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    def _initModels(self, scales):
        """Init theoretical envelope models."""

        self.models = {}

        # generate possible models to fit
        for x in scales:

            CHECK_FORCE_QUIT()

            # make compound
            item = "%s(%s)%d(%s)%d" % (self.formula, self._lossFormula, x,
                                       self._gainFormula, x)
            compound = obj_compound.compound(item)

            # check compound
            if not compound.isvalid(charge=self.charge):
                continue

            # append model [0-compound, 1-pattern, 2-abs abundance, 3-rel abundance]
            self.models[x] = [compound, [], 0.0, 0.0]
Exemple #17
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    def composition(self):
        """Get elemental composition."""

        # check composition buffer
        if self._composition != None:
            return self._composition

        self._composition = {}

        # add monomers to formula
        for monomer in self.chain:
            for el, count in blocks.monomers[monomer].composition.items():
                if el in self._composition:
                    self._composition[el] += count
                else:
                    self._composition[el] = count

        # add modifications and labels
        mods = self.modifications + self.labels
        for name, position, state in mods:
            multi = 1
            if type(position) in (
                    str, unicode
            ) and position != '' and not position in ('nTerm', 'cTerm'):
                multi = self.chain.count(position)
            for el, count in blocks.modifications[name].composition.items():
                if el in self._composition:
                    self._composition[el] += multi * count
                else:
                    self._composition[el] = multi * count

        # add terminal formulae
        if not self.cyclic:
            termCmpd = obj_compound.compound(self.nTermFormula +
                                             self.cTermFormula)
            for el, count in termCmpd.composition().items():
                if el in self._composition:
                    self._composition[el] += count
                else:
                    self._composition[el] = count

        # subtract neutral losses for fragments
        for loss in self.fragmentLosses:
            lossCmpd = obj_compound.compound(loss)
            for el, count in lossCmpd.composition().items():
                if el in self._composition:
                    self._composition[el] -= count
                else:
                    self._composition[el] = -1 * count

        # add neutral gains for fragments
        for gain in self.fragmentGains:
            gainCmpd = obj_compound.compound(gain)
            for el, count in gainCmpd.composition().items():
                if el in self._composition:
                    self._composition[el] += count
                else:
                    self._composition[el] = count

        # remove zeros
        for atom in self._composition.keys():
            if self._composition[atom] == 0:
                del self._composition[atom]

        return self._composition
Exemple #18
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def pattern(compound,
            fwhm=0.1,
            threshold=0.01,
            charge=0,
            agentFormula='H',
            agentCharge=1,
            real=True,
            model='gaussian'):
    """Calculate isotopic pattern for given compound.
        compound (str or mspy.compound) - compound
        fwhm (float) - gaussian peak width
        threshold (float) - relative intensity threshold for isotopes (in %/100)
        charge (int) - charge to be calculated
        agentFormula (str or mspy.compound) - charging agent formula
        agentCharge (int) - charging agent unit charge
        real (bool) - get real peaks from calculated profile
        model (gaussian, lorentzian, gausslorentzian) - peak shape function
    """

    # check compound
    if not isinstance(compound, obj_compound.compound):
        compound = obj_compound.compound(compound)

    # check agent formula
    if agentFormula != 'e' and not isinstance(agentFormula,
                                              obj_compound.compound):
        agentFormula = obj_compound.compound(agentFormula)

    # add charging agent to compound
    if charge and agentFormula != 'e':
        formula = compound.formula()
        for atom, count in agentFormula.composition().items():
            formula += '%s%d' % (atom, count * (charge / agentCharge))
        compound = obj_compound.compound(formula)

    # get composition and check for negative atom counts
    composition = compound.composition()
    for atom in composition:
        if composition[atom] < 0:
            raise ValueError, 'Pattern cannot be calculated for this formula! --> ' + compound.formula(
            )

    # set internal thresholds
    internalThreshold = threshold / 100.
    groupingWindow = fwhm / 4.

    # calculate pattern
    finalPattern = []
    for atom in composition:

        # get isotopic profile for current atom or specified isotope only
        atomCount = composition[atom]
        atomPattern = []
        match = mod_basics.ELEMENT_PATTERN.match(atom)
        symbol, massNumber, tmp = match.groups()
        if massNumber:
            isotope = blocks.elements[symbol].isotopes[int(massNumber)]
            atomPattern.append([isotope[0], 1.])  # [mass, abundance]
        else:
            for massNumber, isotope in blocks.elements[atom].isotopes.items():
                if isotope[1] > 0.:
                    atomPattern.append(list(isotope))  # [mass, abundance]

        # add atoms
        for i in range(atomCount):

            CHECK_FORCE_QUIT()

            # if pattern is empty (first atom) add current atom pattern
            if len(finalPattern) == 0:
                finalPattern = _normalize(atomPattern)
                continue

            # add atom to each peak of final pattern
            currentPattern = []
            for patternIsotope in finalPattern:

                # skip peak under relevant abundance threshold
                if patternIsotope[1] < internalThreshold:
                    continue

                # add each isotope of current atom to peak
                for atomIsotope in atomPattern:
                    mass = patternIsotope[0] + atomIsotope[0]
                    abundance = patternIsotope[1] * atomIsotope[1]
                    currentPattern.append([mass, abundance])

            # group isotopes and normalize pattern
            finalPattern = _consolidate(currentPattern, groupingWindow)
            finalPattern = _normalize(finalPattern)

    # correct charge
    if charge:
        for i in range(len(finalPattern)):
            finalPattern[i][0] = (
                finalPattern[i][0] -
                mod_basics.ELECTRON_MASS * charge) / abs(charge)

    # group isotopes
    finalPattern = _consolidate(finalPattern, groupingWindow)

    # get real peaks from profile
    if real:
        prof = profile(finalPattern, fwhm=fwhm, points=100, model=model)
        finalPattern = []
        for isotope in mod_signal.maxima(prof):
            finalPattern.append(isotope)
            centroid = mod_signal.centroid(prof, isotope[0], isotope[1] * 0.99)
            if abs(centroid - isotope[0]) < fwhm / 100.:
                finalPattern[-1][0] = centroid

    # normalize pattern
    finalPattern = _normalize(finalPattern)

    # discard peaks below threshold
    filteredPeaks = []
    for peak in finalPattern:
        if peak[1] >= threshold:
            filteredPeaks.append(list(peak))
    finalPattern = filteredPeaks

    return finalPattern
Exemple #19
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def frules(compound,
           rules=['HC', 'NOPSC', 'NOPS', 'RDBE', 'RDBEInt'],
           HC=(0.1, 3.0),
           NOPSC=(4, 3, 2, 3),
           RDBE=(-1, 40)):
    """Check formula rules for a given compound.
        compound (str or mspy.compound) - compound
        rules (list of str) - rules to be checked
        HC (tuple) - H/C limits
        NOPSC (tuple) - NOPS/C max values
        RDBE (tuple) - RDBE limits
    """

    # check compound
    if not isinstance(compound, obj_compound.compound):
        compound = obj_compound.compound(compound)

    # get element counts
    countC = float(compound.count('C', groupIsotopes=True))
    countH = float(compound.count('H', groupIsotopes=True))
    countN = float(compound.count('N', groupIsotopes=True))
    countO = float(compound.count('O', groupIsotopes=True))
    countP = float(compound.count('P', groupIsotopes=True))
    countS = float(compound.count('S', groupIsotopes=True))

    # get carbon ratios
    if countC:
        ratioHC = countH / countC
        ratioNC = countN / countC
        ratioOC = countO / countC
        ratioPC = countP / countC
        ratioSC = countS / countC

    # get RDBE
    rdbeValue = rdbe(compound)

    # check HC rule
    if 'HC' in rules and countC:
        if (ratioHC < HC[0] or ratioHC > HC[1]):
            return False

    # check NOPS rule
    if 'NOPSC' in rules and countC:
        if (ratioNC > NOPSC[0] or ratioOC > NOPSC[1] or ratioPC > NOPSC[2]
                or ratioSC > NOPSC[3]):
            return False

    # check NOPS all > 1 rule
    if 'NOPS' in rules and (countN > 1 and countO > 1 and countP > 1
                            and countS > 1):
        if (countN >= 10 or countO >= 20 or countP >= 4 or countS >= 3):
            return False

    # check NOP all > 3 rule
    if 'NOPS' in rules and (countN > 3 and countO > 3 and countP > 3):
        if (countN >= 11 or countO >= 22 or countP >= 6):
            return False

    # check NOS all > 1 rule
    if 'NOPS' in rules and (countN > 1 and countO > 1 and countS > 1):
        if (countN >= 19 or countO >= 14 or countS >= 8):
            return False

    # check NPS all > 1 rule
    if 'NOPS' in rules and (countN > 1 and countP > 1 and countS > 1):
        if (countN >= 3 or countP >= 3 or countS >= 3):
            return False

    # check OPS all > 1 rule
    if 'NOPS' in rules and (countO > 1 and countP > 1 and countS > 1):
        if (countO >= 14 or countP >= 3 or countS >= 3):
            return False

    # check RDBE range
    if 'RDBE' in rules:
        if rdbeValue < RDBE[0] or rdbeValue > RDBE[1]:
            return False

    # check integer RDBE
    if 'RDBEInt' in rules:
        if rdbeValue % 1:
            return False

    # all ok
    return True
Exemple #20
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def formulator(mz, charge=0, tolerance=1., units='ppm', composition={}, agentFormula='H', agentCharge=1, limit=1000):
    """Generate formulae for given mass, tolerance and composition limits.
        mz (float) - searched m/z value
        charge (int) - current charge
        tolerance (float) - mass tolerance
        units (ppm or Da) - mass tolerance units
        composition (dict of 'element':[min count, max count]) - composition limits
        agentFormula (str) - charging agent formula
        agentCharge (int) - charging agent unit charge
        limit (int) - maximum formulae allowed to be calculated
    """
    
    # get neutral mass
    if charge != 0 and agentFormula:
        mass = mod_basics.mz(mz, 0, currentCharge=charge, agentFormula=agentFormula, agentCharge=agentCharge)
    else:
        mass = mz
    
    # check neutral mass
    if mass <= 0:
        return []
    
    # get mass limits
    if units == 'ppm':
        loMass = mass - (mass/1e6) * tolerance
        hiMass = mass + (mass/1e6) * tolerance
    elif charge != 0:
        loMass = mass - abs(charge)*tolerance
        hiMass = mass + abs(charge)*tolerance
    else:
        loMass = mass - tolerance
        hiMass = mass + tolerance
    
    # sort elements by masses to speed up processing
    buff = []
    for el in composition:
        elMass = obj_compound.compound(el).mass(0)
        buff.append([elMass, el])
    buff.sort(reverse=True)
    
    # compile elements and counts
    elementMasses = []
    elements = []
    minComposition = []
    maxComposition = []
    for el in buff:
        elementMasses.append(el[0])
        elements.append(el[1])
        minComposition.append(composition[el[1]][0])
        maxComposition.append(composition[el[1]][1])
    
    # check max composition
    for i in range(len(maxComposition)):
        maxComposition[i] = min(maxComposition[i], int(hiMass/elementMasses[i]))
    
    # generate compositions
    formulae = []
    comps = _compositions(minComposition, maxComposition, elementMasses, loMass, hiMass, limit)
    for comp in comps:
        
        CHECK_FORCE_QUIT()
        
        formula = ''
        for i in range(len(comp)):
            formula += '%s%d' % (elements[i], comp[i])
        
        formulae.append(formula)
    
    return formulae
Exemple #21
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def pattern(compound, fwhm=0.1, threshold=0.01, charge=0, agentFormula='H', agentCharge=1, real=True, model='gaussian'):
    """Calculate isotopic pattern for given compound.
        compound (str or mspy.compound) - compound
        fwhm (float) - gaussian peak width
        threshold (float) - relative intensity threshold for isotopes (in %/100)
        charge (int) - charge to be calculated
        agentFormula (str or mspy.compound) - charging agent formula
        agentCharge (int) - charging agent unit charge
        real (bool) - get real peaks from calculated profile
        model (gaussian, lorentzian, gausslorentzian) - peak shape function
    """

    # check compound
    if not isinstance(compound, obj_compound.compound):
        compound = obj_compound.compound(compound)

    # check agent formula
    if agentFormula != 'e' and not isinstance(agentFormula, obj_compound.compound):
        agentFormula = obj_compound.compound(agentFormula)

    # add charging agent to compound
    if charge and agentFormula != 'e':
        formula = compound.formula()
        for atom, count in agentFormula.composition().items():
            formula += '%s%d' % (atom, count*(charge/agentCharge))
        compound = obj_compound.compound(formula)

    # get composition and check for negative atom counts
    composition = compound.composition()
    for atom in composition:
        if composition[atom] < 0:
            raise ValueError, 'Pattern cannot be calculated for this formula! --> ' + compound.formula()

    # set internal thresholds
    internalThreshold = threshold/100.
    groupingWindow = fwhm/4.

    # calculate pattern
    finalPattern = []
    for atom in composition:

        # get isotopic profile for current atom or specified isotope only
        atomCount = composition[atom]
        atomPattern = []
        match = mod_basics.ELEMENT_PATTERN.match(atom)
        symbol, massNumber, tmp = match.groups()
        if massNumber:
            isotope = blocks.elements[symbol].isotopes[int(massNumber)]
            atomPattern.append([isotope[0], 1.]) # [mass, abundance]
        else:
            for massNumber, isotope in blocks.elements[atom].isotopes.items():
                if isotope[1] > 0.:
                    atomPattern.append(list(isotope)) # [mass, abundance]

        # add atoms
        for i in range(atomCount):

            CHECK_FORCE_QUIT()

            # if pattern is empty (first atom) add current atom pattern
            if len(finalPattern) == 0:
                finalPattern = _normalize(atomPattern)
                continue

            # add atom to each peak of final pattern
            currentPattern = []
            for patternIsotope in finalPattern:

                # skip peak under relevant abundance threshold
                if patternIsotope[1] < internalThreshold:
                    continue

                # add each isotope of current atom to peak
                for atomIsotope in atomPattern:
                    mass = patternIsotope[0] + atomIsotope[0]
                    abundance = patternIsotope[1] * atomIsotope[1]
                    currentPattern.append([mass, abundance])

            # group isotopes and normalize pattern
            finalPattern = _consolidate(currentPattern, groupingWindow)
            finalPattern = _normalize(finalPattern)

    # correct charge
    if charge:
        for i in range(len(finalPattern)):
            finalPattern[i][0] = (finalPattern[i][0] - mod_basics.ELECTRON_MASS*charge) / abs(charge)

    # group isotopes
    finalPattern = _consolidate(finalPattern, groupingWindow)

    # get real peaks from profile
    if real:
        prof = profile(finalPattern, fwhm=fwhm, points=100, model=model)
        finalPattern = []
        for isotope in mod_signal.maxima(prof):
            finalPattern.append(isotope)
            centroid = mod_signal.centroid(prof, isotope[0], isotope[1]*0.99)
            if abs(centroid-isotope[0]) < fwhm/100.:
                finalPattern[-1][0] = centroid

    # normalize pattern
    finalPattern = _normalize(finalPattern)

    # discard peaks below threshold
    filteredPeaks = []
    for peak in finalPattern:
        if peak[1] >= threshold:
            filteredPeaks.append(list(peak))
    finalPattern = filteredPeaks

    return finalPattern
Exemple #22
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def formulator(mz,
               charge=0,
               tolerance=1.,
               units='ppm',
               composition={},
               agentFormula='H',
               agentCharge=1,
               limit=1000):
    """Generate formulae for given mass, tolerance and composition limits.
        mz (float) - searched m/z value
        charge (int) - current charge
        tolerance (float) - mass tolerance
        units (ppm or Da) - mass tolerance units
        composition (dict of 'element':[min count, max count]) - composition limits
        agentFormula (str) - charging agent formula
        agentCharge (int) - charging agent unit charge
        limit (int) - maximum formulae allowed to be calculated
    """

    # get neutral mass
    if charge != 0 and agentFormula:
        mass = mod_basics.mz(mz,
                             0,
                             currentCharge=charge,
                             agentFormula=agentFormula,
                             agentCharge=agentCharge)
    else:
        mass = mz

    # check neutral mass
    if mass <= 0:
        return []

    # get mass limits
    if units == 'ppm':
        loMass = mass - (mass / 1e6) * tolerance
        hiMass = mass + (mass / 1e6) * tolerance
    elif charge != 0:
        loMass = mass - abs(charge) * tolerance
        hiMass = mass + abs(charge) * tolerance
    else:
        loMass = mass - tolerance
        hiMass = mass + tolerance

    # sort elements by masses to speed up processing
    buff = []
    for el in composition:
        elMass = obj_compound.compound(el).mass(0)
        buff.append([elMass, el])
    buff.sort(reverse=True)

    # compile elements and counts
    elementMasses = []
    elements = []
    minComposition = []
    maxComposition = []
    for el in buff:
        elementMasses.append(el[0])
        elements.append(el[1])
        minComposition.append(composition[el[1]][0])
        maxComposition.append(composition[el[1]][1])

    # check max composition
    for i in range(len(maxComposition)):
        maxComposition[i] = min(maxComposition[i],
                                int(hiMass / elementMasses[i]))

    # generate compositions
    formulae = []
    comps = _compositions(minComposition, maxComposition, elementMasses,
                          loMass, hiMass, limit)
    for comp in comps:

        CHECK_FORCE_QUIT()

        formula = ''
        for i in range(len(comp)):
            formula += '%s%d' % (elements[i], comp[i])

        formulae.append(formula)

    return formulae
Exemple #23
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 def composition(self):
     """Get elemental composition."""
     
     # check composition buffer
     if self._composition != None:
         return self._composition
     
     self._composition = {}
     
     # add monomers to formula
     for monomer in self.chain:
         for el, count in blocks.monomers[monomer].composition.items():
             if el in self._composition:
                 self._composition[el] += count
             else:
                 self._composition[el] = count
     
     # add modifications and labels
     mods = self.modifications + self.labels
     for name, position, state in mods:
         multi = 1
         if type(position) in (str, unicode) and position !='' and not position in ('nTerm', 'cTerm'):
             multi = self.chain.count(position)
         for el, count in blocks.modifications[name].composition.items():
             if el in self._composition:
                 self._composition[el] += multi*count
             else:
                 self._composition[el] = multi*count
     
     # add terminal formulae
     if not self.cyclic:
         termCmpd = obj_compound.compound(self.nTermFormula + self.cTermFormula)
         for el, count in termCmpd.composition().items():
             if el in self._composition:
                 self._composition[el] += count
             else:
                 self._composition[el] = count
     
     # subtract neutral losses for fragments
     for loss in self.fragmentLosses:
         lossCmpd = obj_compound.compound(loss)
         for el, count in lossCmpd.composition().items():
             if el in self._composition:
                 self._composition[el] -= count
             else:
                 self._composition[el] = -1*count
     
     # add neutral gains for fragments
     for gain in self.fragmentGains:
         gainCmpd = obj_compound.compound(gain)
         for el, count in gainCmpd.composition().items():
             if el in self._composition:
                 self._composition[el] += count
             else:
                 self._composition[el] = count
     
     # remove zeros
     for atom in self._composition.keys():
         if self._composition[atom] == 0:
             del self._composition[atom]
     
     return self._composition
Exemple #24
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def frules(compound, rules=['HC','NOPSC','NOPS','RDBE','RDBEInt'], HC=(0.1, 3.0), NOPSC=(4,3,2,3), RDBE=(-1,40)):
    """Check formula rules for a given compound.
        compound (str or mspy.compound) - compound
        rules (list of str) - rules to be checked
        HC (tuple) - H/C limits
        NOPSC (tuple) - NOPS/C max values
        RDBE (tuple) - RDBE limits
    """
    
    # check compound
    if not isinstance(compound, obj_compound.compound):
        compound = obj_compound.compound(compound)
    
    # get element counts
    countC = float(compound.count('C', groupIsotopes=True))
    countH = float(compound.count('H', groupIsotopes=True))
    countN = float(compound.count('N', groupIsotopes=True))
    countO = float(compound.count('O', groupIsotopes=True))
    countP = float(compound.count('P', groupIsotopes=True))
    countS = float(compound.count('S', groupIsotopes=True))
    
    # get carbon ratios
    if countC:
        ratioHC = countH / countC
        ratioNC = countN / countC
        ratioOC = countO / countC
        ratioPC = countP / countC
        ratioSC = countS / countC
    
    # get RDBE
    rdbeValue = rdbe(compound)
    
    # check HC rule
    if 'HC' in rules and countC:
        if (ratioHC < HC[0] or ratioHC > HC[1]):
            return False
    
    # check NOPS rule
    if 'NOPSC' in rules and countC:
        if (ratioNC > NOPSC[0] or ratioOC > NOPSC[1] or ratioPC > NOPSC[2] or ratioSC > NOPSC[3]):
            return False
    
    # check NOPS all > 1 rule
    if 'NOPS' in rules and (countN > 1 and countO > 1 and countP > 1 and countS > 1):
        if (countN >= 10 or countO >= 20 or countP >= 4 or countS >= 3):
            return False
    
    # check NOP all > 3 rule
    if 'NOPS' in rules and (countN > 3 and countO > 3 and countP > 3):
        if (countN >= 11 or countO >= 22 or countP >= 6):
            return False
    
    # check NOS all > 1 rule
    if 'NOPS' in rules and (countN > 1 and countO > 1 and countS > 1):
        if (countN >= 19 or countO >= 14 or countS >= 8):
            return False
    
    # check NPS all > 1 rule
    if 'NOPS' in rules and (countN > 1 and countP > 1 and countS > 1):
        if (countN >= 3 or countP >= 3 or countS >= 3):
            return False
    
    # check OPS all > 1 rule
    if 'NOPS' in rules and (countO > 1 and countP > 1 and countS > 1):
        if (countO >= 14 or countP >= 3 or countS >= 3):
            return False
    
    # check RDBE range
    if 'RDBE' in rules:
        if rdbeValue < RDBE[0] or rdbeValue > RDBE[1]:
            return False
    
    # check integer RDBE
    if 'RDBEInt' in rules:
        if rdbeValue % 1:
            return False
    
    # all ok
    return True