Calculate the mass of a peptide.

    :param aaMass: A dictionary with the monoisotopic masses of amino acid
        residues, by default :attr:`maspy.constants.aaMass`
    :param aaModMass: A dictionary with the monoisotopic mass changes of
        modications, by default :attr:`maspy.constants.aaModMass`
    :param elementMass: A dictionary with the masses of chemical elements, by
        default ``pyteomics.mass.nist_mass``
    :param peptide: peptide sequence, modifications have to be written in the
        format "[modificationId]" and "modificationId" has to be present in
        :attr:`maspy.constants.aaModMass`

    #TODO: change to a more efficient way of calculating the modified mass, by
    first extracting all present modifications and then looking up their masses.

def calcPeptideMass(peptide, **kwargs):
    """Calculate the mass of a peptide.

    :param aaMass: A dictionary with the monoisotopic masses of amino acid
        residues, by default :attr:`maspy.constants.aaMass`
    :param aaModMass: A dictionary with the monoisotopic mass changes of
        modications, by default :attr:`maspy.constants.aaModMass`
    :param elementMass: A dictionary with the masses of chemical elements, by
        default ``pyteomics.mass.nist_mass``
    :param peptide: peptide sequence, modifications have to be written in the
        format "[modificationId]" and "modificationId" has to be present in
        :attr:`maspy.constants.aaModMass`

    #TODO: change to a more efficient way of calculating the modified mass, by
    first extracting all present modifications and then looking up their masses.
    """
    aaMass = kwargs.get('aaMass', maspy.constants.aaMass)
    aaModMass = kwargs.get('aaModMass', maspy.constants.aaModMass)
    elementMass = kwargs.get('elementMass', pyteomics.mass.nist_mass)

    addModMass = float()
    unmodPeptide = peptide
    for modId, modMass in viewitems(aaModMass):
        modSymbol = '[' + modId + ']'
        numMod = peptide.count(modSymbol)
        if numMod > 0:
            unmodPeptide = unmodPeptide.replace(modSymbol, '')
            addModMass += modMass * numMod

    if unmodPeptide.find('[') != -1:
        print(unmodPeptide)
        raise Exception('The peptide contains modification, ' +
                        'not present in maspy.constants.aaModMass'
                        )

    unmodPeptideMass = sum(aaMass[i] for i in unmodPeptide)
    unmodPeptideMass += elementMass['H'][0][0]*2 + elementMass['O'][0][0]
    modPeptideMass = unmodPeptideMass + addModMass
    return modPeptideMass