How to use the pdb2pqr.propka30.Source.determinant.Determinant function in pdb2pqr

def addCoulombBasePair(object1, object2, value):
    """
    Adding the Coulomb interaction (a base pair):
    the lower pKa is lowered
    """
    label1 = object1.label
    label2 = object2.label
    if object1.pKa_mod < object2.pKa_mod:
        newDeterminant = Determinant(label2, -value)
        object1.determinants[2].append(newDeterminant)
    else:
        newDeterminant = Determinant(label1, -value)
        object2.determinants[2].append(newDeterminant)

def addCoulombAcidPair(object1, object2, value):
    """
    Adding the Coulomb interaction (an acid pair):
    the higher pKa is raised
    """
    label1 = object1.label
    label2 = object2.label
    if object1.pKa_mod > object2.pKa_mod:
        newDeterminant = Determinant(label2, value)
        object1.determinants[2].append(newDeterminant)
    else:
        newDeterminant = Determinant(label1, value)
        object2.determinants[2].append(newDeterminant)

def setIonDeterminants(protein, version=None):
    """
    adding ion determinants/perturbations
    """
    ionizable_residues = lib.residueList("propka1")
    for residue in protein.propka_residues:
        if residue.resName in ionizable_residues:
            for ion in protein.residue_dictionary["ION"]:
                distance = calculate.InterResidueDistance(residue, ion)
                if distance < version.coulomb_cutoff[1]:
                    label = "%s%4d%2s" % (ion.resName, ion.resNumb, ion.chainID)
                    weight = version.calculatePairWeight(residue.Nmass, ion.Nmass)
                    # the pKa of both acids and bases are shifted up by negative ions (and vice versa)
                    value = (-ion.Q) * version.calculateCoulombEnergy(distance, weight)
                    newDeterminant = Determinant(label, value)
                    residue.determinants[2].append(newDeterminant)

weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
        exception, value = version.checkExceptions(residue1, residue2)
        # exception = False # circumventing exception
        if exception == True:
            """ do nothing, value should have been assigned """
            #pka_print(" exception for %s %s %6.2lf" % (residue1.label, residue2.label, value))
        else:
            value = version.calculateSideChainEnergy(distance, dpka_max, cutoff, weight, f_angle)
        if residue1.Q == residue2.Q:
            # acid pair or base pair
            if residue1.pKa_mod < residue2.pKa_mod:
                newDeterminant1 = Determinant(residue2.label, -value)
                newDeterminant2 = Determinant(residue1.label,  value)
            else:
                newDeterminant1 = Determinant(residue2.label,  value)
                newDeterminant2 = Determinant(residue1.label, -value)
        else:
            newDeterminant1 = Determinant(residue2.label, value*residue1.Q)
            newDeterminant2 = Determinant(residue1.label, value*residue2.Q)
        if residue1.resName not in version.exclude_sidechain_interactions:
            residue1.determinants[0].append(newDeterminant1)
        if residue2.resName not in version.exclude_sidechain_interactions:
            residue2.determinants[0].append(newDeterminant2)

def addCoulombAcidPair(object1, object2, value):
    """
    Adding the Coulomb interaction (an acid pair):
    the higher pKa is raised
    """
    label1 = object1.label
    label2 = object2.label
    if object1.pKa_mod > object2.pKa_mod:
        newDeterminant = Determinant(label2, value)
        object1.determinants[2].append(newDeterminant)
    else:
        newDeterminant = Determinant(label1, value)
        object2.determinants[2].append(newDeterminant)

else:
            # i.e. no angular dependence
            f_angle = 1.0

        weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
        exception, value = version.checkExceptions(residue1, residue2)
        # exception = False # circumventing exception
        if exception == True:
            """ do nothing, value should have been assigned """
            #pka_print(" exception for %s %s %6.2lf" % (residue1.label, residue2.label, value))
        else:
            value = version.calculateSideChainEnergy(distance, dpka_max, cutoff, weight, f_angle)
        if residue1.Q == residue2.Q:
            # acid pair or base pair
            if residue1.pKa_mod < residue2.pKa_mod:
                newDeterminant1 = Determinant(residue2.label, -value)
                newDeterminant2 = Determinant(residue1.label,  value)
            else:
                newDeterminant1 = Determinant(residue2.label,  value)
                newDeterminant2 = Determinant(residue1.label, -value)
        else:
            newDeterminant1 = Determinant(residue2.label, value*residue1.Q)
            newDeterminant2 = Determinant(residue1.label, value*residue2.Q)
        if residue1.resName not in version.exclude_sidechain_interactions:
            residue1.determinants[0].append(newDeterminant1)
        if residue2.resName not in version.exclude_sidechain_interactions:
            residue2.determinants[0].append(newDeterminant2)

weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
        exception, value = version.checkExceptions(residue1, residue2)
        # exception = False # circumventing exception
        if exception == True:
            """ do nothing, value should have been assigned """
            #pka_print(" exception for %s %s %6.2lf" % (residue1.label, residue2.label, value))
        else:
            value = version.calculateSideChainEnergy(distance, dpka_max, cutoff, weight, f_angle)
        if residue1.Q == residue2.Q:
            # acid pair or base pair
            if residue1.pKa_mod < residue2.pKa_mod:
                newDeterminant1 = Determinant(residue2.label, -value)
                newDeterminant2 = Determinant(residue1.label,  value)
            else:
                newDeterminant1 = Determinant(residue2.label,  value)
                newDeterminant2 = Determinant(residue1.label, -value)
        else:
            newDeterminant1 = Determinant(residue2.label, value*residue1.Q)
            newDeterminant2 = Determinant(residue1.label, value*residue2.Q)
        if residue1.resName not in version.exclude_sidechain_interactions:
            residue1.determinants[0].append(newDeterminant1)
        if residue2.resName not in version.exclude_sidechain_interactions:
            residue2.determinants[0].append(newDeterminant2)