mm.py

mm.py

class MassActionFluxProcess:
    def __init__(self, k_value, volume, reactants):
        self.volume = volume
        self.k_value = k_value
        self.reactants = reactants
        self.N_A = 6.0221367e+23

    def __call__(self, variable_array, time):
        velocity = self.k_value * self.volume * self.N_A
        for r in self.reactants:
            coefficient = r['coef']
            value = variable_array[r['id']]
            while coefficient > 0:
                velocity *= value / (self.volume * self.N_A)
                coefficient -= 1
        return velocity

    def __str__(self):
        retval = 'MassAction('
        retval += 'k=%f, ' % self.k_value
        retval += 'reactants=%s' % self.reactants
        retval += ')'
        return retval

class MichaelisMentenFluxProcess:
    def __init__(self, KcR, KcF, KmS, KmP, volume, substrate, product, effector):
        self.volume = volume

        self.KcF = KcF
        self.KmS = KmS
        self.kmP = KmP

        KmSP = KmS * KmP

        self.substrate = substrate
        self.product   = product
        self.catalysts = effector

    def __fire__(self, time):
        self.KmP_S = KmP * conc(self.substrate)
        self.KmS_P = KmS * conc(self.product)

        velocity = KcF * KmP_S
        velocity -= KcR * KmS_P
        velocity *= conc(self.catalysts)

        velocity /= KmS_P + KmP_S + KmSP

        return velocity