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MichaelisMentenHeterodimerizationReaction.cpp

Go to the documentation of this file.

// MichaelisMentenHeterodimerizationReaction.cpp: implementation of the CMichaelisMentenHeterodimerizationReaction class.  Difference from regular MM reaction is that here the "enzyme" concentration decreases by 1, it is a sigma looking heterodimerization rxn
//

#include "MichaelisMentenHeterodimerizationReaction.h"

// Construction/Destruction

CMichaelisMentenHeterodimerizationReaction::CMichaelisMentenHeterodimerizationReaction(Chemical *Enzyme, Chemical *Substrate, Chemical *Product, RateConstant *k_2, RateConstant *K_m, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->Enzyme = chemicals.size();
        chemicals.push_back(Enzyme);
        numberOfEachChemicalChangedByReaction.push_back(-1);

        this->Substrate = chemicals.size();
        chemicals.push_back(Substrate);
        numberOfEachChemicalChangedByReaction.push_back(-1);

        this->Product = chemicals.size();
        chemicals.push_back(Product);
        numberOfEachChemicalChangedByReaction.push_back(+1);

        // rates
        this->k_2 = rateConstants.size();
        rateConstants.push_back(k_2);

        this->K_m = rateConstants.size();
        rateConstants.push_back(K_m);

        // put enough dummy chemicalJacobian elements on the vector 
        // - they are recomputed every time you ask for the chemicalJacobian
        chemicalJacobian.push_back(new JElement(-1,-1));
        chemicalJacobian.push_back(new JElement(-1,-1));

        this->SetTeXForm();
}

CMichaelisMentenHeterodimerizationReaction::~CMichaelisMentenHeterodimerizationReaction()
{

}

double CMichaelisMentenHeterodimerizationReaction::GetRate() const
{
        return rateConstants[k_2]->GetValue()*chemicals[Enzyme]->GetAmount()*
                (chemicals[Substrate]->GetAmount()/(chemicals[Substrate]->GetAmount() + rateConstants[K_m]->GetValue()));
}

void CMichaelisMentenHeterodimerizationReaction::SetTeXForm()
{
//      strstream stream;
        std::ostringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_2]->GetTeXName().c_str();
        stream << " \\left[" << chemicals[Enzyme]->GetTeXName().c_str() << "\\right]";
        stream << " {\\left[" << chemicals[Substrate]->GetTeXName().c_str() << "\\right]";
        stream << "\\over {";
        stream << "\\left[" << chemicals[Substrate]->GetTeXName().c_str() << "\\right]";
        stream << " + " << rateConstants[K_m]->GetTeXName().c_str() << "}}";
        // add a NULL
        stream << std::ends;
        // set the TeX string equal to what's in the stream
        m_sTeXForm = stream.str();
        // allow memory to be freed
//      stream.rdbuf()->freeze(0);
}

std::vector<Reaction::JElement *> *CMichaelisMentenHeterodimerizationReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[Enzyme]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue((rateConstants[k_2]->GetValue()*chemicals[Substrate]->GetAmount())/(chemicals[Substrate]->GetAmount() + rateConstants[K_m]->GetValue()));
        
        chemicalJacobian[1]->SetWithRespectTo(chemicals[Substrate]->GetChemicalNumber());
        chemicalJacobian[1]->SetWithRespectTo((rateConstants[k_2]->GetValue()*rateConstants[K_m]->GetValue()*chemicals[Enzyme]->GetAmount())
                / ((chemicals[Substrate]->GetAmount() + rateConstants[K_m]->GetValue())*(chemicals[Substrate]->GetAmount() + rateConstants[K_m]->GetValue())) );

        return &chemicalJacobian;
}

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