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MichaelisMentenReaction.cpp

Go to the documentation of this file.

// MichaelisMentenReaction.cpp: implementation of the MichaelisMentenReaction class.
//

#include "MichaelisMentenReaction.h"

// Construction/Destruction

MichaelisMentenReaction::MichaelisMentenReaction(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(0);

        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();
}

MichaelisMentenReaction::~MichaelisMentenReaction()
{

}

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

void MichaelisMentenReaction::SetTeXForm()
{
        std::stringstream 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 << 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 *> *MichaelisMentenReaction::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]->SetJValue((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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