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HeterodimerizationReaction.cpp

Go to the documentation of this file.

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

#include "HeterodimerizationReaction.h"

// Construction/Destruction

HeterodimerizationReaction::HeterodimerizationReaction(Chemical *ReactantA, Chemical *ReactantB, Chemical *Heterodimer, RateConstant *k_dim, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->ReactantA = chemicals.size();
        chemicals.push_back(ReactantA);
        numberOfEachChemicalChangedByReaction.push_back(-1);

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

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

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

        // 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();
}

HeterodimerizationReaction::~HeterodimerizationReaction()
{

}

double HeterodimerizationReaction::GetRate() const
{
        return ((rateConstants[k_dim]->GetValue())*(chemicals[ReactantA]->GetAmount())*(chemicals[ReactantB]->GetAmount()));
}

void HeterodimerizationReaction::SetTeXForm()
{
        std::stringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_dim]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[ReactantA]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << "\\left [" << chemicals[ReactantB]->GetTeXName().c_str();
        stream << "\\right ]";
        // 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 *> *HeterodimerizationReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[ReactantA]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue((rateConstants[k_dim]->GetValue())*(chemicals[ReactantB]->GetAmount()));
        
        chemicalJacobian[1]->SetWithRespectTo(chemicals[ReactantB]->GetChemicalNumber());
        chemicalJacobian[1]->SetJValue((rateConstants[k_dim]->GetValue())*(chemicals[ReactantA]->GetAmount()));

        return &chemicalJacobian;
}

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