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HomodimerDissociationReaction.cpp

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

#include "HomodimerDissociationReaction.h"

// Construction/Destruction

HomodimerDissociationReaction::HomodimerDissociationReaction(Chemical *Homodimer, Chemical *Monomer, RateConstant *k_udim, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->Homodimer = chemicals.size();
        chemicals.push_back(Homodimer);
        numberOfEachChemicalChangedByReaction.push_back(-1);

        this->Monomer = chemicals.size();
        chemicals.push_back(Monomer);
        numberOfEachChemicalChangedByReaction.push_back(+2);

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

        // 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));

        this->SetTeXForm();
}

HomodimerDissociationReaction::~HomodimerDissociationReaction()
{

}

double HomodimerDissociationReaction::GetRate() const
{
        return rateConstants[k_udim]->GetValue() * chemicals[Homodimer]->GetAmount();
}

void HomodimerDissociationReaction::SetTeXForm()
{
        std::stringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_udim]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[Homodimer]->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 *> *HomodimerDissociationReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[Homodimer]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(rateConstants[k_udim]->GetValue());
        
        return &chemicalJacobian;
}

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