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HomodimerizationReaction.cpp

Go to the documentation of this file.

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

#include "HomodimerizationReaction.h"

// Construction/Destruction

HomodimerizationReaction::HomodimerizationReaction(Chemical *Monomer, Chemical *Homodimer, RateConstant *k_dim, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->Monomer = chemicals.size();
        chemicals.push_back(Monomer);
        numberOfEachChemicalChangedByReaction.push_back(-2);

        this->Homodimer = chemicals.size();
        chemicals.push_back(Homodimer);
        numberOfEachChemicalChangedByReaction.push_back(+1);
        
        // rates
        this->k_dim = rateConstants.size();
        rateConstants.push_back(k_dim);

        // dummy jacobian
        chemicalJacobian.push_back(new JElement(-1,-1));

        this->SetTeXForm();
}

HomodimerizationReaction::~HomodimerizationReaction()
{

}

double HomodimerizationReaction::GetRate() const
{
        return (rateConstants[k_dim]->GetValue() * chemicals[Monomer]->GetAmount() * (chemicals[Monomer]->GetAmount() - 1.0));
}

void HomodimerizationReaction::SetTeXForm()
{
        std::stringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_dim]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[Monomer]->GetTeXName().c_str();
        stream << "\\right ]" << "\\left(";
        stream << "\\left [" << chemicals[Monomer]->GetTeXName().c_str() << " - 1 ";
        stream << "\\right)";
        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 *> *HomodimerizationReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[Monomer]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue((rateConstants[k_dim]->GetValue())*(2*(chemicals[Monomer]->GetAmount()) - 1));
        
        return &chemicalJacobian;
}

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