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TransformationReaction.cpp

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

#include "TransformationReaction.h"

// Construction/Destruction

TransformationReaction::TransformationReaction(Chemical *OldForm, Chemical *NewForm, RateConstant *k_trans, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->OldForm = chemicals.size();
        chemicals.push_back(OldForm);
        numberOfEachChemicalChangedByReaction.push_back(-1);

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

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

        // 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();
}

TransformationReaction::~TransformationReaction()
{

}

double TransformationReaction::GetRate() const
{
        return rateConstants[k_trans]->GetValue() * chemicals[OldForm]->GetAmount();
}

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

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