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CatalyzedTranslationReaction.cpp

Go to the documentation of this file.

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

#include "CatalyzedTranslationReaction.h"

// Construction/Destruction

CatalyzedTranslationReaction::CatalyzedTranslationReaction(Chemical *mRNA, Chemical *catalyst, Chemical *protein, RateConstant *k_tr, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->mRNA = chemicals.size();
        chemicals.push_back(mRNA);
        numberOfEachChemicalChangedByReaction.push_back(0);

        this->catalyst = chemicals.size();
        chemicals.push_back(catalyst);
        numberOfEachChemicalChangedByReaction.push_back(0);

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

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

        // 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();

}

CatalyzedTranslationReaction::~CatalyzedTranslationReaction()
{

}

double CatalyzedTranslationReaction::GetRate() const
{
        return ((rateConstants[k_tr]->GetValue())*(chemicals[mRNA]->GetAmount())*(chemicals[catalyst]->GetAmount()));
}

void CatalyzedTranslationReaction::SetTeXForm()
{
//      strstream stream;
        std::ostringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_tr]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[mRNA]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << "\\left [" << chemicals[catalyst]->GetTeXName().c_str();
        stream << "\\right ]";
        // add a NULL
        stream << std::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 *> *CatalyzedTranslationReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[mRNA]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue((rateConstants[k_tr]->GetValue())*(chemicals[catalyst]->GetAmount()));
        
        chemicalJacobian[1]->SetWithRespectTo(chemicals[catalyst]->GetChemicalNumber());
        chemicalJacobian[1]->SetJValue((rateConstants[k_tr]->GetValue())*(chemicals[mRNA]->GetAmount()));

        return &chemicalJacobian;
}

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