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FirstOrderDestructionReaction.cpp

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// FirstOrderDestructionReaction.cpp: implementation of the CFirstOrderDestructionReaction class.
//

#include "FirstOrderDestructionReaction.h"

// Construction/Destruction

CFirstOrderDestructionReaction::CFirstOrderDestructionReaction(Chemical *DestroyingEnzyme, Chemical *Substrate, RateConstant *k_fod, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->DestroyingEnzyme = chemicals.size();
        chemicals.push_back(DestroyingEnzyme);
        numberOfEachChemicalChangedByReaction.push_back(0);

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

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

        // 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();

}

CFirstOrderDestructionReaction::~CFirstOrderDestructionReaction()
{

}

double CFirstOrderDestructionReaction::GetRate() const
{
        double kfod = rateConstants[k_fod]->GetValue();
        double de = chemicals[DestroyingEnzyme]->GetAmount();
        double su = chemicals[Substrate]->GetAmount();
        return kfod*de*su; 
}

void CFirstOrderDestructionReaction::SetTeXForm()
{
        std::stringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_fod]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[DestroyingEnzyme]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << " \\left [" << chemicals[Substrate]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << ends;
        // set the TeX string equal to what's in the stream
        m_sTeXForm = stream.str();
        // free up the string
//      stream.rdbuf()->freeze(0);
}

std::vector<Reaction::JElement *> *CFirstOrderDestructionReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[DestroyingEnzyme]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(rateConstants[k_fod]->GetValue()*chemicals[Substrate]->GetAmount());

        chemicalJacobian[1]->SetWithRespectTo(chemicals[Substrate]->GetChemicalNumber());
        chemicalJacobian[1]->SetJValue(rateConstants[k_fod]->GetValue()*chemicals[DestroyingEnzyme]->GetAmount());
        
        return &chemicalJacobian;
}

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