---

PoolTransitionReaction.cpp

Go to the documentation of this file.

#include "pooltransitionreaction.h"

CPoolTransitionReaction::CPoolTransitionReaction(Chemical *OldPoolForm, Chemical *NewPoolForm, RateConstant *k_t, RateConstant *K, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->OldPoolForm = chemicals.size();
        chemicals.push_back(OldPoolForm);
        numberOfEachChemicalChangedByReaction.push_back(-1);

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

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

        this->K = rateConstants.size();
        rateConstants.push_back(K);

        // 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();
}

CPoolTransitionReaction::~CPoolTransitionReaction(void)
{
}

double CPoolTransitionReaction::GetRate() const
{
        return (rateConstants[k_t]->GetValue()*chemicals[OldPoolForm]->GetAmount())/(rateConstants[K]->GetValue() + chemicals[NewPoolForm]->GetAmount());
}

void CPoolTransitionReaction::SetTeXForm()
{
        strstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_t]->GetTeXName().c_str();
        stream << " {\\left[" << chemicals[OldPoolForm]->GetTeXName().c_str() << "\\right]";
        stream << "\\over {";
        stream <<  rateConstants[K]->GetTeXName().c_str() << " + ";
        stream << "\\left[" << chemicals[NewPoolForm]->GetTeXName().c_str() << "\\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 *> *CPoolTransitionReaction::GetChemicalJacobian()
{
        double denom = rateConstants[K]->GetValue() + chemicals[NewPoolForm]->GetAmount();
        
        chemicalJacobian[0]->SetWithRespectTo(chemicals[OldPoolForm]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(rateConstants[k_t]->GetValue()/denom);
        
        chemicalJacobian[1]->SetWithRespectTo(chemicals[NewPoolForm]->GetChemicalNumber());
        chemicalJacobian[1]->SetJValue(-1.0*(rateConstants[k_t]->GetValue()*chemicals[OldPoolForm]->GetAmount())/(denom*denom));

        return &chemicalJacobian;
}

---