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PlasmidReplicationReaction.cpp

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

#include "PlasmidReplicationReaction.h"

// Construction/Destruction

PlasmidReplicationReaction::PlasmidReplicationReaction(Chemical *Generator, std::vector<Chemical *> Products, RateConstant *k_g, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->Generator = chemicals.size();
        chemicals.push_back(Generator);
        numberOfEachChemicalChangedByReaction.push_back(0);

        this->ProductNum = Products.size();
        for (int productcounter = 0; productcounter < Products.size(); ++productcounter)
        {
                this->Product = chemicals.size();
                chemicals.push_back(Products[productcounter]);
                numberOfEachChemicalChangedByReaction.push_back(+1);
//              this->Product.push_back(Products[productcounter]);
//              chemicals.push_back(Products[productcounter]);
//              numberOfEachChemicalChangedByReaction.push_back(+1);
        }

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

        // 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();
}

PlasmidReplicationReaction::~PlasmidReplicationReaction()
{

}

double PlasmidReplicationReaction::GetRate() const
{
        double temp = 0.0;
        int productcounter;
        // initialize productcounter to 1 to avoid including TraRDimer
/*      for (productcounter = 1; productcounter <= ProductNum; ++productcounter)
        {
                temp += chemicals[productcounter]->GetAmount();
        }
        temp = temp/ProductNum;
        temp += rateConstants[k_g]->GetValue() * chemicals[Generator]->GetAmount();
        return temp;
*/      return rateConstants[k_g]->GetValue() * chemicals[Generator]->GetAmount();
}

void PlasmidReplicationReaction::SetTeXForm()
{
        int productcounter;
//      strstream stream;
        std::ostringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_g]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[Generator]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << "\\left (\\right )";
        //initialize productcounter to 1 to avoid TraRDimer
        stream << " \\left [" << chemicals[1]->GetTeXName().c_str();
        stream  << "\\right ] \\\\ \n";
        for (productcounter = 2; productcounter <= ProductNum; ++productcounter)
        {
                stream << " + \\left [" << chemicals[productcounter]->GetTeXName().c_str();
                stream << "\\right ] \\\\ \n";
        }
        stream << " \\left (\\right )"<< " / " << ProductNum;
        // add a NULL
        //int namesize = (chemicals[Generator]->GetName()).length();
        //stream << (chemicals[Generator]->GetName())[namesize];
        stream << std::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 *> *PlasmidReplicationReaction::GetChemicalJacobian()
{
/*      double temp = 0.0;
        int productcounter;
        for (productcounter=1; productcounter <= ProductNum; productcounter++)
        {
                temp += chemicals[productcounter]->GetAmount();
        }
*/
        chemicalJacobian[0]->SetWithRespectTo(chemicals[Generator]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(rateConstants[k_g]->GetValue());
//      chemicalJacobian[0]->SetJValue(rateConstants[k_g]->GetValue()*temp);
        
/*      for (productcounter=1; productcounter<=ProductNum; productcounter++)
        {
                chemicalJacobian[productcounter]->SetWithRespectTo(chemicals[productcounter]->GetChemicalNumber());
                chemicalJacobian[productcounter]->SetJValue(rateConstants[k_g]->GetValue()*chemicals[Generator]->GetAmount());
        }
*/
        return &chemicalJacobian;
}

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