---

Reaction.h

Go to the documentation of this file.

// Reaction.h: interface for the Reaction class.
//

#if !defined(AFX_REACTION_H__17E9EE60_DB43_11D3_8099_00A0C9B3BB18__INCLUDED_)
#define AFX_REACTION_H__17E9EE60_DB43_11D3_8099_00A0C9B3BB18__INCLUDED_

#ifndef SWIG
#if _MSC_VER > 1000
#pragma once
#endif // _MSC_VER > 1000
#endif

#ifdef _WIN32
#include <strstream>
#endif

#include <vector>
#include <string>
//#include <strstrea.h>
#include <sstream>
#include <iostream>
#include "Chemical.h"
#include "RateConstant.h"

class Chemical; // Both files refer to one another


class Reaction  
{
public:
        class JElement
        {
        public:
                JElement() {return;}
                JElement(int withRespectTo, double jValue)
                {
                        _withRespectTo = withRespectTo;
                        _jValue = jValue;
                }
                virtual ~JElement() {return;}
                int GetWithRespectTo() const {return _withRespectTo;}
                double GetJValue() const {return _jValue;}
                void SetWithRespectTo(int withRespectTo) {_withRespectTo = withRespectTo;}
                void SetJValue(double jValue) {_jValue = jValue;}
        private:
                int _withRespectTo;
                double _jValue;
        };
        int GetNumberChangedByReaction(int chemicalNumber);
        void DoReactionOnce();
        Reaction();
        Reaction(std::string reactionName);
        virtual ~Reaction();    
        std::vector<Chemical *> *GetChemicals();
        virtual double GetRate() const = 0;     
        virtual std::vector<JElement *> *GetChemicalJacobian() = 0;
        virtual std::string GetTeXForm() const {return m_sTeXForm;}
        virtual void SetTeXForm() = 0;
        std::string GetName() const {return reactionName;}
protected:
        // For stochastic simulations, should probably store the rate last
        // calculated, and store a bool that tells whether any neighboring 
        // chemical has changed concentration. Would need a member function
        // for alerting the reaction, called in SetAmount for the chemical.

        // Reactions that depend or affect the chemical
        std::vector<Chemical *> chemicals;      
        // Name explains it all
        std::vector<int> numberOfEachChemicalChangedByReaction; 
        // Rate constants for this reaction
        std::vector<RateConstant *> rateConstants;
        // Jacobian w.r.t. variables (chemicals)
        std::vector<JElement *> chemicalJacobian;
        // string for name of reaction
        std::string reactionName;
        // string giving TeX formatted reaction term
        std::string m_sTeXForm;
};

#endif // !defined(AFX_REACTION_H__17E9EE60_DB43_11D3_8099_00A0C9B3BB18__INCLUDED_)

---