#include <set>
#include <vector>
#include <sstream>
#include <fstream>
#include <cstdlib>
#include <new>
#include "copasi/trajectory/CTrajectoryMethod.h"
#include "copasi/utilities/CVersion.h"
#include "copasi/core/CMatrix.h"
#include "copasi/core/CDataVector.h"
#include "copasi/trajectory/CRungeKutta.h"

Classes
class	CHybridMethodODE45

struct	CHybridMethodODE45::Data

Macros
#define	FAST true

#define	INT_EPSILON 0.1

#define	RANDOM_SEED 1

#define	SLOW false

#define	SLOW_REACT -1

#define	SUBTYPE 1

#define	USE_RANDOM_SEED false

Macro Definition Documentation

◆ FAST

#define FAST true

◆ INT_EPSILON

#define INT_EPSILON 0.1

CHybridMethodODE45

This class implements an hybrid algorithm to simulate a biochemical system over time.

File name: CHybridMethodODE45.h Author: Shuo Wang Email: shuow.nosp@m.ang..nosp@m.learn.nosp@m.er@g.nosp@m.mail..nosp@m.com

Last change: 11, Aug 2014

Partition the system into a deterministic part and a stochastic part. That is, every reaction is either classified deterministic or stochastic. Deterministic reactions involve only those metabolites (on substrate and product side), which have a high particle number. Therefore it is legal to integrate this part of the system with e.g. a numerical integrator. The concentration and relative particle number change should be low enough, so that the probabilities of all the reactions in the system show only little changes. The stochastic reactions must be simulated with an exact stochastic method (e.g. next reaction method (Gibson)), because their firing changes the reaction probabilities in the system significantly.

◆ RANDOM_SEED

#define RANDOM_SEED 1

◆ SLOW

#define SLOW false

◆ SLOW_REACT

#define SLOW_REACT -1

◆ SUBTYPE

#define SUBTYPE 1

◆ USE_RANDOM_SEED

#define USE_RANDOM_SEED false

Classes

Macros