#include <RateTerm.h>

Inheritance diagram for RateTerm:

Collaboration diagram for RateTerm:

Public Member Functions
virtual RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const =0

virtual double	getR1 () const =0
	Used by Zombie to return rate terms. More...

virtual double	getR2 () const =0
	Used by Zombie to return rate terms. More...

virtual unsigned int	getReactants (vector< unsigned int > &molIndex) const =0

virtual double	operator() (const double *S) const =0
	Computes the rate. The argument is the molecule array. More...

	RateTerm ()

virtual void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)=0

virtual void	setR1 (double k1)=0
	Used by Zombie to assign rate terms. More...

virtual void	setR2 (double k2)=0
	Used by Zombie to assign rate terms. More...

virtual void	setRates (double k1, double k2)=0

virtual	~RateTerm ()

Static Public Attributes
static const double	EPSILON = 1.0e-6

Detailed Description

Definition at line 18 of file RateTerm.h.

Constructor & Destructor Documentation

RateTerm::RateTerm ( )

inline

Definition at line 21 of file RateTerm.h.

21 {;}

virtual RateTerm::~RateTerm ( )

inlinevirtual

Definition at line 22 of file RateTerm.h.

22 {;}

Member Function Documentation

virtual RateTerm* RateTerm::copyWithVolScaling	(	double	vol,
		double	sub,
		double	prd
	)		const

pure virtual

Duplicates rate term and then applies volume scaling. Arguments are volume of reference voxel, product of vol/refVol for all substrates: applied to R1 product of vol/refVol for all products: applied to R2

Note that unless the reaction is cross-compartment, the vol/refVol will be one.

Implemented in BidirectionalReaction, StochNOrder, NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, Flux, ZeroOrder, ExternReac, MMEnzyme, MMEnzyme1, FuncReac, and FuncRate.

virtual double RateTerm::getR1 ( ) const

pure virtual

Used by Zombie to return rate terms.

Implemented in BidirectionalReaction, ZeroOrder, ExternReac, and MMEnzymeBase.

Referenced by Stoich::convertRatesToStochasticForm().

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virtual double RateTerm::getR2 ( ) const

pure virtual

Used by Zombie to return rate terms.

Implemented in BidirectionalReaction, ZeroOrder, ExternReac, and MMEnzymeBase.

virtual unsigned int RateTerm::getReactants ( vector< unsigned int > & molIndex ) const

pure virtual

This function finds the reactant indices in the vector S. It returns the number of substrates found, which are the first entries in molIndex. The products are the remaining ones. Note that it does NOT find products for unidirectional reactions, which is a bit of a problem.

Implemented in BidirectionalReaction, NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, Flux, ZeroOrder, ExternReac, MMEnzyme, MMEnzyme1, FuncReac, and FuncRate.

Referenced by Gsolve::fillMmEnzDep(), and MMEnzyme::getReactants().

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virtual double RateTerm::operator() ( const double * S ) const

pure virtual

Computes the rate. The argument is the molecule array.

Implemented in BidirectionalReaction, StochNOrder, NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, Flux, ZeroOrder, ExternReac, MMEnzyme, MMEnzyme1, FuncReac, and FuncRate.

virtual void RateTerm::rescaleVolume	(	short	comptIndex,
		const vector< short > &	compartmentLookup,
		double	ratio
	)

pure virtual

This is used to rescale the RateTerm kinetics when the compartment volume changes. This is needed because the kinetics are in extensive units, that is, mol numbers, rather than in intensive units like concentration. So when the volume changes the rate terms change. Each Rate term checks if any of its reactant molecules are affected, and if so, rescales. Ratio is newVol / oldVol

Implemented in BidirectionalReaction, NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, Flux, ZeroOrder, ExternReac, FuncReac, and MMEnzymeBase.