RateTerm Class Reference

#include <RateTerm.h>

Inheritance diagram for RateTerm:

Public Member Functions
	RateTerm ()
virtual	~RateTerm ()
virtual double	operator() (const double *S) const =0
	Computes the rate. The argument is the molecule array.
virtual void	setRates (double k1, double k2)=0
virtual void	setR1 (double k1)=0
	Used by Zombie to assign rate terms.
virtual void	setR2 (double k2)=0
	Used by Zombie to assign rate terms.
virtual double	getR1 () const =0
	Used by Zombie to return rate terms.
virtual double	getR2 () const =0
	Used by Zombie to return rate terms.
virtual unsigned int	getReactants (vector< unsigned int > &molIndex) const =0
virtual void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)=0
virtual RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const =0
Static Public Attributes
static const double	EPSILON = 1.0e-6

Constructor & Destructor Documentation

RateTerm::RateTerm ( ) [inline]

virtual RateTerm::~RateTerm ( ) [inline, virtual]

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

virtual double RateTerm::getR1 ( ) const [pure virtual]

Used by Zombie to return rate terms.

Implemented in MMEnzymeBase, ExternReac, ZeroOrder, and BidirectionalReaction.

Referenced by Stoich::convertRatesToStochasticForm().

virtual double RateTerm::getR2 ( ) const [pure virtual]

Used by Zombie to return rate terms.

Implemented in MMEnzymeBase, ExternReac, ZeroOrder, and BidirectionalReaction.

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

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

virtual double RateTerm::operator() ( const double * S ) const [pure virtual]

Computes the rate. The argument is the molecule array.

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

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