BidirectionalReaction Class Reference

#include <RateTerm.h>

Inheritance diagram for BidirectionalReaction:

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Public Member Functions
	BidirectionalReaction (ZeroOrder forward, ZeroOrder backward)
	~BidirectionalReaction ()
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array.
void	setRates (double kf, double kb)
void	setR1 (double kf)
	Used by Zombie to assign rate terms.
void	setR2 (double kb)
	Used by Zombie to assign rate terms.
double	getR1 () const
	Used by Zombie to return rate terms.
double	getR2 () const
	Used by Zombie to return rate terms.
unsigned int	getReactants (vector< unsigned int > &molIndex) const
void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const

Constructor & Destructor Documentation

BidirectionalReaction::BidirectionalReaction	(	ZeroOrder *	forward,
		ZeroOrder *	backward
	)			`[inline]`

Referenced by copyWithVolScaling().

BidirectionalReaction::~BidirectionalReaction ( ) [inline]

Member Function Documentation

RateTerm* BidirectionalReaction::copyWithVolScaling	(	double	vol,
		double	sub,
		double	prd
	)			const `[inline, 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.

Implements RateTerm.

References BidirectionalReaction(), and ZeroOrder::copyWithVolScaling().

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double BidirectionalReaction::getR1 ( ) const [inline, virtual]

Used by Zombie to return rate terms.

Implements RateTerm.

References ZeroOrder::getR1().

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double BidirectionalReaction::getR2 ( ) const [inline, virtual]

Used by Zombie to return rate terms.

Implements RateTerm.

References ZeroOrder::getR1().

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unsigned int BidirectionalReaction::getReactants ( vector< unsigned int > & molIndex ) const [inline, 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.

Implements RateTerm.

References ZeroOrder::getReactants().

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double BidirectionalReaction::operator() ( const double * S ) const [inline, virtual]

Computes the rate. The argument is the molecule array.

Implements RateTerm.

void BidirectionalReaction::rescaleVolume	(	short	comptIndex,
		const vector< short > &	compartmentLookup,
		double	ratio
	)			`[inline, 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

Implements RateTerm.

References ZeroOrder::rescaleVolume().

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