NOrder Class Reference

#include <RateTerm.h>

Inheritance diagram for NOrder:

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Collaboration diagram for NOrder:

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List of all members.

Public Member Functions
	NOrder (double k, vector< unsigned int > v)
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array.
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
Protected Attributes
vector< unsigned int >	v_

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Constructor & Destructor Documentation

NOrder::NOrder	(	double	k,
		vector< unsigned int >	v
	)			[inline]

Referenced by copyWithVolScaling().

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Member Function Documentation

RateTerm* NOrder::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.

Reimplemented from ZeroOrder.

Reimplemented in StochNOrder.

References ZeroOrder::k_, NA, NOrder(), and v_.

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unsigned int NOrder::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.

Reimplemented from ZeroOrder.

References v_.

double NOrder::operator()

(

const double *

S

)

const [inline, virtual]

Computes the rate. The argument is the molecule array.

Reimplemented from ZeroOrder.

Reimplemented in StochNOrder.

References ZeroOrder::k_, and v_.

void NOrder::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

Reimplemented from ZeroOrder.

References ZeroOrder::k_, and v_.

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Member Data Documentation

vector< unsigned int > NOrder::v_ [protected]

Referenced by StochNOrder::copyWithVolScaling(), copyWithVolScaling(), getReactants(), operator()(), StochNOrder::operator()(), and rescaleVolume().

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The documentation for this class was generated from the following file:

• ksolve/RateTerm.h