ZeroOrder Class Reference

#include <RateTerm.h>

Inheritance diagram for ZeroOrder:

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Collaboration diagram for ZeroOrder:

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List of all members.

Public Member Functions
	ZeroOrder (double k)
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array.
void	setK (double k)
void	setRates (double k1, double k2)
void	setR1 (double k1)
	Used by Zombie to assign rate terms.
void	setR2 (double k2)
	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
Protected Attributes
double	k_

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Constructor & Destructor Documentation

ZeroOrder::ZeroOrder

(

double

k

)

[inline]

References k_.

Referenced by copyWithVolScaling().

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Member Function Documentation

RateTerm* ZeroOrder::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.

Reimplemented in Flux, FirstOrder, SecondOrder, StochSecondOrderSingleSubstrate, NOrder, and StochNOrder.

References k_, and ZeroOrder().

Referenced by BidirectionalReaction::copyWithVolScaling().

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double ZeroOrder::getR1

(

)

const [inline, virtual]

Used by Zombie to return rate terms.

Implements RateTerm.

References k_.

Referenced by BidirectionalReaction::getR1(), and BidirectionalReaction::getR2().

double ZeroOrder::getR2

(

)

const [inline, virtual]

Used by Zombie to return rate terms.

Implements RateTerm.

unsigned int ZeroOrder::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.

Reimplemented in Flux, FirstOrder, SecondOrder, StochSecondOrderSingleSubstrate, and NOrder.

Referenced by BidirectionalReaction::getReactants().

double ZeroOrder::operator()

(

const double *

S

)

const [inline, virtual]

Computes the rate. The argument is the molecule array.

Implements RateTerm.

Reimplemented in Flux, FirstOrder, SecondOrder, StochSecondOrderSingleSubstrate, NOrder, and StochNOrder.

References k_.

void ZeroOrder::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.

Reimplemented in Flux, FirstOrder, SecondOrder, StochSecondOrderSingleSubstrate, and NOrder.

Referenced by BidirectionalReaction::rescaleVolume().

void ZeroOrder::setK

(

double

k

)

[inline]

References k_.

Referenced by BidirectionalReaction::setR1(), setR1(), BidirectionalReaction::setR2(), BidirectionalReaction::setRates(), and setRates().

void ZeroOrder::setR1

(

double

k1

)

[inline, virtual]

Used by Zombie to assign rate terms.

Implements RateTerm.

References setK().

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void ZeroOrder::setR2

(

double

k2

)

[inline, virtual]

Used by Zombie to assign rate terms.

Implements RateTerm.

void ZeroOrder::setRates	(	double	k1,
		double	k2
	)			[inline, virtual]

Assign the rates.

Implements RateTerm.

References setK().

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Member Data Documentation

double ZeroOrder::k_ [protected]

Referenced by StochNOrder::copyWithVolScaling(), NOrder::copyWithVolScaling(), StochSecondOrderSingleSubstrate::copyWithVolScaling(), SecondOrder::copyWithVolScaling(), FirstOrder::copyWithVolScaling(), Flux::copyWithVolScaling(), copyWithVolScaling(), getR1(), NOrder::operator()(), StochSecondOrderSingleSubstrate::operator()(), SecondOrder::operator()(), FirstOrder::operator()(), Flux::operator()(), operator()(), StochNOrder::operator()(), NOrder::rescaleVolume(), StochSecondOrderSingleSubstrate::rescaleVolume(), SecondOrder::rescaleVolume(), setK(), and ZeroOrder().

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

• ksolve/RateTerm.h