FuncRate Class Reference

#include <FuncRateTerm.h>

Inheritance diagram for FuncRate:

Collaboration diagram for FuncRate:

Public Member Functions
	FuncRate (double k, unsigned int targetPoolIndex)
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array.
unsigned int	getReactants (vector< unsigned int > &molIndex) const
void	setReactants (const vector< unsigned int > &molIndex)
const vector< unsigned int > &	getFuncArgIndex ()
void	setFuncArgIndex (const vector< unsigned int > &mol)
void	setExpr (const string &s)
const string &	getExpr () const
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
Protected Attributes
FuncTerm	func_
double	k_
double	funcVolPower_

Detailed Description

This FuncRate manages a one-way reaction whose rate is determined by a Function. It has no substrates, just controls the rate of change of a target molecule.

dtarget/dt = func( x0, x1, x2..., t )

The values x0, x1, x2 are expected to be concentrations so that they do not depend on volume.

Constructor & Destructor Documentation

FuncRate::FuncRate	(	double	k,
		unsigned int	targetPoolIndex
	)			`[inline]`

References func_, and FuncTerm::setTarget().

Referenced by copyWithVolScaling().

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Member Function Documentation

RateTerm* FuncRate::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 ExternReac.

Reimplemented in FuncReac.

References func_, FuncRate(), funcVolPower_, FuncTerm::getTarget(), k_, and NA.

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const string& FuncRate::getExpr ( ) const [inline]

References func_, and FuncTerm::getExpr().

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const vector< unsigned int >& FuncRate::getFuncArgIndex ( ) [inline]

References func_, and FuncTerm::getReactantIndex().

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unsigned int FuncRate::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 ExternReac.

Reimplemented in FuncReac.

References func_, and FuncTerm::getTarget().

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