MMEnzymeBase Class Reference

#include <RateTerm.h>

Inheritance diagram for MMEnzymeBase:

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Collaboration diagram for MMEnzymeBase:

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List of all members.

Public Member Functions
	MMEnzymeBase (double Km, double kcat, unsigned int enz)
void	setKm (double Km)
void	setKcat (double kcat)
void	setRates (double Km, double kcat)
void	setR1 (double Km)
	Used by Zombie to assign rate terms.
void	setR2 (double kcat)
	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.
void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)
unsigned int	getEnzIndex () const
Protected Attributes
double	Km_
double	kcat_
unsigned int	enz_

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Constructor & Destructor Documentation

MMEnzymeBase::MMEnzymeBase	(	double	Km,
		double	kcat,
		unsigned int	enz
	)			[inline]

References Km_.

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Member Function Documentation

unsigned int MMEnzymeBase::getEnzIndex

(

)

const [inline]

References enz_.

double MMEnzymeBase::getR1

(

)

const [inline, virtual]

Used by Zombie to return rate terms.

Implements RateTerm.

References Km_.

double MMEnzymeBase::getR2

(

)

const [inline, virtual]

Used by Zombie to return rate terms.

Implements RateTerm.

References kcat_.

void MMEnzymeBase::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 Km_.

void MMEnzymeBase::setKcat

(

double

kcat

)

[inline]

References kcat_.

Referenced by setR2(), and setRates().

void MMEnzymeBase::setKm

(

double

Km

)

[inline]

References Km_.

Referenced by setR1(), and setRates().

void MMEnzymeBase::setR1

(

double

k1

)

[inline, virtual]

Used by Zombie to assign rate terms.

Implements RateTerm.

References setKm().

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void MMEnzymeBase::setR2

(

double

k2

)

[inline, virtual]

Used by Zombie to assign rate terms.

Implements RateTerm.

References setKcat().

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

Assign the rates.

Implements RateTerm.

References setKcat(), and setKm().

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Member Data Documentation

unsigned int MMEnzymeBase::enz_ [protected]

Referenced by MMEnzyme::copyWithVolScaling(), MMEnzyme1::copyWithVolScaling(), getEnzIndex(), MMEnzyme::getReactants(), MMEnzyme1::getReactants(), MMEnzyme::operator()(), and MMEnzyme1::operator()().

double MMEnzymeBase::kcat_ [protected]

Referenced by MMEnzyme::copyWithVolScaling(), MMEnzyme1::copyWithVolScaling(), getR2(), MMEnzyme::operator()(), MMEnzyme1::operator()(), and setKcat().

double MMEnzymeBase::Km_ [protected]

Referenced by MMEnzyme::copyWithVolScaling(), MMEnzyme1::copyWithVolScaling(), getR1(), MMEnzymeBase(), MMEnzyme::operator()(), MMEnzyme1::operator()(), rescaleVolume(), and setKm().

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

• ksolve/RateTerm.h