EnzBase Class Reference

#include <EnzBase.h>

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List of all members.

Public Member Functions
	EnzBase ()
virtual	~EnzBase ()
void	setKm (const Eref &e, double v)
double	getKm (const Eref &e) const
void	setNumKm (const Eref &e, double v)
double	getNumKm (const Eref &e) const
void	setKcat (const Eref &e, double v)
double	getKcat (const Eref &e) const
unsigned int	getNumSub (const Eref &e) const
virtual void	vSetKm (const Eref &e, double v)=0
virtual double	vGetKm (const Eref &e) const =0
virtual void	vSetNumKm (const Eref &e, double v)=0
virtual double	vGetNumKm (const Eref &e) const =0
virtual void	vSetKcat (const Eref &e, double v)=0
virtual double	vGetKcat (const Eref &e) const =0
void	process (const Eref &e, ProcPtr p)
void	reinit (const Eref &e, ProcPtr p)
void	sub (double n)
void	enz (double n)
void	prd (double n)
void	remesh (const Eref &e)
virtual void	vProcess (const Eref &e, ProcPtr p)
virtual void	vReinit (const Eref &e, ProcPtr p)
virtual void	vSub (double n)
virtual void	vEnz (double n)
virtual void	vRemesh (const Eref &e)
virtual void	setSolver (Id solver, Id orig)
	Assign solver info.
Static Public Member Functions
static void	zombify (Element *original, const Cinfo *zClass, Id solver)
static const Cinfo *	initCinfo ()

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Detailed Description

This class is the base class for enzymes, both the classical Michaelis- Menten form and the form with explicit enz-substrate complexes that MOOSE prefers.

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Constructor & Destructor Documentation

EnzBase::EnzBase

(

)

EnzBase::~EnzBase

(

)

[virtual]

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Member Function Documentation

void EnzBase::enz

(

double

n

)

References vEnz().

Referenced by initCinfo(), and CplxEnzBase::initCinfo().

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double EnzBase::getKcat

(

const Eref &

e

)

const

References vGetKcat().

Referenced by initCinfo(), CplxEnzBase::initCinfo(), ZombieEnz::vGetKm(), ZombieEnz::vGetRatio(), ZombieEnz::vSetKm(), ZombieEnz::vSetNumKm(), ZombieEnz::vSetRatio(), zombify(), and CplxEnzBase::zombify().

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double EnzBase::getKm

(

const Eref &

e

)

const

References vGetKm().

Referenced by initCinfo(), ZombieEnz::vSetRatio(), and zombify().

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double EnzBase::getNumKm

(

const Eref &

e

)

const

References vGetNumKm().

Referenced by initCinfo().

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unsigned int EnzBase::getNumSub

(

const Eref &

e

)

const

References Eref::element(), and Element::getMsgAndFunc().

Referenced by initCinfo().

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const Cinfo * EnzBase::initCinfo

(

)

[static]

Reimplemented in CplxEnzBase, Enz, MMenz, ZombieEnz, and ZombieMMenz.

References enz(), enzDest(), getKcat(), getKm(), getNumKm(), getNumSub(), Neutral::initCinfo(), prd(), process(), reinit(), remesh(), setKcat(), setKm(), setNumKm(), and sub().

Referenced by enzDest(), findMeshOfEnz(), ZombieMMenz::initCinfo(), MMenz::initCinfo(), and CplxEnzBase::initCinfo().

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void EnzBase::prd

(

double

n

)

Referenced by initCinfo().

void EnzBase::process	(	const Eref &	e,
		ProcPtr	p
	)

References vProcess().

Referenced by initCinfo().

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void EnzBase::reinit	(	const Eref &	e,
		ProcPtr	p
	)

References vReinit().

Referenced by initCinfo().

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void EnzBase::remesh

(

const Eref &

e

)

References vRemesh().

Referenced by initCinfo().

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void EnzBase::setKcat	(	const Eref &	e,
		double	v
	)

References vSetKcat().

Referenced by initCinfo(), CplxEnzBase::initCinfo(), zombify(), and CplxEnzBase::zombify().

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void EnzBase::setKm	(	const Eref &	e,
		double	v
	)

References vSetKm().

Referenced by initCinfo(), Enz::vRemesh(), and zombify().

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void EnzBase::setNumKm	(	const Eref &	e,
		double	v
	)

References vSetNumKm().

Referenced by initCinfo().

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void EnzBase::setSolver	(	Id	solver,
		Id	orig
	)			[virtual]

Assign solver info.

Reimplemented in ZombieEnz, and ZombieMMenz.

Referenced by zombify(), and CplxEnzBase::zombify().

void EnzBase::sub

(

double

n

)

References vSub().

Referenced by initCinfo().

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void EnzBase::vEnz

(

double

n

)

[virtual]

Reimplemented in Enz, and MMenz.

Referenced by enz().

virtual double EnzBase::vGetKcat

(

const Eref &

e

)

const [pure virtual]

Implemented in Enz, MMenz, ZombieEnz, and ZombieMMenz.

Referenced by getKcat().

virtual double EnzBase::vGetKm

(

const Eref &

e

)

const [pure virtual]

Implemented in Enz, MMenz, ZombieEnz, and ZombieMMenz.

Referenced by getKm().

virtual double EnzBase::vGetNumKm

(

const Eref &

e

)

const [pure virtual]

Implemented in Enz, MMenz, ZombieEnz, and ZombieMMenz.

Referenced by getNumKm().

void EnzBase::vProcess	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

Reimplemented in Enz, and MMenz.

Referenced by process().

void EnzBase::vReinit	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

Reimplemented in Enz, and MMenz.

Referenced by reinit().

void EnzBase::vRemesh

(

const Eref &

e

)

[virtual]

Reimplemented in Enz, and MMenz.

Referenced by remesh().

virtual void EnzBase::vSetKcat	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in Enz, MMenz, ZombieEnz, and ZombieMMenz.

Referenced by setKcat().

virtual void EnzBase::vSetKm	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in Enz, MMenz, ZombieEnz, and ZombieMMenz.

Referenced by setKm().

virtual void EnzBase::vSetNumKm	(	const Eref &	e,
		double	v
	)			[pure virtual]

Implemented in Enz, MMenz, ZombieEnz, and ZombieMMenz.

Referenced by setNumKm().

void EnzBase::vSub

(

double

n

)

[virtual]

Reimplemented in Enz, and MMenz.

Referenced by sub().

void EnzBase::zombify	(	Element *	orig,
		const Cinfo *	zClass,
		Id	solver
	)			[static]

This function helps the conversion between Enzyme subclasses. Note that we may need a second zombify function to convert to and from explicit enz classes because there is information lost if we go right down to the EnzBase. Specifically, EnzBase only knows about two parameters, the Km and kcat. Explicit enzymes also need to know a k2, or equivalently a ratio between kcat and k2. But in principle this function allows conversion between the two cases.

Reimplemented in CplxEnzBase.

References Element::cinfo(), Eref::data(), getKcat(), getKm(), Element::id(), Element::localDataStart(), Element::numLocalData(), setKcat(), setKm(), setSolver(), and Element::zombieSwap().

Referenced by Stoich::unZombifyModel().

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

• kinetics/EnzBase.h
• kinetics/EnzBase.cpp