#include <MMenz.h>

Inheritance diagram for MMenz:

Collaboration diagram for MMenz:

Public Member Functions
	MMenz ()

void	vEnz (double n)

double	vGetKcat (const Eref &e) const

double	vGetKm (const Eref &e) const

double	vGetNumKm (const Eref &e) const

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

void	vRemesh (const Eref &e)

void	vSetKcat (const Eref &e, double v)

void	vSetKm (const Eref &e, double v)

void	vSetNumKm (const Eref &e, double v)

void	vSub (double n)

virtual	~MMenz ()

Public Member Functions inherited from EnzBase
void	enz (double n)

	EnzBase ()

double	getKcat (const Eref &e) const

double	getKm (const Eref &e) const

double	getNumKm (const Eref &e) const

unsigned int	getNumPrd (const Eref &e) const

unsigned int	getNumSub (const Eref &e) const

void	prd (double n)

void	process (const Eref &e, ProcPtr p)

void	reinit (const Eref &e, ProcPtr p)

void	remesh (const Eref &e)

void	setKcat (const Eref &e, double v)

void	setKm (const Eref &e, double v)

void	setNumKm (const Eref &e, double v)

virtual void	setSolver (Id solver, Id orig)
	Assign solver info. More...

void	sub (double n)

virtual	~EnzBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from EnzBase
static const Cinfo *	initCinfo ()

static void	zombify (Element original, const Cinfo zClass, Id solver)

Private Attributes
double	enz_
	State variable: substrate (in num units) * numKm. More...

double	kcat_
	Km in number units. More...

double	Km_

double	numKm_
	Km in Concentration units, millimolar. More...

double	sub_
	kcat in 1/sec More...

Detailed Description

This class represents the Michaelis-Menten type enzyme, obeying the equation V = kcat.[Etot].[S]/( Km + [S] )

Definition at line 18 of file MMenz.h.

Constructor & Destructor Documentation

MMenz::MMenz ( )

Definition at line 58 of file MMenz.cpp.

     : Km_( 0.005 ), kcat_( 0.1 ), sub_( 0.0 ), enz_( 0.0 )
 {
     ;
 }

MMenz::~MMenz ( )

virtual

Definition at line 64 of file MMenz.cpp.

65 {;}

Member Function Documentation

const Cinfo * MMenz::initCinfo ( )

static

Definition at line 18 of file MMenz.cpp.

References EnzBase::initCinfo(), and mmEnzCinfo.

 {
         // Field Definitions: Inherited from base class.
         // Shared Msg Definitions: Inherited from base class.
         // MsgDest Definitions: inherited
 
     static Dinfo< MMenz > dinfo;
     static Cinfo mmEnzCinfo (
         "MMenz",
         EnzBase::initCinfo(),
         0,
         0,
         &dinfo
     );
 
     return &mmEnzCinfo;
 }

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void MMenz::vEnz ( double n )

virtual

Reimplemented from EnzBase.

Definition at line 77 of file MMenz.cpp.

References enz_.

Referenced by testMMenz().

 {
     enz_ = n;
 }

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double MMenz::vGetKcat ( const Eref & e ) const

virtual

Implements EnzBase.

Definition at line 141 of file MMenz.cpp.

References kcat_.

Referenced by testMMenz().

 {
     return kcat_;
 }

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double MMenz::vGetKm ( const Eref & e ) const

virtual

Implements EnzBase.

Definition at line 115 of file MMenz.cpp.

References Km_.

Referenced by testMMenz().

 {
     return Km_;
 }

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double MMenz::vGetNumKm ( const Eref & e ) const

virtual

Implements EnzBase.

Definition at line 127 of file MMenz.cpp.

References convertConcToNumRateUsingMesh(), and Km_.

 {
     double volScale = convertConcToNumRateUsingMesh( enz, subOut, 1 );
     return Km_ * volScale;
 }

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void MMenz::vProcess	(	const Eref &	e,
		ProcPtr	p
	)

virtual

Reimplemented from EnzBase.

Definition at line 82 of file MMenz.cpp.

References enz_, kcat_, numKm_, SrcFinfo2< T1, T2 >::send(), and sub_.

Referenced by testMMenz().

 {
     double rate = kcat_ * enz_ * sub_ / ( numKm_ + sub_ );
     subOut->send( e, 0, rate );
     prdOut->send( e, rate, 0 );
 
     sub_ = 1.0;
 }

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void MMenz::vReinit	(	const Eref &	e,
		ProcPtr	p
	)

virtual

Reimplemented from EnzBase.

Definition at line 91 of file MMenz.cpp.

References enz_, and sub_.

Referenced by testMMenz().

 {
     sub_ = 1.0;
     enz_ = 0.0;
 }

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void MMenz::vRemesh ( const Eref & e )

virtual

Reimplemented from EnzBase.

Definition at line 97 of file MMenz.cpp.

References convertConcToNumRateUsingMesh(), Km_, and numKm_.

 {
 //  cout << "MMenz::remesh for " << e << endl;
     double volScale = convertConcToNumRateUsingMesh( e, subOut, 1 );
     numKm_ = Km_ * volScale;
 }

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void MMenz::vSetKcat	(	const Eref &	e,
		double	v
	)

virtual

Implements EnzBase.

Definition at line 134 of file MMenz.cpp.

References EPSILON, and kcat_.

Referenced by testMMenz().

 {
     if ( v < EPSILON )
         v = EPSILON;
     kcat_ = v;
 }

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void MMenz::vSetKm	(	const Eref &	e,
		double	v
	)

virtual

Implements EnzBase.

Definition at line 108 of file MMenz.cpp.

References convertConcToNumRateUsingMesh(), Km_, and numKm_.

Referenced by testMMenz().

 {
     Km_ = v;
     double volScale = convertConcToNumRateUsingMesh( enz, subOut, 1 );
     numKm_ = v * volScale;
 }

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void MMenz::vSetNumKm	(	const Eref &	e,
		double	v
	)

virtual

Implements EnzBase.

Definition at line 120 of file MMenz.cpp.

References convertConcToNumRateUsingMesh(), Km_, and numKm_.

 {
     double volScale = convertConcToNumRateUsingMesh( enz, subOut, 1 );
     numKm_ = v;
     Km_ = v / volScale;
 }

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void MMenz::vSub ( double n )

virtual

Reimplemented from EnzBase.

Definition at line 72 of file MMenz.cpp.

References sub_.

Referenced by testMMenz().

 {
     sub_ *= n;
 }

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Member Data Documentation

double MMenz::enz_

private

State variable: substrate (in num units) * numKm.

Definition at line 51 of file MMenz.h.

Referenced by vEnz(), vProcess(), and vReinit().

double MMenz::kcat_

private

Km in number units.

Definition at line 49 of file MMenz.h.

Referenced by vGetKcat(), vProcess(), and vSetKcat().

double MMenz::Km_

private

Definition at line 47 of file MMenz.h.

Referenced by vGetKm(), vGetNumKm(), vRemesh(), vSetKm(), and vSetNumKm().

double MMenz::numKm_

private

Km in Concentration units, millimolar.

Definition at line 48 of file MMenz.h.

Referenced by vProcess(), vRemesh(), vSetKm(), and vSetNumKm().

double MMenz::sub_

private

kcat in 1/sec

Definition at line 50 of file MMenz.h.

Referenced by vProcess(), vReinit(), and vSub().

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

moose-core/kinetics/MMenz.h
moose-core/kinetics/MMenz.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation