#include <Enz.h>

Inheritance diagram for Enz:

Collaboration diagram for Enz:

Public Member Functions
	Enz ()

void	setKmK1 (double Km, double k1)

void	vCplx (double n)

void	vEnz (double n)

double	vGetConcK1 (const Eref &e) const

double	vGetK1 (const Eref &e) const

double	vGetK2 (const Eref &e) const

double	vGetKcat (const Eref &e) const

double	vGetKm (const Eref &e) const

double	vGetNumKm (const Eref &e) const

double	vGetRatio (const Eref &e) const

void	vPrd (double n)

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

void	vRemesh (const Eref &e)

void	vSetConcK1 (const Eref &e, double v)

void	vSetK1 (const Eref &e, double v)

void	vSetK2 (const Eref &e, double v)

void	vSetKcat (const Eref &e, double v)

void	vSetKm (const Eref &e, double v)

void	vSetNumKm (const Eref &e, double v)

void	vSetRatio (const Eref &e, double v)

void	vSub (double n)

	~Enz ()

Public Member Functions inherited from CplxEnzBase
void	cplx (double n)

	CplxEnzBase ()

double	getConcK1 (const Eref &e) const

double	getK1 (const Eref &e) const

double	getK2 (const Eref &e) const

double	getRatio (const Eref &e) const

void	setConcK1 (const Eref &e, double v)

void	setK1 (const Eref &e, double v)

void	setK2 (const Eref &e, double v)

void	setRatio (const Eref &e, double v)

virtual	~CplxEnzBase ()

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 CplxEnzBase
static const Cinfo *	initCinfo ()

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

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

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

Private Attributes
double	k1_
	Km in concentration units: millimolar. More...

double	k2_
	in # and time units More...

double	k3_
	in time More...

double	Km_

double	r1_
	in time More...

double	r2_

double	r3_

Detailed Description

Definition at line 13 of file Enz.h.

Constructor & Destructor Documentation

Enz::Enz ( )

Definition at line 75 of file Enz.cpp.

     : Km_(5.0e-3), k1_( 0.1 ), k2_( 0.4 ), k3_( 0.1 )
 {
     ;
 }

Enz::~Enz ( )

Definition at line 81 of file Enz.cpp.

82 {;}

Member Function Documentation

const Cinfo * Enz::initCinfo ( )

static

Definition at line 18 of file Enz.cpp.

References enzCinfo, CplxEnzBase::initCinfo(), and setKmK1().

 {
         // Field Definitions: all inherited
         // MsgDest Definitions
         static DestFinfo setKmK1Dest( "setKmK1",
             "Low-level function used when you wish to explicitly set "
             "Km and k1, without doing any of the volume calculations."
             "Needed by ReadKkit and other situations where the numbers "
             "must be set before all the messaging is in place."
             "Not relevant for zombie enzymes.",
             new OpFunc2< Enz, double, double >( &Enz::setKmK1 )
         );
         // Shared Msg Definitions
     static Dinfo< Enz > dinfo;
     static Finfo* enzFinfos[] = {
         &setKmK1Dest,   // DestFinfo
     };
 
     static Cinfo enzCinfo (
         "Enz",
         CplxEnzBase::initCinfo(),
         enzFinfos,
         sizeof( enzFinfos ) / sizeof ( Finfo* ),
         &dinfo
     );
 
     return &enzCinfo;
 }

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void Enz::setKmK1	(	double	Km,
		double	k1
	)

Definition at line 88 of file Enz.cpp.

References k1_, Km_, and r1_.

Referenced by initCinfo().

 {
     r1_ = k1_ = k1;
     Km_ = Km;
 }

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void Enz::vCplx ( double n )

virtual

Reimplemented from CplxEnzBase.

Definition at line 104 of file Enz.cpp.

References k2_, k3_, r2_, and r3_.

 {
     r2_ = k2_ * n;
     r3_ = k3_ * n;
 }

void Enz::vEnz ( double n )

virtual

Reimplemented from EnzBase.

Definition at line 99 of file Enz.cpp.

References r1_.

 {
     r1_ *= n;
 }

double Enz::vGetConcK1 ( const Eref & e ) const

virtual

Implements CplxEnzBase.

Definition at line 236 of file Enz.cpp.

References EPSILON, k2_, k3_, and Km_.

 {
     if ( Km_ < EPSILON ) {
         cout << "Enz::vGetConcK1: Warning: Km_ too small\n";
         return 1.0;
     }
     return ( k2_ + k3_ ) / Km_;
 }

double Enz::vGetK1 ( const Eref & e ) const

virtual

Implements CplxEnzBase.

Definition at line 143 of file Enz.cpp.

References k1_, Km_, and vSetKm().

 {
     Enz* temp = const_cast< Enz* >( this );
     temp->vSetKm( e, Km_ );
     return k1_;
 }

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double Enz::vGetK2 ( const Eref & e ) const

virtual

Implements CplxEnzBase.

Definition at line 156 of file Enz.cpp.

References k2_.

 {
     return k2_;
 }

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

virtual

Implements EnzBase.

Definition at line 173 of file Enz.cpp.

References k3_.

 {
     return k3_;
 }

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

virtual

Implements EnzBase.

Definition at line 193 of file Enz.cpp.

References Km_.

 {
     return Km_;
 }

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

virtual

Implements EnzBase.

Definition at line 205 of file Enz.cpp.

References convertConcToNumRateUsingMesh(), and Km_.

 {
     double volScale = convertConcToNumRateUsingMesh( e, enzOut, 1 );
     return Km_ * volScale;
 }

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double Enz::vGetRatio ( const Eref & e ) const

virtual

Implements CplxEnzBase.

Definition at line 220 of file Enz.cpp.

References k2_, and k3_.

 {
     return k2_ / k3_;
 }

void Enz::vPrd ( double n )

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

virtual

Reimplemented from EnzBase.

Definition at line 110 of file Enz.cpp.

References k1_, r1_, r2_, r3_, and SrcFinfo2< T1, T2 >::send().

 {
     subOut->send( e, r2_, r1_ );
     prdOut->send( e, r3_, 0 );
     enzOut->send( e, r3_ + r2_, r1_ );
     cplxOut->send( e, r1_, r3_ + r2_ );
 
     // cout << "    proc: " << r1_ << ", " << r2_ << ", " << r3_ << endl;
 
     r1_ = k1_;
 }

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

virtual

Reimplemented from EnzBase.

Definition at line 122 of file Enz.cpp.

References k1_, and r1_.

 {
     r1_ = k1_;
 }

void Enz::vRemesh ( const Eref & e )

virtual

Reimplemented from EnzBase.

Definition at line 127 of file Enz.cpp.

References Km_, and EnzBase::setKm().

 {
     setKm( e, Km_ );
 }

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void Enz::vSetConcK1	(	const Eref &	e,
		double	v
	)

virtual

Implements CplxEnzBase.

Definition at line 225 of file Enz.cpp.

References convertConcToNumRateUsingMesh(), EPSILON, k1_, k2_, k3_, Km_, and r1_.

 {
     if ( v < EPSILON ) {
         cout << "Enz::vSetConcK1: Warning: value " << v << " too small\n";
         return;
     }
     double volScale = convertConcToNumRateUsingMesh( e, enzOut, 1 );
     r1_ = k1_ = v * volScale;
     Km_ = ( k2_ + k3_ ) / ( v );
 }

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void Enz::vSetK1	(	const Eref &	e,
		double	v
	)

virtual

Implements CplxEnzBase.

Definition at line 136 of file Enz.cpp.

References convertConcToNumRateUsingMesh(), k1_, k2_, k3_, Km_, and r1_.

 {
     r1_ = k1_ = v;
     double volScale = convertConcToNumRateUsingMesh( e, enzOut, 1 );
     Km_ = ( k2_ + k3_ ) / ( k1_ * volScale );
 }

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void Enz::vSetK2	(	const Eref &	e,
		double	v
	)

virtual

Implements CplxEnzBase.

Definition at line 150 of file Enz.cpp.

References k2_, Km_, and vSetKm().

 {
     k2_ = v; // Assume this overrides the default ratio.
     vSetKm( e, Km_ ); // Update k1_ here as well.
 }

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

virtual

Implements EnzBase.

Definition at line 161 of file Enz.cpp.

References EPSILON, k2_, k3_, Km_, and vSetKm().

 {
     double ratio = 4.0;
     if ( v < EPSILON )
             v = EPSILON;
     if (k3_ > EPSILON)
         ratio = k2_ / k3_;
     k3_ = v;
     k2_ = v * ratio;
     vSetKm( e, Km_ ); // Update k1_ here as well.
 }

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

virtual

Implements EnzBase.

Definition at line 185 of file Enz.cpp.

References convertConcToNumRateUsingMesh(), k1_, k2_, k3_, and Km_.

Referenced by vGetK1(), vSetK2(), and vSetKcat().

 {
     Km_ = v;
     double volScale =
         convertConcToNumRateUsingMesh( e, enzOut, 1 );
     k1_ = ( k2_ + k3_ ) / ( v * volScale );
 }

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

virtual

Implements EnzBase.

Definition at line 198 of file Enz.cpp.

References convertConcToNumRateUsingMesh(), k1_, k2_, k3_, and Km_.

 {
     double volScale = convertConcToNumRateUsingMesh( e, enzOut, 1 );
     k1_ = ( k2_ + k3_ ) / v;
     Km_ = v / volScale;
 }

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void Enz::vSetRatio	(	const Eref &	e,
		double	v
	)

virtual

Implements CplxEnzBase.

Definition at line 211 of file Enz.cpp.

References convertConcToNumRateUsingMesh(), k1_, k2_, k3_, and Km_.

 {
     k2_ = v * k3_;
     double volScale =
         convertConcToNumRateUsingMesh( e, enzOut, 1 );
 
     k1_ = ( k2_ + k3_ ) / ( Km_ * volScale );
 }

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void Enz::vSub ( double n )

virtual

Reimplemented from EnzBase.

Definition at line 94 of file Enz.cpp.

References r1_.

 {
     r1_ *= n;
 }

Member Data Documentation

double Enz::k1_

private

Km in concentration units: millimolar.

Definition at line 63 of file Enz.h.

Referenced by setKmK1(), vGetK1(), vProcess(), vReinit(), vSetConcK1(), vSetK1(), vSetKm(), vSetNumKm(), and vSetRatio().

double Enz::k2_

private

in # and time units

Definition at line 64 of file Enz.h.

Referenced by vCplx(), vGetConcK1(), vGetK2(), vGetRatio(), vSetConcK1(), vSetK1(), vSetK2(), vSetKcat(), vSetKm(), vSetNumKm(), and vSetRatio().

double Enz::k3_

private

in time

Definition at line 65 of file Enz.h.

Referenced by vCplx(), vGetConcK1(), vGetKcat(), vGetRatio(), vSetConcK1(), vSetK1(), vSetKcat(), vSetKm(), vSetNumKm(), and vSetRatio().

double Enz::Km_

private

Definition at line 62 of file Enz.h.

Referenced by setKmK1(), vGetConcK1(), vGetK1(), vGetKm(), vGetNumKm(), vRemesh(), vSetConcK1(), vSetK1(), vSetK2(), vSetKcat(), vSetKm(), vSetNumKm(), and vSetRatio().

double Enz::r1_

private

in time

Definition at line 66 of file Enz.h.

Referenced by setKmK1(), vEnz(), vProcess(), vReinit(), vSetConcK1(), vSetK1(), and vSub().

double Enz::r2_

private

Definition at line 67 of file Enz.h.

Referenced by vCplx(), and vProcess().

double Enz::r3_

private

Definition at line 68 of file Enz.h.

Referenced by vCplx(), and vProcess().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation