ZombieMMenz Class Reference

#include <ZombieMMenz.h>

Inheritance diagram for ZombieMMenz:

Collaboration diagram for ZombieMMenz:

Public Member Functions
void	setSolver (Id solver, Id orig)
double	vGetKcat (const Eref &e) const
double	vGetKm (const Eref &e) const
double	vGetNumKm (const Eref &e) const
void	vSetKcat (const Eref &e, double v)
void	vSetKm (const Eref &e, double v)
void	vSetNumKm (const Eref &e, double v)
	ZombieMMenz ()
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)
void	sub (double n)
virtual void	vEnz (double n)
virtual void	vProcess (const Eref &e, ProcPtr p)
virtual void	vReinit (const Eref &e, ProcPtr p)
virtual void	vRemesh (const Eref &e)
virtual void	vSub (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	Km_
Stoich *	stoich_

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 ZombieMMenz.h.

Constructor & Destructor Documentation

ZombieMMenz::ZombieMMenz

(

)

Definition at line 75 of file ZombieMMenz.cpp.

    : Km_( 0.005 )
{;}

Member Function Documentation

const Cinfo * ZombieMMenz::initCinfo ( )

static

Definition at line 27 of file ZombieMMenz.cpp.

References EnzBase::initCinfo(), and zombieMMenzCinfo.

{
        // Field Definitions
        // MsgDest Definitions
        // Shared Msg Definitions

    static string doc[] = {
        "Name", "ZombieMMenz",
        "Author", "Upi Bhalla",
        "Description", "Zombie class for MM (Michaelis-Menten) enzyme."
    };
    static Dinfo< ZombieMMenz > dinfo;
    static Cinfo zombieMMenzCinfo (
        "ZombieMMenz",
        EnzBase::initCinfo(),
        0,
        0,
        &dinfo,
        doc,
        sizeof(doc)/sizeof(string)
    );

    return &zombieMMenzCinfo;
}

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void ZombieMMenz::setSolver ( Id  solver, Id  orig  )

virtual

Does ZombieMMenz specific functions during conversion to zombie virtual func overrides default.

Now set up the RateTerm

Reimplemented from EnzBase.

Definition at line 140 of file ZombieMMenz.cpp.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Cinfo::findFinfo(), Element::getNeighbors(), EnzBase::initCinfo(), Cinfo::isA(), and stoich_.

{
    static const DestFinfo* enzFinfo = dynamic_cast< const DestFinfo* >(
        EnzBase::initCinfo()->findFinfo( "enzDest" ) );
    static const SrcFinfo* subFinfo = dynamic_cast< const SrcFinfo* >(
        EnzBase::initCinfo()->findFinfo( "subOut" ) );
    static const SrcFinfo* prdFinfo = dynamic_cast< const SrcFinfo* >(
        EnzBase::initCinfo()->findFinfo( "prdOut" ) );
    assert( enzFinfo );
    assert( subFinfo );
    assert( prdFinfo );

    assert( solver.element()->cinfo()->isA( "Stoich" ) );
    stoich_ = reinterpret_cast< Stoich* >( solver.eref().data() );

    vector< Id > enzvec;
    vector< Id > subvec;
    vector< Id > prdvec;
    unsigned int num = enzId.element()->getNeighbors( enzvec, enzFinfo );
    num = enzId.element()->getNeighbors( subvec, subFinfo );
    num = enzId.element()->getNeighbors( prdvec, prdFinfo );
    stoich_->installMMenz( enzId, enzvec, subvec, prdvec );
}

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

virtual

Implements EnzBase.

Definition at line 131 of file ZombieMMenz.cpp.

References Stoich::getMMenzKcat(), and stoich_.

{
    return stoich_->getMMenzKcat( e );
}

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

virtual

Implements EnzBase.

Definition at line 105 of file ZombieMMenz.cpp.

References Km_.

{
    return Km_;
}

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

virtual

Implements EnzBase.

Definition at line 117 of file ZombieMMenz.cpp.

References convertConcToNumRateUsingMesh(), and Km_.

{
    double volScale = convertConcToNumRateUsingMesh( e, subOut, 1 );
    return Km_ * volScale;
    // return stoich_->getMMenzNumKm( e );
}

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

virtual

Implements EnzBase.

Definition at line 124 of file ZombieMMenz.cpp.

References EPSILON, Stoich::setMMenzKcat(), and stoich_.

{
    if ( v < EPSILON )
        v = EPSILON;
    stoich_->setMMenzKcat( e, v );
}

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

virtual

Implements EnzBase.

Definition at line 97 of file ZombieMMenz.cpp.

References Km_, Stoich::setMMenzKm(), and stoich_.

{
    Km_ = v;
    stoich_->setMMenzKm( e, v );
    //double volScale = convertConcToNumRateUsingMesh( e, subOut, 1 );
    //stoich_->setMMenzKm( e, v * volScale );
}

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

virtual

Implements EnzBase.

Definition at line 110 of file ZombieMMenz.cpp.

References convertConcToNumRateUsingMesh(), Km_, Stoich::setMMenzKm(), and stoich_.

{
    double volScale = convertConcToNumRateUsingMesh( e, subOut, 1 );
    Km_ = v / volScale;
    stoich_->setMMenzKm( e, Km_ );
}

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Member Data Documentation

double ZombieMMenz::Km_

private

Definition at line 51 of file ZombieMMenz.h.

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

Stoich* ZombieMMenz::stoich_

private

Definition at line 50 of file ZombieMMenz.h.

Referenced by setSolver(), vGetKcat(), vSetKcat(), vSetKm(), and vSetNumKm().

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

• moose-core/ksolve/ZombieMMenz.h
• moose-core/ksolve/ZombieMMenz.cpp