EnzBase Class Reference

#include <EnzBase.h>

Inheritance diagram for EnzBase:

Collaboration diagram for EnzBase:

Public Member Functions
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 void	vEnz (double n)
virtual double	vGetKcat (const Eref &e) const =0
virtual double	vGetKm (const Eref &e) const =0
virtual double	vGetNumKm (const Eref &e) const =0
virtual void	vProcess (const Eref &e, ProcPtr p)
virtual void	vReinit (const Eref &e, ProcPtr p)
virtual void	vRemesh (const Eref &e)
virtual void	vSetKcat (const Eref &e, double v)=0
virtual void	vSetKm (const Eref &e, double v)=0
virtual void	vSetNumKm (const Eref &e, double v)=0
virtual void	vSub (double n)
virtual	~EnzBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()
static void	zombify (Element *original, const Cinfo *zClass, Id solver)

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.

Definition at line 18 of file EnzBase.h.

Constructor & Destructor Documentation

EnzBase::EnzBase

(

)

Definition at line 169 of file EnzBase.cpp.

{;}

EnzBase::~EnzBase ( )

virtual

Definition at line 172 of file EnzBase.cpp.

{;}

Member Function Documentation

void EnzBase::enz

(

double

n

)

Definition at line 187 of file EnzBase.cpp.

References vEnz().

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

{
    vEnz( n );
}

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double EnzBase::getKcat

(

const Eref &

e

)

const

Definition at line 256 of file EnzBase.cpp.

References vGetKcat().

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

{
        return vGetKcat( e );
}

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double EnzBase::getKm

(

const Eref &

e

)

const

Definition at line 235 of file EnzBase.cpp.

References vGetKm().

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

{
        return vGetKm( enz );
}

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double EnzBase::getNumKm

(

const Eref &

e

)

const

Definition at line 245 of file EnzBase.cpp.

References vGetNumKm().

Referenced by initCinfo().

{
        return vGetNumKm( enz );
}

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unsigned int EnzBase::getNumPrd

(

const Eref &

e

)

const

Definition at line 269 of file EnzBase.cpp.

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

Referenced by initCinfo().

{
    const vector< MsgFuncBinding >* mfb =
        e.element()->getMsgAndFunc( prdOut()->getBindIndex() );
    assert( mfb );
    return ( mfb->size() );
}

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unsigned int EnzBase::getNumSub

(

const Eref &

e

)

const

Definition at line 261 of file EnzBase.cpp.

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

Referenced by initCinfo().

{
    const vector< MsgFuncBinding >* mfb =
        e.element()->getMsgAndFunc( subOut()->getBindIndex() );
    assert( mfb );
    return ( mfb->size() );
}

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const Cinfo * EnzBase::initCinfo ( )

static

Definition at line 33 of file EnzBase.cpp.

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

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

{
        // Field Definitions
        static ElementValueFinfo< EnzBase, double > Km(
            "Km",
            "Michaelis-Menten constant in SI conc units (milliMolar)",
            &EnzBase::setKm,
            &EnzBase::getKm
        );

        static ElementValueFinfo< EnzBase, double > numKm(
            "numKm",
            "Michaelis-Menten constant in number units, volume dependent",
            &EnzBase::setNumKm,
            &EnzBase::getNumKm
        );

        static ElementValueFinfo< EnzBase, double > kcat(
            "kcat",
            "Forward rate constant for enzyme, units 1/sec",
            &EnzBase::setKcat,
            &EnzBase::getKcat
        );

        static ReadOnlyElementValueFinfo< EnzBase, unsigned int > numSub(
            "numSubstrates",
            "Number of substrates in this MM reaction. Usually 1."
            "Does not include the enzyme itself",
            &EnzBase::getNumSub
        );

        static ReadOnlyElementValueFinfo< EnzBase, unsigned int > numPrd(
            "numProducts",
            "Number of products in this MM reaction. Usually 1.",
            &EnzBase::getNumPrd
        );


        // Shared Msg Definitions
        static DestFinfo process( "process",
            "Handles process call",
            new ProcOpFunc< EnzBase >( &EnzBase::process ) );

        static DestFinfo reinit( "reinit",
            "Handles reinit call",
            new ProcOpFunc< EnzBase >( &EnzBase::reinit ) );

        /*
        static DestFinfo group( "group",
            "Handle for group msgs. Doesn't do anything",
            new OpFuncDummy() );
            */

        static DestFinfo remesh( "remesh",
            "Tells the MMEnz to recompute its numKm after remeshing",
            new EpFunc0< EnzBase >( &EnzBase::remesh ) );

        // MsgDest Definitions
        static DestFinfo enzDest( "enzDest",
                "Handles # of molecules of Enzyme",
                new OpFunc1< EnzBase, double >( &EnzBase::enz ) );
        static DestFinfo subDest( "subDest",
                "Handles # of molecules of substrate",
                new OpFunc1< EnzBase, double >( &EnzBase::sub ) );
        static DestFinfo prdDest( "prdDest",
                "Handles # of molecules of product. Dummy.",
                new OpFunc1< EnzBase, double >( &EnzBase::prd ) );
        static Finfo* subShared[] = {
            subOut(), &subDest
        };

        static Finfo* prdShared[] = {
            prdOut(), &prdDest
        };
        static SharedFinfo sub( "sub",
            "Connects to substrate molecule",
            subShared, sizeof( subShared ) / sizeof( const Finfo* )
        );
        static SharedFinfo prd( "prd",
            "Connects to product molecule",
            prdShared, sizeof( prdShared ) / sizeof( const Finfo* )
        );
        static Finfo* procShared[] = {
            &process, &reinit
        };
        static SharedFinfo proc( "proc",
            "Shared message for process and reinit",
            procShared, sizeof( procShared ) / sizeof( const Finfo* )
        );

    static Finfo* enzBaseFinfos[] = {
        &Km,    // ElementValue
        &numKm, // ElementValue
        &kcat,  // Value
        &numSub,    // ReadOnlyElementValue
        &numPrd,    // ReadOnlyElementValue
        &enzDest,           // DestFinfo
        &sub,               // SharedFinfo
        &prd,               // SharedFinfo
        &proc,              // SharedFinfo
        &remesh,            // Destfinfo
    };

    static string doc[] =
    {
        "Name", "EnzBase",
        "Author", "Upi Bhalla",
        "Description", "Abstract base class for enzymes."
    };
    static ZeroSizeDinfo< int > dinfo;
    static Cinfo enzBaseCinfo (
        "EnzBase",
        Neutral::initCinfo(),
        enzBaseFinfos,
        sizeof( enzBaseFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof( doc )/sizeof( string ),
        true // Don't create it, it is a an astract base class.
    );

    return &enzBaseCinfo;
}

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void EnzBase::prd

(

double

n

)

Definition at line 184 of file EnzBase.cpp.

Referenced by initCinfo().

{;}

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

Definition at line 192 of file EnzBase.cpp.

References vProcess().

Referenced by initCinfo().

{
    vProcess( e, p );
}

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

Definition at line 197 of file EnzBase.cpp.

References vReinit().

Referenced by initCinfo().

{
    vReinit( e, p );
}

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void EnzBase::remesh

(

const Eref &

e

)

Definition at line 202 of file EnzBase.cpp.

References vRemesh().

Referenced by initCinfo().

{
    vRemesh( e );
}

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

Definition at line 251 of file EnzBase.cpp.

References vSetKcat().

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

{
        vSetKcat( e, v );
}

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

Definition at line 230 of file EnzBase.cpp.

References vSetKm().

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

{
        vSetKm( enz, v );
}

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

Definition at line 240 of file EnzBase.cpp.

References vSetNumKm().

Referenced by initCinfo().

{
        vSetNumKm( enz, v );
}

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

virtual

Assign solver info.

Reimplemented in ZombieEnz, and ZombieMMenz.

Definition at line 319 of file EnzBase.cpp.

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

{
    ;
}

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void EnzBase::sub

(

double

n

)

Definition at line 179 of file EnzBase.cpp.

References vSub().

Referenced by initCinfo().

{
    vSub( n );
}

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void EnzBase::vEnz ( double  n )

virtual

Reimplemented in Enz, and MMenz.

Definition at line 214 of file EnzBase.cpp.

Referenced by enz().

{;}

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virtual double EnzBase::vGetKcat ( const Eref &  e ) const

pure virtual

Implemented in MMenz, ZombieMMenz, ZombieEnz, and Enz.

Referenced by getKcat().

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virtual double EnzBase::vGetKm ( const Eref &  e ) const

pure virtual

Implemented in ZombieEnz, MMenz, ZombieMMenz, and Enz.

Referenced by getKm().

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virtual double EnzBase::vGetNumKm ( const Eref &  e ) const

pure virtual

Implemented in ZombieEnz, MMenz, ZombieMMenz, and Enz.

Referenced by getNumKm().

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

virtual

Reimplemented in Enz, and MMenz.

Definition at line 217 of file EnzBase.cpp.

Referenced by process().

{;}

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

virtual

Reimplemented in Enz, and MMenz.

Definition at line 220 of file EnzBase.cpp.

Referenced by reinit().

{;}

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void EnzBase::vRemesh ( const Eref &  e )

virtual

Reimplemented in Enz, and MMenz.

Definition at line 223 of file EnzBase.cpp.

Referenced by remesh().

{;}

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

pure virtual

Implemented in MMenz, ZombieMMenz, ZombieEnz, and Enz.

Referenced by setKcat().

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

pure virtual

Implemented in ZombieEnz, MMenz, ZombieMMenz, and Enz.

Referenced by setKm().

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

pure virtual

Implemented in ZombieEnz, MMenz, ZombieMMenz, and Enz.

Referenced by setNumKm().

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void EnzBase::vSub ( double  n )

virtual

Reimplemented in Enz, and MMenz.

Definition at line 211 of file EnzBase.cpp.

Referenced by sub().

{;}

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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.

Definition at line 291 of file EnzBase.cpp.

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

Referenced by Stoich::unZombifyModel(), and Stoich::zombifyModel().

{
    if ( orig->cinfo() == zClass )
        return;
    unsigned int start = orig->localDataStart();
    unsigned int num = orig->numLocalData();
    if ( num == 0 )
            return;
    vector< double > Km( num, 0.0 );
    vector< double > kcat( num, 0.0 );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        const EnzBase* eb =
            reinterpret_cast< const EnzBase* >( er.data() );
        kcat[ i ] = eb->getKcat( er );
        Km[ i ] = eb->getKm( er );
    }
    orig->zombieSwap( zClass );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        EnzBase* eb = reinterpret_cast< EnzBase* >( er.data() );
        eb->setSolver( solver, orig->id() );
        eb->setKcat( er, kcat[i] );
        eb->setKm( er, Km[i] );
    }
}

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

• moose-core/kinetics/EnzBase.h
• moose-core/kinetics/EnzBase.cpp