CplxEnzBase Class Reference

#include <CplxEnzBase.h>

Inheritance diagram for CplxEnzBase:

Collaboration diagram for CplxEnzBase:

Public Member Functions
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 void	vCplx (double n)
virtual double	vGetConcK1 (const Eref &e) const =0
virtual double	vGetK1 (const Eref &e) const =0
virtual double	vGetK2 (const Eref &e) const =0
virtual double	vGetRatio (const Eref &e) const =0
virtual void	vSetConcK1 (const Eref &e, double v)=0
virtual void	vSetK1 (const Eref &e, double v)=0
virtual void	vSetK2 (const Eref &e, double v)=0
virtual void	vSetRatio (const Eref &e, double v)=0
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 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)
Static Public Member Functions inherited from EnzBase
static const Cinfo *	initCinfo ()
static void	zombify (Element *original, const Cinfo *zClass, Id solver)

Detailed Description

This class is for mass-action enzymes, in which there is an explict pool for the enzyme-substrate complex. It models the reaction E + S <===> E.S -—> E + P

Definition at line 18 of file CplxEnzBase.h.

Constructor & Destructor Documentation

CplxEnzBase::CplxEnzBase

(

)

Definition at line 175 of file CplxEnzBase.cpp.

{ ; }

CplxEnzBase::~CplxEnzBase ( )

virtual

Definition at line 177 of file CplxEnzBase.cpp.

{ ; }

Member Function Documentation

void CplxEnzBase::cplx

(

double

n

)

Definition at line 184 of file CplxEnzBase.cpp.

References vCplx().

Referenced by initCinfo().

{
    vCplx( n );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double CplxEnzBase::getConcK1

(

const Eref &

e

)

const

Definition at line 238 of file CplxEnzBase.cpp.

References vGetConcK1().

Referenced by initCinfo(), and zombify().

{
    return vGetConcK1( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double CplxEnzBase::getK1

(

const Eref &

e

)

const

Definition at line 201 of file CplxEnzBase.cpp.

References vGetK1().

Referenced by initCinfo().

{
    return vGetK1( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double CplxEnzBase::getK2

(

const Eref &

e

)

const

Definition at line 211 of file CplxEnzBase.cpp.

References vGetK2().

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

{
    return vGetK2( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

double CplxEnzBase::getRatio

(

const Eref &

e

)

const

Definition at line 228 of file CplxEnzBase.cpp.

References vGetRatio().

Referenced by initCinfo().

{
    return vGetRatio( e );
}

Here is the call graph for this function:

Here is the caller graph for this function:

const Cinfo * CplxEnzBase::initCinfo ( )

static

Definition at line 49 of file CplxEnzBase.cpp.

References cplx(), cplxEnzCinfo, cplxOut(), EnzBase::enz(), enzDest(), enzOut(), getConcK1(), getK1(), getK2(), EnzBase::getKcat(), getRatio(), EnzBase::initCinfo(), setConcK1(), setK1(), setK2(), EnzBase::setKcat(), and setRatio().

Referenced by Enz::initCinfo(), and ZombieEnz::initCinfo().

{
        // Field Definitions
        static ElementValueFinfo< CplxEnzBase, double > k1(
            "k1",
            "Forward reaction from enz + sub to complex, in # units."
            "This parameter is subordinate to the Km. This means that"
            "when Km is changed, this changes. It also means that when"
            "k2 or k3 (aka kcat) are changed, we assume that Km remains"
            "fixed, and as a result k1 must change. It is only when"
            "k1 is assigned directly that we assume that the user knows"
            "what they are doing, and we adjust Km accordingly."
            "k1 is also subordinate to the 'ratio' field, since setting "
            "the ratio reassigns k2."
            "Should you wish to assign the elementary rates k1, k2, k3,"
            "of an enzyme directly, always assign k1 last.",
            &CplxEnzBase::setK1,
            &CplxEnzBase::getK1
        );

        static ElementValueFinfo< CplxEnzBase, double > k2(
            "k2",
            "Reverse reaction from complex to enz + sub",
            &CplxEnzBase::setK2,
            &CplxEnzBase::getK2
        );

        static ElementValueFinfo< CplxEnzBase, double > k3(
            "k3",
            "Forward rate constant from complex to product + enz",
            &CplxEnzBase::setKcat,
            &CplxEnzBase::getKcat
        );

        static ElementValueFinfo< CplxEnzBase, double > ratio(
            "ratio",
            "Ratio of k2/k3",
            &CplxEnzBase::setRatio,
            &CplxEnzBase::getRatio
        );

        static ElementValueFinfo< CplxEnzBase, double > concK1(
            "concK1",
            "K1 expressed in concentration (1/millimolar.sec) units"
            "This parameter is subordinate to the Km. This means that"
            "when Km is changed, this changes. It also means that when"
            "k2 or k3 (aka kcat) are changed, we assume that Km remains"
            "fixed, and as a result concK1 must change. It is only when"
            "concK1 is assigned directly that we assume that the user knows"
            "what they are doing, and we adjust Km accordingly."
            "concK1 is also subordinate to the 'ratio' field, since"
            "setting the ratio reassigns k2."
            "Should you wish to assign the elementary rates concK1, k2, k3,"
            "of an enzyme directly, always assign concK1 last.",
            &CplxEnzBase::setConcK1,
            &CplxEnzBase::getConcK1
        );

        // MsgDest Definitions: most are inherited from EnzBase.
        static DestFinfo cplxDest( "cplxDest",
                "Handles # of molecules of enz-sub complex",
                new OpFunc1< CplxEnzBase, double >( &CplxEnzBase::cplx ) );

        // Shared Msg Definitions
        static Finfo* enzShared[] = {
            enzOut(), enzDest()
        };
        static Finfo* cplxShared[] = {
            cplxOut(), &cplxDest
        };

        static SharedFinfo enz( "enz",
            "Connects to enzyme pool",
            enzShared, sizeof( enzShared ) / sizeof( const Finfo* )
        );
        static SharedFinfo cplx( "cplx",
            "Connects to enz-sub complex pool",
            cplxShared, sizeof( cplxShared ) / sizeof( const Finfo* )
        );

    static Finfo* cplxEnzFinfos[] = {
        &k1,    // Value
        &k2,    // Value
        &k3,    // Value
        &ratio, // Value
        &concK1,    // Value
        &enz,               // SharedFinfo
        &cplx,              // SharedFinfo
    };

    static string doc[] =
    {
            "Name", "CplxEnzBase",
            "Author", "Upi Bhalla",
            "Description:",
            "Base class for mass-action enzymes in which there is an "
            " explicit pool for the enzyme-substrate complex. "
            "It models the reaction: "
            "E + S <===> E.S ----> E + P"
    };

    static ZeroSizeDinfo< int > dinfo;
    static Cinfo cplxEnzCinfo (
        "CplxEnzBase",
        EnzBase::initCinfo(),
        cplxEnzFinfos,
        sizeof( cplxEnzFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof( doc )/sizeof( string )
    );

    return &cplxEnzCinfo;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CplxEnzBase::setConcK1	(	const Eref &	e,
		double	v
	)

Definition at line 233 of file CplxEnzBase.cpp.

References vSetConcK1().

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

{
    vSetConcK1( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CplxEnzBase::setK1	(	const Eref &	e,
		double	v
	)

Definition at line 196 of file CplxEnzBase.cpp.

References vSetK1().

Referenced by initCinfo().

{
    vSetK1( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CplxEnzBase::setK2	(	const Eref &	e,
		double	v
	)

Definition at line 206 of file CplxEnzBase.cpp.

References vSetK2().

Referenced by initCinfo(), and zombify().

{
    vSetK2( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CplxEnzBase::setRatio	(	const Eref &	e,
		double	v
	)

Definition at line 223 of file CplxEnzBase.cpp.

References vSetRatio().

Referenced by initCinfo().

{
    vSetRatio( e, v );
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CplxEnzBase::vCplx ( double  n )

virtual

Reimplemented in Enz.

Definition at line 189 of file CplxEnzBase.cpp.

Referenced by cplx().

{;}

Here is the caller graph for this function:

virtual double CplxEnzBase::vGetConcK1 ( const Eref &  e ) const

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by getConcK1().

Here is the caller graph for this function:

virtual double CplxEnzBase::vGetK1 ( const Eref &  e ) const

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by getK1().

Here is the caller graph for this function:

virtual double CplxEnzBase::vGetK2 ( const Eref &  e ) const

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by getK2().

Here is the caller graph for this function:

virtual double CplxEnzBase::vGetRatio ( const Eref &  e ) const

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by getRatio().

Here is the caller graph for this function:

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

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by setConcK1().

Here is the caller graph for this function:

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

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by setK1().

Here is the caller graph for this function:

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

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by setK2().

Here is the caller graph for this function:

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

pure virtual

Implemented in Enz, and ZombieEnz.

Referenced by setRatio().

Here is the caller graph for this function:

void CplxEnzBase::zombify ( Element *  orig, const Cinfo *  zClass, Id  solver  )

static

This function helps the conversion between CplxEnz subclasses, these are the ones that have an explicit enzyme-substrate complex molecule. Note that I use the ConcK1 terms because those are independent of the volume decomposition. K2 and kcat (ie., k3) only have time units.

Definition at line 254 of file CplxEnzBase.cpp.

References Element::cinfo(), Eref::data(), getConcK1(), getK2(), EnzBase::getKcat(), Element::id(), Element::localDataStart(), Element::numLocalData(), setConcK1(), setK2(), EnzBase::setKcat(), EnzBase::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 > concK1( num, 0.0 );
    vector< double > k2( num, 0.0 );
    vector< double > kcat( num, 0.0 );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        const CplxEnzBase* ceb =
            reinterpret_cast< const CplxEnzBase* >( er.data() );
        concK1[ i ] = ceb->getConcK1( er );
        k2[ i ] = ceb->getK2( er );
        kcat[ i ] = ceb->getKcat( er );
    }
    orig->zombieSwap( zClass );
    for ( unsigned int i = 0; i < num; ++i ) {
        Eref er( orig, i + start );
        CplxEnzBase* ceb = reinterpret_cast< CplxEnzBase* >( er.data() );
        ceb->setSolver( solver, orig->id() );
        ceb->setKcat( er, kcat[i] );
        ceb->setK2( er, k2[i] );
        ceb->setConcK1( er, concK1[i] );
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

---

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

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