MMEnzymeBase Class Reference

#include <RateTerm.h>

Inheritance diagram for MMEnzymeBase:

Collaboration diagram for MMEnzymeBase:

Public Member Functions
unsigned int	getEnzIndex () const
double	getR1 () const
	Used by Zombie to return rate terms. More...
double	getR2 () const
	Used by Zombie to return rate terms. More...
	MMEnzymeBase (double Km, double kcat, unsigned int enz)
void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)
void	setKcat (double kcat)
void	setKm (double Km)
void	setR1 (double Km)
	Used by Zombie to assign rate terms. More...
void	setR2 (double kcat)
	Used by Zombie to assign rate terms. More...
void	setRates (double Km, double kcat)
Public Member Functions inherited from RateTerm
virtual RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const =0
virtual unsigned int	getReactants (vector< unsigned int > &molIndex) const =0
virtual double	operator() (const double *S) const =0
	Computes the rate. The argument is the molecule array. More...
	RateTerm ()
virtual	~RateTerm ()

Protected Attributes
unsigned int	enz_
double	kcat_
double	Km_

Additional Inherited Members
Static Public Attributes inherited from RateTerm
static const double	EPSILON = 1.0e-6

Detailed Description

Definition at line 81 of file RateTerm.h.

Constructor & Destructor Documentation

MMEnzymeBase::MMEnzymeBase ( double  Km, double  kcat, unsigned int  enz  )

inline

Definition at line 84 of file RateTerm.h.

References Km_.

            : Km_( Km ), kcat_( kcat ), enz_( enz )
        {
            assert( Km_ > 0.0 );
        }

Member Function Documentation

unsigned int MMEnzymeBase::getEnzIndex ( ) const

inline

Definition at line 127 of file RateTerm.h.

References enz_.

        {
            return enz_;
        }

double MMEnzymeBase::getR1 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 113 of file RateTerm.h.

References Km_.

                             {
            return Km_;
        }

double MMEnzymeBase::getR2 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 117 of file RateTerm.h.

References kcat_.

                             {
            return kcat_;
        }

void MMEnzymeBase::rescaleVolume ( short  comptIndex, const vector< short > &  compartmentLookup, double  ratio  )

inlinevirtual

This is used to rescale the RateTerm kinetics when the compartment volume changes. This is needed because the kinetics are in extensive units, that is, mol numbers, rather than in intensive units like concentration. So when the volume changes the rate terms change. Each Rate term checks if any of its reactant molecules are affected, and if so, rescales. Ratio is newVol / oldVol

Implements RateTerm.

Definition at line 121 of file RateTerm.h.

References Km_.

        {
            Km_ *= ratio;
        }

void MMEnzymeBase::setKcat ( double  kcat )

inline

Definition at line 95 of file RateTerm.h.

References kcat_.

Referenced by setR2(), and setRates().

                                    {
            if ( kcat > 0 )
                kcat_ = kcat;
        }

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void MMEnzymeBase::setKm ( double  Km )

inline

Definition at line 90 of file RateTerm.h.

References Km_.

Referenced by setR1(), and setRates().

                                {
            if ( Km > 0.0 )
                Km_ = Km;
        }

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void MMEnzymeBase::setR1 ( double  k1 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 105 of file RateTerm.h.

References setKm().

                                {
            setKm( Km );
        }

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void MMEnzymeBase::setR2 ( double  k2 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 109 of file RateTerm.h.

References setKcat().

                                  {
            setKcat( kcat );
        }

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void MMEnzymeBase::setRates ( double  k1, double  k2  )

inlinevirtual

Assign the rates.

Implements RateTerm.

Definition at line 100 of file RateTerm.h.

References setKcat(), and setKm().

                                                {
            setKm( Km );
            setKcat( kcat );
        }

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Member Data Documentation

unsigned int MMEnzymeBase::enz_

protected

Definition at line 135 of file RateTerm.h.

Referenced by MMEnzyme1::copyWithVolScaling(), MMEnzyme::copyWithVolScaling(), getEnzIndex(), MMEnzyme1::getReactants(), MMEnzyme::getReactants(), MMEnzyme1::operator()(), and MMEnzyme::operator()().

double MMEnzymeBase::kcat_

protected

Definition at line 134 of file RateTerm.h.

Referenced by MMEnzyme1::copyWithVolScaling(), MMEnzyme::copyWithVolScaling(), getR2(), MMEnzyme1::operator()(), MMEnzyme::operator()(), and setKcat().

double MMEnzymeBase::Km_

protected

Definition at line 133 of file RateTerm.h.

Referenced by MMEnzyme1::copyWithVolScaling(), MMEnzyme::copyWithVolScaling(), getR1(), MMEnzymeBase(), MMEnzyme1::operator()(), MMEnzyme::operator()(), rescaleVolume(), and setKm().

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

• moose-core/ksolve/RateTerm.h