MMEnzyme Class Reference

#include <RateTerm.h>

Inheritance diagram for MMEnzyme:

Collaboration diagram for MMEnzyme:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
unsigned int	getReactants (vector< unsigned int > &molIndex) const
	MMEnzyme (double Km, double kcat, unsigned int enz, RateTerm *sub)
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array. More...
Public Member Functions inherited from MMEnzymeBase
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
	RateTerm ()
virtual	~RateTerm ()

Private Attributes
RateTerm *	substrates_

Additional Inherited Members
Static Public Attributes inherited from RateTerm
static const double	EPSILON = 1.0e-6
Protected Attributes inherited from MMEnzymeBase
unsigned int	enz_
double	kcat_
double	Km_

Detailed Description

Definition at line 172 of file RateTerm.h.

Constructor & Destructor Documentation

MMEnzyme::MMEnzyme ( double  Km, double  kcat, unsigned int  enz, RateTerm *  sub  )

inline

Definition at line 175 of file RateTerm.h.

Referenced by copyWithVolScaling().

            : MMEnzymeBase( Km, kcat, enz ), substrates_( sub )
        {
            ;
        }

Here is the caller graph for this function:

Member Function Documentation

RateTerm* MMEnzyme::copyWithVolScaling ( double  vol, double  sub, double  prd  ) const

inlinevirtual

Duplicates rate term and then applies volume scaling. Arguments are volume of reference voxel, product of vol/refVol for all substrates: applied to R1 product of vol/refVol for all products: applied to R2

Note that unless the reaction is cross-compartment, the vol/refVol will be one.

Implements RateTerm.

Definition at line 195 of file RateTerm.h.

References MMEnzymeBase::enz_, MMEnzymeBase::kcat_, MMEnzymeBase::Km_, MMEnzyme(), NA, and substrates_.

        {
            double ratio = sub * vol * NA;
            return new MMEnzyme( ratio * Km_, kcat_, enz_, substrates_ );
        }

Here is the call graph for this function:

unsigned int MMEnzyme::getReactants ( vector< unsigned int > &  molIndex ) const

inlinevirtual

This function finds the reactant indices in the vector S. It returns the number of substrates found, which are the first entries in molIndex. The products are the remaining ones. Note that it does NOT find products for unidirectional reactions, which is a bit of a problem.

Implements RateTerm.

Definition at line 189 of file RateTerm.h.

References MMEnzymeBase::enz_, RateTerm::getReactants(), and substrates_.

                                                                           {
            substrates_->getReactants( molIndex );
            molIndex.insert( molIndex.begin(), enz_ );
            return molIndex.size();
        }

Here is the call graph for this function:

double MMEnzyme::operator() ( const double *  S ) const

inlinevirtual

Computes the rate. The argument is the molecule array.

Implements RateTerm.

Definition at line 182 of file RateTerm.h.

References MMEnzymeBase::enz_, RateTerm::EPSILON, MMEnzymeBase::kcat_, and MMEnzymeBase::Km_.

                                                    {
            double sub = (*substrates_)( S );
            // the subtrates_() operator returns the conc product.
            assert( sub >= -EPSILON );
            return ( sub * kcat_ * S[ enz_ ] ) / ( Km_ + sub );
        }

Member Data Documentation

RateTerm* MMEnzyme::substrates_

private

Definition at line 202 of file RateTerm.h.

Referenced by copyWithVolScaling(), and getReactants().

---

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

• moose-core/ksolve/RateTerm.h