SecondOrder Class Reference

#include <RateTerm.h>

Inheritance diagram for SecondOrder:

Collaboration diagram for SecondOrder:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
unsigned int	getReactants (vector< unsigned int > &molIndex) const
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array. More...
void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)
	SecondOrder (double k, unsigned int y1, unsigned int y2)
Public Member Functions inherited from ZeroOrder
double	getR1 () const
	Used by Zombie to return rate terms. More...
double	getR2 () const
	Used by Zombie to return rate terms. More...
void	setK (double k)
void	setR1 (double k1)
	Used by Zombie to assign rate terms. More...
void	setR2 (double k2)
	Used by Zombie to assign rate terms. More...
void	setRates (double k1, double k2)
	ZeroOrder (double k)
Public Member Functions inherited from RateTerm
	RateTerm ()
virtual	~RateTerm ()

Private Attributes
unsigned int	y1_
unsigned int	y2_

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

Detailed Description

Definition at line 387 of file RateTerm.h.

Constructor & Destructor Documentation

SecondOrder::SecondOrder ( double  k, unsigned int  y1, unsigned int  y2  )

inline

Definition at line 390 of file RateTerm.h.

Referenced by copyWithVolScaling().

            : ZeroOrder( k ), y1_( y1 ), y2_( y2 )
        {;}

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Member Function Documentation

RateTerm* SecondOrder::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.

Reimplemented from ZeroOrder.

Definition at line 415 of file RateTerm.h.

References ZeroOrder::k_, NA, SecondOrder(), y1_, and y2_.

        {
            double ratio = sub * vol * NA;
            return new SecondOrder( k_ / ratio, y1_, y2_ );
        }

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unsigned int SecondOrder::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.

Reimplemented from ZeroOrder.

Definition at line 400 of file RateTerm.h.

References y1_, and y2_.

                                                                           {
            molIndex.resize( 2 );
            molIndex[0] = y1_;
            molIndex[1] = y2_;
            return 2;
        }

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

inlinevirtual

Computes the rate. The argument is the molecule array.

Reimplemented from ZeroOrder.

Definition at line 394 of file RateTerm.h.

References ZeroOrder::k_, y1_, and y2_.

                                                    {
            assert( !std::isnan( S[ y1_ ] ) );
            assert( !std::isnan( S[ y2_ ] ) );
            return k_ * S[ y1_ ] * S[ y2_ ];
        }

void SecondOrder::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

Reimplemented from ZeroOrder.

Definition at line 407 of file RateTerm.h.

References ZeroOrder::k_, y1_, and y2_.

        {
            if ( comptIndex == compartmentLookup[ y1_ ] ||
                comptIndex == compartmentLookup[ y2_ ] )
            k_ /= ratio;
        }

Member Data Documentation

unsigned int SecondOrder::y1_

private

Definition at line 423 of file RateTerm.h.

Referenced by copyWithVolScaling(), getReactants(), operator()(), and rescaleVolume().

unsigned int SecondOrder::y2_

private

Definition at line 424 of file RateTerm.h.

Referenced by copyWithVolScaling(), getReactants(), operator()(), and rescaleVolume().

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

• moose-core/ksolve/RateTerm.h