ZeroOrder Class Reference

#include <RateTerm.h>

Inheritance diagram for ZeroOrder:

Collaboration diagram for ZeroOrder:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
double	getR1 () const
	Used by Zombie to return rate terms. More...
double	getR2 () const
	Used by Zombie to return rate terms. More...
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)
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 ()

Protected Attributes
double	k_

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

Detailed Description

Definition at line 254 of file RateTerm.h.

Constructor & Destructor Documentation

ZeroOrder::ZeroOrder ( double  k )

inline

Definition at line 257 of file RateTerm.h.

References k_.

Referenced by copyWithVolScaling().

            : k_( k )
        {
            assert( !std::isnan( k_ ) );
        }

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Member Function Documentation

RateTerm* ZeroOrder::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.

Reimplemented in StochNOrder, NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, and Flux.

Definition at line 305 of file RateTerm.h.

References k_, and ZeroOrder().

Referenced by BidirectionalReaction::copyWithVolScaling().

        {
            return new ZeroOrder( k_ );
        }

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double ZeroOrder::getR1 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 286 of file RateTerm.h.

References k_.

Referenced by BidirectionalReaction::getR1(), and BidirectionalReaction::getR2().

                             {
            return k_;
        }

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double ZeroOrder::getR2 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 290 of file RateTerm.h.

                             {
            return 0.0;
        }

unsigned int ZeroOrder::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.

Reimplemented in NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, and Flux.

Definition at line 294 of file RateTerm.h.

Referenced by BidirectionalReaction::getReactants(), Stoich::innerInstallReaction(), and Stoich::installEnzyme().

                                                                           {
            molIndex.resize( 0 );
            return 0;
        }

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

inlinevirtual

Computes the rate. The argument is the molecule array.

Implements RateTerm.

Reimplemented in StochNOrder, NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, and Flux.

Definition at line 263 of file RateTerm.h.

References k_.

                                                    {
            assert( !std::isnan( k_ ) );
            return k_;
        }

void ZeroOrder::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.

Reimplemented in NOrder, StochSecondOrderSingleSubstrate, SecondOrder, FirstOrder, and Flux.

Definition at line 299 of file RateTerm.h.

Referenced by BidirectionalReaction::rescaleVolume().

        {
            return; // Nothing needs to be scaled.
        }

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void ZeroOrder::setK ( double  k )

inline

Definition at line 268 of file RateTerm.h.

References k_.

Referenced by setR1(), BidirectionalReaction::setR1(), BidirectionalReaction::setR2(), setRates(), and BidirectionalReaction::setRates().

                              {
            assert( !std::isnan( k ) );
            if ( k >= 0.0 )
                k_ = k;
        }

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void ZeroOrder::setR1 ( double  k1 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 278 of file RateTerm.h.

References setK().

                                {
            setK( k1 );
        }

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void ZeroOrder::setR2 ( double  k2 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 282 of file RateTerm.h.

                                {
            ;
        }

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

inlinevirtual

Assign the rates.

Implements RateTerm.

Definition at line 274 of file RateTerm.h.

References setK().

                                              {
            setK( k1 );
        }

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Member Data Documentation

double ZeroOrder::k_

protected

Definition at line 311 of file RateTerm.h.

Referenced by copyWithVolScaling(), Flux::copyWithVolScaling(), FirstOrder::copyWithVolScaling(), SecondOrder::copyWithVolScaling(), StochSecondOrderSingleSubstrate::copyWithVolScaling(), NOrder::copyWithVolScaling(), StochNOrder::copyWithVolScaling(), getR1(), operator()(), Flux::operator()(), FirstOrder::operator()(), SecondOrder::operator()(), StochSecondOrderSingleSubstrate::operator()(), NOrder::operator()(), StochNOrder::operator()(), SecondOrder::rescaleVolume(), StochSecondOrderSingleSubstrate::rescaleVolume(), NOrder::rescaleVolume(), setK(), and ZeroOrder().

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

• moose-core/ksolve/RateTerm.h