BidirectionalReaction Class Reference

#include <RateTerm.h>

Inheritance diagram for BidirectionalReaction:

Collaboration diagram for BidirectionalReaction:

Public Member Functions
	BidirectionalReaction (ZeroOrder *forward, ZeroOrder *backward)
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	setR1 (double kf)
	Used by Zombie to assign rate terms. More...
void	setR2 (double kb)
	Used by Zombie to assign rate terms. More...
void	setRates (double kf, double kb)
	~BidirectionalReaction ()
Public Member Functions inherited from RateTerm
	RateTerm ()
virtual	~RateTerm ()

Private Attributes
ZeroOrder *	backward_
ZeroOrder *	forward_

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

Detailed Description

Definition at line 541 of file RateTerm.h.

Constructor & Destructor Documentation

BidirectionalReaction::BidirectionalReaction ( ZeroOrder *  forward, ZeroOrder *  backward  )

inline

Definition at line 544 of file RateTerm.h.

Referenced by copyWithVolScaling().

            : forward_( forward ), backward_( backward )
        { // Here we allocate internal forward and backward terms
        // with the correct number of args.
        ;
        }

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BidirectionalReaction::~BidirectionalReaction ( )

inline

Definition at line 551 of file RateTerm.h.

References backward_, and forward_.

        {
            delete forward_;
            delete backward_;
        }

Member Function Documentation

RateTerm* BidirectionalReaction::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 597 of file RateTerm.h.

References backward_, BidirectionalReaction(), ZeroOrder::copyWithVolScaling(), and forward_.

        {
            ZeroOrder* f = static_cast< ZeroOrder* >(
                            forward_->copyWithVolScaling( vol, sub, 1 ) );
            ZeroOrder* b = static_cast< ZeroOrder* >(
                            backward_->copyWithVolScaling( vol, prd, 1 ) );
            return new BidirectionalReaction( f, b );
        }

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double BidirectionalReaction::getR1 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 574 of file RateTerm.h.

References forward_, and ZeroOrder::getR1().

                             {
            return forward_->getR1();
        }

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double BidirectionalReaction::getR2 ( ) const

inlinevirtual

Used by Zombie to return rate terms.

Implements RateTerm.

Definition at line 578 of file RateTerm.h.

References backward_, and ZeroOrder::getR1().

                             {
            return backward_->getR1();
        }

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unsigned int BidirectionalReaction::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 582 of file RateTerm.h.

References backward_, forward_, and ZeroOrder::getReactants().

                                                                           {
            forward_->getReactants( molIndex );
            unsigned int ret = molIndex.size();
            vector< unsigned int > temp;
            backward_->getReactants( temp );
            molIndex.insert( molIndex.end(), temp.begin(), temp.end() );
            return ret;
        }

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

inlinevirtual

Computes the rate. The argument is the molecule array.

Implements RateTerm.

Definition at line 557 of file RateTerm.h.

References backward_, and forward_.

                                                    {
            return (*forward_)( S ) - (*backward_)( S );
        }

void BidirectionalReaction::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 591 of file RateTerm.h.

References backward_, forward_, and ZeroOrder::rescaleVolume().

        {
            forward_->rescaleVolume( comptIndex, compartmentLookup, ratio );
            backward_->rescaleVolume( comptIndex, compartmentLookup, ratio);
        }

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void BidirectionalReaction::setR1 ( double  k1 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 566 of file RateTerm.h.

References forward_, and ZeroOrder::setK().

                                {
            forward_->setK( kf );
        }

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void BidirectionalReaction::setR2 ( double  k2 )

inlinevirtual

Used by Zombie to assign rate terms.

Implements RateTerm.

Definition at line 570 of file RateTerm.h.

References backward_, and ZeroOrder::setK().

                                {
            backward_->setK( kb );
        }

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

inlinevirtual

Assign the rates.

Implements RateTerm.

Definition at line 561 of file RateTerm.h.

References backward_, forward_, and ZeroOrder::setK().

                                              {
            forward_->setK( kf );
            backward_->setK( kb );
        }

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Member Data Documentation

ZeroOrder* BidirectionalReaction::backward_

private

Definition at line 609 of file RateTerm.h.

Referenced by copyWithVolScaling(), getR2(), getReactants(), operator()(), rescaleVolume(), setR2(), setRates(), and ~BidirectionalReaction().

ZeroOrder* BidirectionalReaction::forward_

private

Definition at line 608 of file RateTerm.h.

Referenced by copyWithVolScaling(), getR1(), getReactants(), operator()(), rescaleVolume(), setR1(), setRates(), and ~BidirectionalReaction().

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

• moose-core/ksolve/RateTerm.h