FuncRate Class Reference

#include <FuncRateTerm.h>

Inheritance diagram for FuncRate:

Collaboration diagram for FuncRate:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
	FuncRate (double k, unsigned int targetPoolIndex)
const string &	getExpr () const
const vector< unsigned int > &	getFuncArgIndex ()
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	setExpr (const string &s)
void	setFuncArgIndex (const vector< unsigned int > &mol)
void	setReactants (const vector< unsigned int > &molIndex)
Public Member Functions inherited from ExternReac
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 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)
Public Member Functions inherited from RateTerm
	RateTerm ()
virtual	~RateTerm ()

Protected Attributes
FuncTerm	func_
double	funcVolPower_
double	k_

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

Detailed Description

This FuncRate manages a one-way reaction whose rate is determined by a Function. It has no substrates, just controls the rate of change of a target molecule.

dtarget/dt = func( x0, x1, x2..., t )

The values x0, x1, x2.. are numbers at this point. So is the rate output of this function. There may be a problem if there is a volume change.

Definition at line 22 of file FuncRateTerm.h.

Constructor & Destructor Documentation

FuncRate::FuncRate ( double  k, unsigned int  targetPoolIndex  )

inline

Definition at line 25 of file FuncRateTerm.h.

References func_, and FuncTerm::setTarget().

Referenced by copyWithVolScaling().

            : k_( k ), funcVolPower_( 0.0 )
        {
            func_.setTarget( targetPoolIndex );
        }

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Member Function Documentation

RateTerm* FuncRate::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 FuncReac.

Definition at line 66 of file FuncRateTerm.h.

References func_, FuncRate(), funcVolPower_, FuncTerm::getTarget(), k_, and NA.

        {
            double ratio = sub * pow( NA * vol, funcVolPower_ );
            FuncRate* ret = new FuncRate( k_ / ratio, func_.getTarget() );
            ret->funcVolPower_ = funcVolPower_;
            ret->func_ = func_;
            // return new FuncRate( k_ / ratio );
            return ret;
        }

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const string& FuncRate::getExpr ( ) const

inline

Definition at line 62 of file FuncRateTerm.h.

References func_, and FuncTerm::getExpr().

                                      {
            return func_.getExpr();
        }

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const vector< unsigned int >& FuncRate::getFuncArgIndex ( )

inline

Definition at line 50 of file FuncRateTerm.h.

References func_, and FuncTerm::getReactantIndex().

        {
            return func_.getReactantIndex();
        }

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unsigned int FuncRate::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 FuncReac.

Definition at line 36 of file FuncRateTerm.h.

References func_, and FuncTerm::getTarget().

                                                                           {
            molIndex.resize( 1 );
            molIndex[0] = func_.getTarget();

            // This is the number of substrates to the reac. It is zero.
            return 0;
            // The target molecule is handled as a product.
        }

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

inlinevirtual

Computes the rate. The argument is the molecule array.

Implements RateTerm.

Reimplemented in FuncReac.

Definition at line 31 of file FuncRateTerm.h.

References func_, and Field< A >::get().

                                                    {
            double t = Field< double >::get( Id(1), "currentTime" );
            return func_( S, t ); // get rate from func calculation.
        }

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void FuncRate::setExpr ( const string &  s )

inline

Definition at line 59 of file FuncRateTerm.h.

References func_, and FuncTerm::setExpr().

Referenced by Stoich::installAndUnschedFuncRate(), Stoich::installAndUnschedFuncReac(), and Stoich::setFunctionExpr().

                                        {
            func_.setExpr( s );
        }

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void FuncRate::setFuncArgIndex ( const vector< unsigned int > &  mol )

inline

Definition at line 55 of file FuncRateTerm.h.

References func_, and FuncTerm::setReactantIndex().

Referenced by Stoich::installAndUnschedFuncRate(), and Stoich::installAndUnschedFuncReac().

                                                                  {
            func_.setReactantIndex( mol );
        }

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void FuncRate::setReactants ( const vector< unsigned int > &  molIndex )

inline

Definition at line 45 of file FuncRateTerm.h.

References func_, and FuncTerm::setTarget().

                                                                    {
            assert( molIndex.size() > 0 );
            func_.setTarget( molIndex[0] );
        }

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Member Data Documentation

FuncTerm FuncRate::func_

protected

Definition at line 78 of file FuncRateTerm.h.

Referenced by copyWithVolScaling(), FuncReac::copyWithVolScaling(), FuncRate(), getExpr(), getFuncArgIndex(), getReactants(), operator()(), FuncReac::operator()(), setExpr(), setFuncArgIndex(), and setReactants().

double FuncRate::funcVolPower_

protected

Definition at line 80 of file FuncRateTerm.h.

Referenced by copyWithVolScaling(), and FuncReac::copyWithVolScaling().

double FuncRate::k_

protected

Definition at line 79 of file FuncRateTerm.h.

Referenced by copyWithVolScaling(), FuncReac::copyWithVolScaling(), and FuncReac::rescaleVolume().

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

• moose-core/ksolve/FuncRateTerm.h