StochNOrder Class Reference

#include <RateTerm.h>

Inheritance diagram for StochNOrder:

Collaboration diagram for StochNOrder:

Public Member Functions
RateTerm *	copyWithVolScaling (double vol, double sub, double prd) const
double	operator() (const double *S) const
	Computes the rate. The argument is the molecule array. More...
	StochNOrder (double k, vector< unsigned int > v)
Public Member Functions inherited from NOrder
unsigned int	getReactants (vector< unsigned int > &molIndex) const
	NOrder (double k, vector< unsigned int > v)
void	rescaleVolume (short comptIndex, const vector< short > &compartmentLookup, double ratio)
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 ()

Additional Inherited Members
Static Public Attributes inherited from RateTerm
static const double	EPSILON = 1.0e-6
Protected Attributes inherited from NOrder
vector< unsigned int >	v_
Protected Attributes inherited from ZeroOrder
double	k_

Detailed Description

This is an unpleasant case, like the StochSecondOrderSingleSubstrate. Here we deal with the possibility that one or more of the substrates may be of order greater than one. If so, we need to diminish the N of each substrate by one for each time the substrate is factored into the rate.

Definition at line 522 of file RateTerm.h.

Constructor & Destructor Documentation

StochNOrder::StochNOrder	(	double	k,
		vector< unsigned int >	v
	)

Definition at line 21 of file RateTerm.cpp.

References NOrder::v_.

Referenced by copyWithVolScaling().

    : NOrder( k, v )
{
    // Here we sort the y vector so that if there are repeated
    // substrates, they are put consecutively. This lets us use
    // the algorithm below to deal with repeats.
    sort( v_.begin(), v_.end() );
}

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Member Function Documentation

RateTerm* StochNOrder::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 NOrder.

Definition at line 529 of file RateTerm.h.

References ZeroOrder::k_, NA, StochNOrder(), and NOrder::v_.

        {
            assert( v_.size() > 0 );
            double ratio = sub * pow( vol * NA, (int)( v_.size() ) -1);
            return new StochNOrder( k_ / ratio, v_ );
        }

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

virtual

Computes the rate. The argument is the molecule array.

Reimplemented from NOrder.

Definition at line 30 of file RateTerm.cpp.

References ZeroOrder::k_, and NOrder::v_.

                                                       {
    double ret = k_;
    vector< unsigned int >::const_iterator i;
    unsigned int lasty = 0;
    double y = 0.0;
    for ( i = v_.begin(); i != v_.end(); i++) {
        assert( !std::isnan( S[ *i ] ) );
        if ( lasty == *i )
            y -= 1.0;
        else
            y = S[ *i ];
        ret *= y;
        lasty = *i;
    }
    return ret;
}

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

• moose-core/ksolve/RateTerm.h
• moose-core/ksolve/RateTerm.cpp