RateTerm.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
** also known as GENESIS 3 base code.
**           copyright (C) 2003-2010 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/

/*
double assignRates( RateCalculation& r )
{
    return r();
}
*/
#include "../utility/numutil.h"
class RateTerm
{
    public:
        RateTerm() {;}
        virtual ~RateTerm() {;}
        virtual double operator() ( const double* S ) const = 0;

        virtual void setRates( double k1, double k2 ) = 0;

        virtual void setR1( double k1 ) = 0;

        virtual void setR2( double k2 ) = 0;

        virtual double getR1() const = 0;

        virtual double getR2() const = 0;

        virtual unsigned int  getReactants(
            vector< unsigned int >& molIndex ) const = 0;
        static const double EPSILON;

        virtual void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio ) = 0;

        virtual RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const = 0;
};

// Base class MMEnzme for the purposes of setting rates
// Pure base class: cannot be instantiated, but useful as a handle.
class MMEnzymeBase: public RateTerm
{
    public:
        MMEnzymeBase( double Km, double kcat, unsigned int enz )
            : Km_( Km ), kcat_( kcat ), enz_( enz )
        {
            assert( Km_ > 0.0 );
        }

        void setKm( double Km ) {
            if ( Km > 0.0 )
                Km_ = Km;
        }

        void setKcat( double kcat ) {
            if ( kcat > 0 )
                kcat_ = kcat;
        }

        void setRates( double Km, double kcat ) {
            setKm( Km );
            setKcat( kcat );
        }

        void setR1( double Km ) {
            setKm( Km );
        }

        void setR2( double kcat ) {
            setKcat( kcat );
        }

        double getR1() const {
            return Km_;
        }

        double getR2() const {
            return kcat_;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            Km_ *= ratio;
        }

        unsigned int getEnzIndex() const
        {
            return enz_;
        }

    protected:
        double Km_; // In # units, not conc units.
        double kcat_;
        unsigned int enz_;
};

// Single substrate MMEnzyme: by far the most common.
class MMEnzyme1: public MMEnzymeBase
{
    public:
        MMEnzyme1( double Km, double kcat,
            unsigned int enz, unsigned int sub )
            : MMEnzymeBase( Km, kcat, enz ), sub_( sub )
        {
            ;
        }

        double operator() ( const double* S ) const {
        //  assert( S[ sub_ ] >= -EPSILON );
            return ( kcat_ * S[ sub_ ] * S[ enz_ ] ) / ( Km_ + S[ sub_ ] );
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 2 );
            molIndex[0] = enz_;
            molIndex[1] = sub_;
            return 2;
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            double ratio = vol * sub * NA;
            return new MMEnzyme1( ratio * Km_, kcat_, enz_, sub_);
        }

    private:
        unsigned int sub_;
};

class MMEnzyme: public MMEnzymeBase
{
    public:
        MMEnzyme( double Km, double kcat,
            unsigned int enz, RateTerm* sub )
            : MMEnzymeBase( Km, kcat, enz ), substrates_( sub )
        {
            ;
        }

        double operator() ( const double* S ) const {
            double sub = (*substrates_)( S );
            // the subtrates_() operator returns the conc product.
            assert( sub >= -EPSILON );
            return ( sub * kcat_ * S[ enz_ ] ) / ( Km_ + sub );
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            substrates_->getReactants( molIndex );
            molIndex.insert( molIndex.begin(), enz_ );
            return molIndex.size();
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            double ratio = sub * vol * NA;
            return new MMEnzyme( ratio * Km_, kcat_, enz_, substrates_ );
        }
    private:
        RateTerm* substrates_;
};

class ExternReac: public RateTerm
{
    public:
        // All the terms will have been updated separately, and
        // a reply obtained to this pointer here:
        double operator() ( const double* S ) const {
            double ret = 0.0;
            return ret;
        }
        void setRates( double k1, double k2 ) {
            ; // Dummy function to keep compiler happy
        }

        void setR1( double k1 ) {
            ;
        }

        void setR2( double k2 ) {
            ;
        }

        double getR1() const {
            return 0.0;
        }

        double getR2() const {
            return 0.0;
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 0 );
            return 0;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            return; // Need to figure out what to do here.
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            return new ExternReac();
        }

    private:
};

class ZeroOrder: public RateTerm
{
    public:
        ZeroOrder( double k )
            : k_( k )
        {
            assert( !std::isnan( k_ ) );
        }

        double operator() ( const double* S ) const {
            assert( !std::isnan( k_ ) );
            return k_;
        }

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

        void setRates( double k1, double k2 ) {
            setK( k1 );
        }

        void setR1( double k1 ) {
            setK( k1 );
        }

        void setR2( double k2 ) {
            ;
        }

        double getR1() const {
            return k_;
        }

        double getR2() const {
            return 0.0;
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 0 );
            return 0;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            return; // Nothing needs to be scaled.
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            return new ZeroOrder( k_ );
        }
    protected:
        double k_;
};

class Flux: public ZeroOrder
{
    public:
        Flux( double k, unsigned int y )
            : ZeroOrder( k ), y_( y )
        {;}

        double operator() ( const double* S ) const {
            assert( !std::isnan( S[ y_ ] ) );
            return k_ * S[ y_ ];
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 0 );
            return 0;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            return; // Nothing needs to be scaled.
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            return new Flux( k_, y_ );
        }

    private:
        unsigned int y_;
};

class FirstOrder: public ZeroOrder
{
    public:
        FirstOrder( double k, unsigned int y )
            : ZeroOrder( k ), y_( y )
        {;}

        double operator() ( const double* S ) const {
            assert( !std::isnan( S[ y_ ] ) );
            return k_ * S[ y_ ];
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 1 );
            molIndex[0] = y_;
            return 1;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            return; // Nothing needs to be scaled.
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            return new FirstOrder( k_ / sub, y_ );
        }

    private:
        unsigned int y_;
};

class SecondOrder: public ZeroOrder
{
    public:
        SecondOrder( double k, unsigned int y1, unsigned int y2 )
            : ZeroOrder( k ), y1_( y1 ), y2_( y2 )
        {;}

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

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 2 );
            molIndex[0] = y1_;
            molIndex[1] = y2_;
            return 2;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            if ( comptIndex == compartmentLookup[ y1_ ] ||
                comptIndex == compartmentLookup[ y2_ ] )
            k_ /= ratio;
        }

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

    private:
        unsigned int y1_;
        unsigned int y2_;
};

class StochSecondOrderSingleSubstrate: public ZeroOrder
{
    public:
        StochSecondOrderSingleSubstrate( double k, unsigned int y )
            : ZeroOrder( k ), y_( y )
        {;}

        double operator() ( const double* S ) const {
            double y = S[ y_ ];
            assert( !std::isnan( y ) );
            return k_ * ( y - 1 ) * y;
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex.resize( 2 );
            molIndex[0] = y_;
            molIndex[1] = y_;
            return 2;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            if ( comptIndex == compartmentLookup[ y_ ] )
                k_ /= ratio;
        }

        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            double ratio = sub * vol * NA;
            return new StochSecondOrderSingleSubstrate( k_ / ratio, y_ );
        }

    private:
        const unsigned int y_;
};

class NOrder: public ZeroOrder
{
    public:
        NOrder( double k, vector< unsigned int > v )
            : ZeroOrder( k ), v_( v )
        {;}

        double operator() ( const double* S ) const {
            double ret = k_;
            vector< unsigned int >::const_iterator i;
            for ( i = v_.begin(); i != v_.end(); i++) {
                assert( !std::isnan( S[ *i ] ) );
                ret *= S[ *i ];
            }
            return ret;
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            molIndex = v_;
            return v_.size();
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            for ( unsigned int i = 1; i < v_.size(); ++i ) {
                if ( comptIndex == compartmentLookup[ v_[i] ] )
                    k_ /= ratio;
            }
        }

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

    protected:
        vector< unsigned int > v_;
};

class StochNOrder: public NOrder
{
    public:
        StochNOrder( double k, vector< unsigned int > v );

        double operator() ( const double* S ) const;

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

extern class ZeroOrder*
    makeHalfReaction( double k, vector< unsigned int > v );

class BidirectionalReaction: public RateTerm
{
    public:
        BidirectionalReaction(
            ZeroOrder* forward, ZeroOrder* backward)
            : forward_( forward ), backward_( backward )
        { // Here we allocate internal forward and backward terms
        // with the correct number of args.
        ;
        }
        ~BidirectionalReaction()
        {
            delete forward_;
            delete backward_;
        }

        double operator() ( const double* S ) const {
            return (*forward_)( S ) - (*backward_)( S );
        }

        void setRates( double kf, double kb ) {
            forward_->setK( kf );
            backward_->setK( kb );
        }

        void setR1( double kf ) {
            forward_->setK( kf );
        }

        void setR2( double kb ) {
            backward_->setK( kb );
        }

        double getR1() const {
            return forward_->getR1();
        }

        double getR2() const {
            return backward_->getR1();
        }

        unsigned int getReactants( vector< unsigned int >& molIndex ) const{
            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;
        }

        void rescaleVolume( short comptIndex,
            const vector< short >& compartmentLookup, double ratio )
        {
            forward_->rescaleVolume( comptIndex, compartmentLookup, ratio );
            backward_->rescaleVolume( comptIndex, compartmentLookup, ratio);
        }
        RateTerm* copyWithVolScaling(
                double vol, double sub, double prd ) const
        {
            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 );
        }

    private:
        ZeroOrder* forward_;
        ZeroOrder* backward_;
};