kinetics/ReadCspace.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
**           copyright (C) 2003-2004 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.
**********************************************************************/

#ifndef _READCSPACE_H
#define _READCSPACE_H

class CspaceMolInfo 
{
    public:
        CspaceMolInfo( char name, double conc )
            : name_( name ), conc_( conc )
        {
            ;
        }
        CspaceMolInfo( )
            : name_( 'a' ), conc_( 0.0 )
        {
            ;
        }

        bool operator<( const CspaceMolInfo& other ) const
        {
            return ( name_ < other.name_ );
        }

        double conc() {
            return conc_;
        }
    private:
        char name_;
        double conc_;
};

class CspaceReacInfo 
{
    public:
        CspaceReacInfo( const string& name, double r1, double r2 )
            : name_( name ), r1_( r1 ), r2_( r2 )
        {
            ;   
        }
        CspaceReacInfo( )
            : name_( "" ), r1_( 0.1 ), r2_( 0.1 )
        {
            ;   
        }

        bool operator<( const CspaceReacInfo& other ) const
        {
            return ( name_ < other.name_ );
        }

        string name() {
            return name_;
        }
        double r1() {
            return r1_;
        }
        double r2() {
            return r2_;
        }
    private:
        string name_;
        double r1_;
        double r2_;
};

class ReadCspace
{
    public:
        ReadCspace();

        void printHeader();
        void printFooter();
        

        void printMol(Id id, double conc, double concinit, double vol);

        void printReac( Id id, double kf, double kb);

        void printEnz( Id id, Id cplx, double k1, double k2, double k3);

        Id readModelString( const string& model,
            const string& modelname, Id pa, const string& solverClass );
        // void setupGslRun( double plotdt );
        void makePlots( double plotdt );

        void build( const char* name );
        void expandEnzyme( 
            const char* name, int e, int s, int p, int p2 = 0);
        void expandReaction( const char* name, int nm1 );

        void deployParameters();
        void testReadModel( );

        void makeMolecule( char name ); 
        
    private:
        static const double SCALE;
        static const double DEFAULT_CONC;
        static const double DEFAULT_RATE;
        static const double DEFAULT_KM;
        static const bool USE_PIPE;

        Id base_; // manager of model tree. A SimManager
        Id compt_; // compartment holding model tree.
        Id mesh_; // mesh entry below compartment
        ostream* fout_;

        // All the molecules, in alphabetical order.
        vector< Id > mol_;
        vector< unsigned int > molseq_;
        // Just a list of reactions and enzymes, in order of occurrence
        vector< Id > reac_;
        // All the model parameters. First are the mol concs, then rates
        vector< double > parms_;
        // Temporary storage for default molecular concs.
        vector< double > molparms_;

        vector< CspaceMolInfo > mollist_;
        vector< CspaceReacInfo > reaclist_;
};

#endif // _READCSPACE_H

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