Reaction.hh

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#ifndef GGL_CHEM_REACTION_HH_
#define GGL_CHEM_REACTION_HH_


#include <string>
#include <set>
#include <ostream>

namespace ggl {
 namespace chem {

      /*! @brief Reaction description
       *
       * A data container describing information of a chemical reaction.
       * 
       * @author Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/
       * @author Alexander Ullrich
       * 
       */
    class Reaction  {
        
    public:
        
          //! container that stores all metabolites/educts of the reaction
        typedef std::multiset< std::string > Metabolite_Container;

          //! container that stores all products of the reaction
        typedef std::multiset< std::string > Product_Container;
        
    public:

          /*! the identifier of the ggl::chem::ChemRule rule that was applied
           * in this reaction.
           */
        std::string rule_id;
        
          //! the SMILES of the molecules involved in this reaction
        Metabolite_Container metabolites;
        
          //! the SMILES of the produced molecules of this reaction
        Product_Container products;
        
          //! the rate of the reaction
        double rate;
        
          //! The SMILES of the transition state along the reaction. It is used
          //! to calculate appropriate reaction rates.
        std::string transState;
        
    public:
        
          //! Default construction with empty content
        Reaction();
        
          /*! Construction
           * @param rule_id the identifier of the rule that was applied
           * @param metabolites the SMILES of the molecules involved
           * @param products the SMILES of the produced molecules
           * @param rate the rate of the reaction
           * @param transState the SMILES of the transition state
           */
        Reaction(   const std::string& rule_id
                    , const Metabolite_Container& metabolites
                    , const Product_Container& products
                    , const double rate
                    , const std::string& transState );

        //! Destruction
        ~Reaction();
        
          //! resets the content to values of default construction;
        void
        clear( void );
        
          /*! Comparison operator to enable the storage of Reaction objects in
           * ordered containers like std::set that require a strict less
           * ordering.
           * 
           * @param r2 the Reaction to compare to
           * @return true if [
           *      (rule_id < r2.rule_id) or equal and
           *      (less products) or equal and
           *      (less metabolites) or equal and
           *      (equal product number and one SMILES smaller) or equal and
           *      (equal metabolites number and one SMILES smaller) or equal and
           *      (both rates are set) and (rate < r2.rate) ],
           *      false otherwise
           */
        bool
        operator < ( const Reaction& r2 ) const ;
        
        
    };

 } // namespace chem
} // namespace ggl
    
     /*! outstream operator for Reaction class that prints the reaction to stream
      * @param out the stream to write to
      * @param r the Reaction to write
      * @return the modified stream
      */
    std::ostream&
    operator << ( std::ostream& out, const ggl::chem::Reaction& r );

    
#endif /*REACTION_HH_*/