ReactionTransitionState.hh

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#ifndef GGL_CHEM_REACTIONTRANSITIONSTATE_HH_
#define GGL_CHEM_REACTIONTRANSITIONSTATE_HH_

#include "ggl/chem/ChemRule.hh"
#include "ggl/chem/ChemRuleGraph.hh"

#include <sgm/Graph_Interface.hh>
#include <sgm/Match_Reporter.hh>


namespace ggl {
 namespace chem {


    /*! @brief Transition state of a reaction
     *
     * This class encodes an imaginary transition state (ITS) of a chemical
     * reaction. 
     * 
     * @author Martin Mann - http://www.bioinf.uni-freiburg.de/~mmann/
     */
    class ReactionTransitionState : public ChemRule::TransitionState
    {
    public:
        
          //! access to the superclass TransitionState type
        typedef ChemRule::TransitionState SuperClass;
        
        
    protected:
        
          //! the graph encoding of the imaginary transition state
        using SuperClass::tState;
        
          //! SMILES representation of the imaginary transition state
        using SuperClass::tStateSMILES;
        
    public:
        
         /*! Constructs an imaginary transition state based on the educts, 
          * products, and chemical GGL rule applied.
          * 
          * @param leftSide the left side pattern of the chemical rule applied
          * @param molecules the molecules where leftSide was mapped on
          * @param match the mapping of nodes of leftSide on the nodes of the
          *         molecules object
          * @param addEachComponent if set to true, than all components of the
          *        Rules LeftSidePattern are matched to an own molecule graph
          *        copy if two components map to the same molecule graph.
          */
        ReactionTransitionState(
                    const LeftSidePattern & leftSide
                    , const sgm::Graph_Interface & molecules
                    , const sgm::Match & match
                    , const bool addEachComponent = false
                );
        
        virtual ~ReactionTransitionState();
        
    protected:
        
         /*! Merges the given molecules into a rule graph such that the 
          * left side pattern of the rule maps the matched subgraph of the 
          * molecules object. This is the first step to create the imaginary
          * transition state.
          * 
          * @param its the intermediate transition state object to extend
          *        (NOTE : the object will be overwritten during the merge!)
          * @param leftSide the left side pattern of the chemical rule applied
          * @param molecules the molecule information to add to 
          * @param match the mapping of nodes of leftSide on the nodes of the
          *         molecules object
          * @param addEachComponent if set to true, than all components of the
          *        Rules LeftSidePattern are matched to an own molecule graph
          *        copy if two components map to the same molecule graph.
          */
        static
        bool
        mergeGraphs(    ChemRule::CoreGraph & its
                        , const LeftSidePattern & leftSide
                        , const sgm::Graph_Interface & molecules
                        , const sgm::Match & match
                        , const bool addEachComponent = false );
    };
    
    
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////

 } // namespace chem
} // namespace ggl

// implementation
#include "ggl/chem/ReactionTransitionState.icc"

////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////

    
#endif /*REACTIONTRANSITIONSTATE_HH_*/