GS_SMILES_OB.hh

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#ifndef GGL_CHEM_GS_SMILES_OB_HH_
#define GGL_CHEM_GS_SMILES_OB_HH_

#include "ggl/chem/GS_chem.hh"

#include "ggl/chem/Molecule.hh"


#include <iterator>

namespace ggl {
 namespace chem {

#define GGL_CHEM_GS_SMILES_OB_TEMPLATE \
    template <  class STL_INSERTER >

#define GGL_CHEM_GS_SMILES_OB_TYPE \
    GS_SMILES_OB <  STL_INSERTER >

 
 
 
      /*! @brief SMILES graph storage OpenBabel
       *
       * A Graph_Storage implementation that converts each added Molecule graph
       * into a SMILES string representation and adds it to the specified 
       * STL string container.
       * 
       * Usage Examples :
       * \verbatim
       * //////////////////////////////////////////////////////////////////////
       * 
       * std::set< std::string > SMILES_set;
       * typedef std::insert_iterator< SMILES_set > SMILES_set_inserter;
       * 
       * SMILES_set smilesSet;
       * SMILES_set_inserter insertSet(smilesSet, smilesSet.end());
       * 
       * ggl::chem::GS_SMILES_OB< SMILES_set_inserter > gs_set(insertSet);
       * 
       * //////////////////////////////////////////////////////////////////////
       * 
       * std::vector< std::string > SMILES_vector;
       * typedef std::back_insert_iterator< SMILES_vector > SMILES_vector_inserter;
       * 
       * SMILES_vector smilesVec;
       * SMILES_vector_inserter insertVec(smilesVec);
       * 
       * ggl::chem::GS_SMILES_OB< SMILES_vector_inserter > gs_vec(insertVec);
       * 
       * //////////////////////////////////////////////////////////////////////
       * \endverbatim
       * 
       * @author Martin Mann (c) 2008 http://www.bioinf.uni-freiburg.de/~mmann/
       * 
       * @tparam STL_INSERTER an STL insert iterator (e.g. std::insert_iterator)
       *            to add all SMILES to store to
       */
    template <  class STL_INSERTER >
    class GS_SMILES_OB : public GS_chem {
        
    protected:
        
          //! the std::inserter where each SMILES string is reported to
        STL_INSERTER insert;
        

    public:
        
          //! Construction
          //! @param insert the STL inserter to which each generated SMILES
          //!               is assigned to
        GS_SMILES_OB( STL_INSERTER insert );
        
         //! Destruction
        virtual
        ~GS_SMILES_OB();
        
        
          /*! Adds the SMILES string representation of a given graph to a
           * string container.
           * @param graph the Graph object to add.
           */
        virtual
        void
        addMolecule( const Molecule & graph );
    };

 
 }  // namespace chem
}  // namespace ggl


namespace ggl {
 namespace chem {
 
#define GGL_CHEM_GS_SMILES_OB_MOL_TEMPLATE \
    template <  class SMILES_MOL_MAP >

#define GGL_CHEM_GS_SMILES_OB_MOL_TYPE \
    GS_SMILES_OB_MOL <  SMILES_MOL_MAP >


     /*! @brief SMILES graph storage OpenBabel using STL SMILES-Graph map
      *
      * A Graph_Storage implementation that converts each added Molecule graph
      * into a SMILES string representation and adds it, if not already
      * existing, to the specified STL map container using the SMILES as key
      * and the Molecule object as value.
      *
      * @author Martin Mann (c) 2008 http://www.bioinf.uni-freiburg.de/~mmann/
      *
      * @tparam STL_INSERTER an STL insert iterator (e.g. std::insert_iterator)
      *            to add all SMILES to store to
      */
    template <  class SMILES_MOL_MAP >
    class GS_SMILES_OB_MOL : public GS_chem {
        
    protected:
        
          //! the map where each SMILES string is mapped to the represented
          //! molecule
        SMILES_MOL_MAP* smiles2mol;

    public:
        
          //! Construction
          //! @param smiles2mol the STL inserter to which each generated SMILES
          //!               and its molecule is assigned to
        GS_SMILES_OB_MOL( SMILES_MOL_MAP& smiles2mol );
        
        
        virtual
        ~GS_SMILES_OB_MOL();
        
        
          //! Rewrites a given molecule to SMILES and adds it to a contained.
          //! @param graph the molecule to add.
        virtual
        void
        addMolecule( const Molecule & graph );
        
    protected:
        
        virtual
        bool
        insert2map(const std::string & SMILES, const Molecule& graph );
        
    };

 }  // namespace chem
}  // namespace ggl


namespace ggl {
 namespace chem {

 
#define GGL_CHEM_GS_SMILES_OB_MOLp_TEMPLATE \
    template <  class SMILES_MOL_MAP >

#define GGL_CHEM_GS_SMILES_OB_MOLp_TYPE \
    GS_SMILES_OB_MOL <  SMILES_MOL_MAP >


     /*! @brief SMILES graph storage OpenBabel using STL SMILES-GraphPointer map
      *
      * A Graph_Storage implementation that converts each added Molecule graph
      * into a SMILES string representation and adds it, if not already
      * existing, to the specified STL map container using the SMILES as key
      * and the pointer to the newly allocated Molecule object as value.
      *
      * @author Martin Mann (c) 2008 http://www.bioinf.uni-freiburg.de/~mmann/
      *
      * @tparam STL_INSERTER an STL insert iterator (e.g. std::insert_iterator)
      *            to add all SMILES to store to
      */
    template <  class SMILES_MOL_MAP >
    class GS_SMILES_OB_MOLp : public GS_chem {
        
    protected:
        
          //! the map where each SMILES string is mapped to the represented
          //! molecule
        SMILES_MOL_MAP* smiles2mol;
        

    public:
        
        size_t reportedHits;
        
          //! Construction
          //! @param smiles2mol the STL inserter to which each generated SMILES
          //!               and its molecule is assigned to
        GS_SMILES_OB_MOLp( SMILES_MOL_MAP& smiles2mol );
        
        
        virtual
        ~GS_SMILES_OB_MOLp();
        
        
          //! Rewrites the given molecule to SMILES and adds it to a contained
          //! @param graph the molecule to add.
        virtual
        void
        addMolecule( const Molecule & graph );
        
    protected:
        
        virtual
        bool
        insert2map(const std::string & SMILES, const Molecule& graph );
        
    };

 }  // namespace chem
}  // namespace ggl

#include "ggl/chem/GS_SMILES_OB.icc"


#endif /*GS_SMILES_OB_HH_*/