GS_SMILES.hh

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#ifndef GGL_CHEM_GS_SMILES_HH_
#define GGL_CHEM_GS_SMILES_HH_

#include "ggl/chem/GS_chem.hh"

#include "ggl/chem/Molecule.hh"
#include "ggl/chem/SMILESwriter.hh"

#include <iterator>

namespace ggl {
 namespace chem {

 
#define GGL_CHEM_GS_SMILES_TEMPLATE \
    template <  class STL_INSERTER >

#define GGL_CHEM_GS_SMILES_TYPE \
    GS_SMILES < STL_INSERTER >

 
      /*! @brief SMILES graph storage
       *
       * 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< 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< 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
       * @tparam Molecule the boost graph representing the molecule to convert
       * @tparam NODE_LABEL_PROPERTY property type of the node label
       * @tparam EDGE_LABEL_PROPERTY property type of the edge label
       * @tparam NODE_INDEX_PROPERTY property type of the node indices
       */
    template <  class STL_INSERTER >
    class GS_SMILES : 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( STL_INSERTER insert );
        
        
        virtual
        ~GS_SMILES();
        
        
          //! Writes the SMILES string of a given molecule graph to a string
          //! container.
          //! @param graph the molecule object to add.
        virtual
        void
        addMolecule( const Molecule & graph );
    };

 
 }  // namespace chem
}  // namespace ggl


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

#define GGL_CHEM_GS_SMILES_MOL_TYPE \
    GS_SMILES_MOL < SMILES_MOL_MAP >


     /*! @brief SMILES graph storage 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_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_MOL( SMILES_MOL_MAP& smiles2mol );
        
        
        virtual
        ~GS_SMILES_MOL();
        
        
          //! Converts a given molecule graph to SMILES and adds it to the
          //! storage container.
          //! @param graph the Graph object 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_MOLp_TEMPLATE \
    template <  class SMILES_MOL_MAP >

#define GGL_CHEM_GS_SMILES_MOLp_TYPE \
    GS_SMILES_MOLp <    SMILES_MOL_MAP >

     /*! @brief SMILES graph storage 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_MOLp : public GS_chem {
        
    protected:
        
          //! the map where each SMILES string is mapped to the represented
          //! molecule
        SMILES_MOL_MAP* smiles2mol;
        const SMILES_MOL_MAP* smiles2molCheckOnly1;
        const SMILES_MOL_MAP* smiles2molCheckOnly2;


    public:
        
          //! Construction
          //! @param smiles2mol the map (SMILES->molecule) to that each 
          //!               generated SMILES and its molecule is added to
          //!               if not already present
        GS_SMILES_MOLp( SMILES_MOL_MAP& smiles2mol );
        
          /*! Construction
           * @param smiles2mol the map (SMILES->molecule) to that each
           *                generated SMILES and its molecule is added to
           *                if not already present
           * @param smiles2molCheckOnly an additional map to check for existence
           *                of a new molecule to store
           */ 
        GS_SMILES_MOLp( SMILES_MOL_MAP& smiles2mol 
                        , const SMILES_MOL_MAP& smiles2molCheckOnly );
        
          /*! Construction
           * @param smiles2mol the map (SMILES->molecule) to that each
           *                generated SMILES and its molecule is added to
           *                if not already present
           * @param smiles2molCheckOnly1 an additional map to check for existence
           *                of a new molecule to store
           * @param smiles2molCheckOnly2 an additional map to check for existence
           *                of a new molecule to store
           */ 
        GS_SMILES_MOLp( SMILES_MOL_MAP& smiles2mol 
                        , const SMILES_MOL_MAP& smiles2molCheckOnly1
                        , const SMILES_MOL_MAP& smiles2molCheckOnly2 );
        
        
        virtual
        ~GS_SMILES_MOLp();
        
        
          //! Converts a given molecule graph to SMILES and adds it to the
          //! storage container.
          //! @param graph the Graph object 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.icc"


#endif /*GGL_CHEM_GS_SMILES_HH_*/