smartsMatcher.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_SMARTSMATCHER_H
#define BALL_STRUCTURE_SMARTSMATCHER_H

#ifndef BALL_STRUCTURE_SMARTSPARSER_H
# include <BALL/STRUCTURE/smartsParser.h>
#endif

#include <vector>
#include <set>
#include <map>

#include <boost/shared_ptr.hpp>

namespace BALL 
{
  // forward declaration
  class Molecule;

  class BALL_EXPORT SmartsMatcher
  {
    public: 

      typedef std::vector<std::set<const Atom*> > Match;


      SmartsMatcher();

      virtual ~SmartsMatcher();


      void match(Match& matches, Molecule& mol, const String& smarts);

      void match(Match& matches, Molecule& mol, const String& smarts, const std::set<const Atom*>& start_atoms);

      void match(std::vector<Match>& matches, Molecule& mol, const std::vector<String>& smarts);

      void match(std::vector<Match>& matches, Molecule& mol, const std::vector<String>& smarts, const std::set<const Atom*>& start_atoms);

      void setSSSR(const std::vector<std::vector<Atom*> >& sssr);

      void unsetSSSR();


    private:
      
      SmartsMatcher(const SmartsMatcher& matcher);

      SmartsMatcher& operator = (const SmartsMatcher& matcher);


    protected:

      typedef SmartsParser::SPNode SPNode;
      typedef SmartsParser::SPEdge SPEdge;
      typedef SmartsParser::SPAtom SPAtom;
      typedef SmartsParser::SPBond SPBond;

      class RecStructCore_
      {
        public:
          
          RecStructCore_();

          RecStructCore_(const RecStructCore_&);

          virtual ~RecStructCore_();

          RecStructCore_& operator = (const RecStructCore_&);

          void clear();
      
          std::vector<std::set<const Atom*> > matched_atoms;

          std::vector<std::map<const SPNode*, const Atom*> > mapped_atoms;

          std::vector<std::set<const Atom*> > visited_atoms;

          std::vector<std::set<const Bond*> > visited_bonds;

          std::vector<std::set<const SPEdge*> > visited_edges;

          std::vector<std::pair<const SPNode*, const Atom*> > first_matches;
      };

      class RecStructPool_
      {
        public:
          
          RecStructPool_();

          virtual ~RecStructPool_();

          RecStructCore_* getNextFree();

          Position getLastPosition();

          void destroy(Position pos);

        private:

          void resize_();

          RecStructPool_(const RecStructPool_&);

          RecStructPool_& operator = (const RecStructPool_&);
  
          std::vector<RecStructCore_*> rec_struct_pool_;

          std::vector<Position> free_list_;

          Position last_position_;
      };


      class RecStruct_
      {
        private:
          RecStructCore_* rec_struct_core_;
      
        public:
          
          RecStruct_();

          RecStruct_(const RecStruct_& rec_struct);

          virtual ~RecStruct_();

          RecStruct_& operator = (const RecStruct_&); 

          std::vector<std::set<const Atom*> >& matched_atoms;

          std::vector<std::map<const SPNode*, const Atom*> >& mapped_atoms;

          std::vector<std::set<const Atom*> >& visited_atoms;

          std::vector<std::set<const Bond*> >& visited_bonds;

          std::vector<std::set<const SPEdge*> >& visited_edges;

          std::vector<std::pair<const SPNode*, const Atom*> >& first_matches;

          void add(const RecStruct_& rec_struct);

          void add(const RecStruct_& rec_struct, Size i);

          void clear();

          void dump(const String& name, Size depth_ = 0);

        private:
        
          Position pos_;
      };

      static boost::shared_ptr<RecStructPool_> pool_;

      bool evaluateRingEdges_(const std::set<const Atom*>& matching, const std::map<const SPNode*, const Atom*>& mapping, const String& smarts);
      
      void evaluate_( RecStruct_& rs, SPNode* start_node, const Atom* start_atom);
  
      bool evaluate_node_(RecStruct_& rs, SPNode* start_node, const Atom* start_atom);
  
      bool evaluate_edge_(RecStruct_& rs, SPEdge* start_node, const Atom* start_atom, const Bond* start_bond);

      std::map<SPNode*, std::vector<std::set<const Atom*> > > rec_matches_;

      bool has_user_sssr_;

      std::vector<std::vector<Atom*> > sssr_;

      // debug output depth
      Size depth_;
  };
  
} // namespace BALL

#endif // BALL_STRUCTURE_SMARTSMATCHER_H