isomorphism.h

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/**********************************************************************
  isomophism.h - OBIsomorphismMapper class for finding isomorphisms.

  Copyright (C) 2010 by Tim Vandermeersch

  This file is part of the Open Babel project.
  For more information, see <http://openbabel.org/>

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
  02110-1301, USA.
 **********************************************************************/
#ifndef OB_ISOMORPHISM_H
#define OB_ISOMORPHISM_H

#include <openbabel/bitvec.h>

namespace OpenBabel {

  class OBQuery;
  class OBMol;


  class OBAPI OBIsomorphismMapper
  {
    public:
      typedef std::vector< std::pair<unsigned int,unsigned int> > Mapping;
      typedef std::vector< Mapping > Mappings;

      OBIsomorphismMapper(OBQuery *query);
      virtual ~OBIsomorphismMapper();

      static OBIsomorphismMapper* GetInstance(OBQuery *query, const std::string &algorithm = std::string("VF2"));

      virtual void MapFirst(const OBMol *queried, Mapping &map, const OBBitVec &mask = OBBitVec()) = 0;
      virtual void MapUnique(const OBMol *queried, Mappings &maps, const OBBitVec &mask = OBBitVec()) = 0;
      virtual void MapAll(const OBMol *queried, Mappings &maps, const OBBitVec &mask = OBBitVec(), std::size_t maxMemory = 3000000) = 0;

      class Functor
      {
        public:
          virtual ~Functor() {}
          virtual bool operator()(Mapping &map) = 0;
      };
      virtual void MapGeneric(Functor &functor, const OBMol *queried, const OBBitVec &mask = OBBitVec()) = 0;


      void SetTimeout(unsigned int seconds) { m_timeout = seconds; }

    protected:
      OBQuery *m_query; 
      unsigned int m_timeout; 
  };

  inline bool MapsTo(const OBIsomorphismMapper::Mapping &map, unsigned int queryIndex, unsigned int &queriedIndex)
  {
    OBIsomorphismMapper::Mapping::const_iterator i;
    for (i = map.begin(); i != map.end(); ++i)
      if (i->first == queryIndex) {
        queriedIndex = i->second;
        return true;
      }

    return false;
  }


  typedef OBIsomorphismMapper::Mapping Automorphism;
  typedef OBIsomorphismMapper::Mappings Automorphisms;

  OBAPI bool FindAutomorphisms(OBMol *mol, std::vector<OBIsomorphismMapper::Mapping> &aut, const std::vector<unsigned int> &symmetry_classes,
      const OBBitVec &mask = OBBitVec(), std::size_t maxMemory = 3000000);
  OBAPI bool FindAutomorphisms(OBMol *mol, std::vector<OBIsomorphismMapper::Mapping> &aut, const OBBitVec &mask = OBBitVec(),
      std::size_t maxMemory = 3000000);

  OBAPI void FindAutomorphisms(OBIsomorphismMapper::Functor &functor, OBMol *mol,
      const std::vector<unsigned int> &symmetry_classes, const OBBitVec &mask = OBBitVec());


}

#endif