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