/****************************************************************************
 * Copyright (C) 2009-2013 GGA Software Services LLC
 * 
 * This file is part of Indigo toolkit.
 * 
 * This file may be distributed and/or modified under the terms of the
 * GNU General Public License version 3 as published by the Free Software
 * Foundation and appearing in the file LICENSE.GPL included in the
 * packaging of this file.
 * 
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 ***************************************************************************/

#ifndef __molecule_tautomer_h__
#define __molecule_tautomer_h__

#include "base_cpp/array.h"
#include "base_cpp/tlscont.h"
#include "base_cpp/obj.h"
#include "graph/graph_decomposer.h"
#include "molecule/molecule.h"
#include "molecule/molecule_dearom.h"
#include "molecule/base_molecule.h"

#ifdef _WIN32
#pragma warning(push)
#pragma warning(disable:4251)
#endif


namespace indigo {

class Molecule;
class AromaticityMatcher;
class Dearomatizer;
class DearomatizationMatcher;
struct Atom;

//#define TRACE_TAUTOMER_MATCHING

struct TautomerRule
{
   bool check (BaseMolecule &molecule, int first, int last, char other_arom_first, char other_arom_last) const;

   Array<int> list1;
   Array<int> list2;
   int aromaticity1;
   int aromaticity2;

   static bool atomInAromaticRing (BaseMolecule &mol, int atom_idx);
};

struct TautomerSearchContext
{
   explicit TautomerSearchContext (BaseMolecule &g1_, BaseMolecule &g2_, GraphDecomposer &decomposer1_, GraphDecomposer &decomposer2_,
      const PtrArray<TautomerRule> &rules_list_, const AromaticityOptions &arom_options);
   virtual ~TautomerSearchContext ();

   BaseMolecule &g1;
   BaseMolecule &g2;

   GraphDecomposer &decomposer1;
   GraphDecomposer &decomposer2;

   // amount of metal bonds
   CP_DECL;
   TL_CP_DECL(Array<int>, h_rep_count_1);
   TL_CP_DECL(Array<int>, h_rep_count_2);

   const PtrArray<TautomerRule> &rules_list;

   bool force_hydrogens;
   bool ring_chain;
   int  rules;
   bool substructure;
   bool (*cb_check_rules) (TautomerSearchContext &context, int first1, int first2, int last1, int last2);

   int max_chains;

   AromaticityOptions arom_options;

   TL_CP_DECL(DearomatizationsStorage, dearomatizations);

   TL_CP_DECL(Array<int>, core_1);
   TL_CP_DECL(Array<int>, core_2);

   int initial_g1_vertexend;

   TL_CP_DECL(Array<int>, chains_2);

   TL_CP_DECL(Array<int>, edges_1);
   TL_CP_DECL(Array<int>, edges_2);
   TL_CP_DECL(Array<int>, edge_types_2);

   TL_CP_DECL(Array<int>, n1);
   TL_CP_DECL(Array<int>, n2);

   Obj<Dearomatizer> dearomatizer;
   Obj<DearomatizationMatcher>  dearomatizationMatcher;
};

class TautomerMatcher
{
public:
   explicit TautomerMatcher (TautomerSearchContext &context);
   explicit TautomerMatcher (TautomerSearchContext &context, int start_path_number, int n_chains);
   virtual ~TautomerMatcher ();

   bool findMatch      ();
   void addPair        (int n1, int n2, int arom_bond_idx2, int bond_type2);
   bool nextPair       (int &n1, int &n2, int &h_diff, int prev_n1, int prev_n2);
   bool isFeasiblePair (int n1, int n2, int &h_diff);
   void restore        ();

   static bool matchAtomsTau (BaseMolecule &g1, BaseMolecule &g2, int n1, int n2);
   static bool matchBondsTau (Graph &subgraph, Graph &supergraph,
      int sub_idx, int super_idx, void *userdata);
   static bool matchBondsTauSub (Graph &subgraph, Graph &supergraph,
      int sub_idx, int super_idx, void *userdata);

   static bool fixBondsNotInChains (TautomerSearchContext &context, const int *core1, const int *core2);

private:
   bool _checkInterPathBonds ();

   static int _remainderEmbedding (Graph &g1, Graph &g2,
      int *core1, int *core2, void *userdata);
   static int _preliminaryEmbedding (Graph &g1, Graph &g2,
      int *core1, int *core2, void *userdata);

   static bool _matchAtoms (Graph &subgraph, Graph &supergraph,
      const int *core_sub, int sub_idx, int super_idx, void *userdata);
   static bool _matchAtomsEx (Graph &subgraph, Graph &supergraph,
      const int *core_sub, int sub_idx, int super_idx, void *userdata);

   struct MatchData
   {
      MatchData (TautomerSearchContext &context_) : context(context_) {}

      TautomerSearchContext &context;
      int start_path_number;
   } _d;

   int _n1;
   int _n2;
   int _bond_idx2;
   int _n_chains;
};

class TautomerChainFinder
{
public:
   explicit TautomerChainFinder (TautomerSearchContext &context, int h_difference,
      int start_path_number, int n_chains);
   explicit TautomerChainFinder (TautomerChainFinder &other);
   virtual ~TautomerChainFinder ();

   bool enumeratePaths ();
   void addPair (int n1, int n2, bool is_zero_bond, int arom_bond_idx2, int bond_type2);
   void restore ();

   bool nextPair (int &n1, int &n2, int &e1, int &e2, int prev_e1, int prev_e2);
   int  isFeasiblePair (int n1, int n2, bool &zero_bond, int &arom_bond_idx2, int &bond_type2);

private:
   TautomerSearchContext &_context;

   int _prev_n1;
   int _prev_n2;
   int _bond_idx2;

   int _path_length;

   int _h_difference;

   bool _is_zero_bond_present;

   int _path_number;

   int _start_idx1;
   int _start_idx2;

   int _n_chains;
};

class TautomerChainChecker
{
public:
   explicit TautomerChainChecker (TautomerSearchContext &context,
      const Array<int> &core1, const Array<int> &core2, int start_path_number);
   explicit TautomerChainChecker (TautomerChainChecker &other);
   virtual ~TautomerChainChecker ();

   bool check ();
   void addPair (int n1, int n2);
   void restore();

   bool nextStartingPair (int &n1, int &n2);
   bool isFeasibleStartingPair (int n1, int n2, int &h_diff);

   bool nextPair (int &n1, int &n2, int &e1, int &e2);
   int isFeasiblePair (int n1, int n2, TautomerChainChecker &next1, TautomerChainChecker &next2);

   bool releaseChain ();
   void restoreChain ();

   DECL_ERROR;
private:
   bool _checkInterPathBonds ();

   static bool _matchAromBonds (Graph &subgraph, Graph &supergraph,
      int sub_idx, int super_idx, void *userdata);
   static void _removeAtom (Graph &subgraph, int sub_idx, void *userdata);
   static void _addBond (Graph &subgraph, Graph &supergraph,
      int sub_idx, int super_idx, void *userdata);
   static int _embedding (Graph &subgraph, Graph &supergraph,
                          int *core_sub, int *core_super, void *userdata);
   bool _matchAromatizedQuery();

   TautomerSearchContext &_context;

   int _path_length;
   int _h_difference;

   // at the end of chain
   int _final_path_length;
   int _final_h_difference;

   bool _is_zero_bond_present;
   bool _is_query_bond_present;
   bool _is_non_aromatic_bond_present;

   int _path_number;

   const Array<int> &_core_1;
   const Array<int> &_core_2;

   int _tau_bonds_to_match;

   int _prev_n1;
   int _prev_n2;

   int _bond_idx1;
   int _bond_idx2;
   int _bond_type2;

   int _start_idx1;
   int _start_idx2;
};

class DLLEXPORT TautomerSuperStructure : public Molecule
{
public:
   enum { NONE, TAUTOMER, ORIGINAL };

   TautomerSuperStructure (Molecule &mol);
   virtual ~TautomerSuperStructure ();

   virtual void clear ();

   virtual int getBondOrder    (int idx);
   virtual int getBondTopology (int idx);
   virtual bool possibleBondOrder (int idx, int order);

   virtual int getAtomTotalH (int idx);

   bool isZeroedBond (int idx);

   const int * getMapping ();
   const Array<int> & getInvMapping ();

   int       getSubgraphType  (const Array<int> &vertices, const Array<int> &edges);

protected:
   void  _findMinDistance (int source, int maxDist, Array<int> &dest, int *result);

   void  _collectAtomProperties (void);
   void  _getDoubleBondsCount   (int i, int &double_count, int &arom_count);
   bool  _isAcceptingHeteroatom (int idx);
   bool  _isEmittingHeteroatom  (int idx);
   int   _hetroatomsCount       (int idx);

   int _getBondOrder (int idx);
   int _getBondTopology (int idx);
   
   bool  _inside_ctor;

   CP_DECL;
   TL_CP_DECL(Array<int>,  _atomsEmitBond);
   TL_CP_DECL(Array<int>,  _atomsAcceptBond);
   TL_CP_DECL(Array<bool>, _isBondAttachedArray);
   TL_CP_DECL(Array<int>,  _mapping);
   TL_CP_DECL(Array<int>,  _inv_mapping);
   TL_CP_DECL(Array<int>,  _edge_mapping);
   TL_CP_DECL(Array<int>,  _total_h);
};

}

#ifdef _WIN32
#pragma warning(pop)
#endif

#endif