/****************************************************************************
 * Copyright (C) 2009-2015 EPAM Systems
 * 
 * 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.
 ***************************************************************************/

#include "molecule/molecule_arom.h"

#include "base_c/bitarray.h"
#include "base_cpp/gray_codes.h"
#include "graph/cycle_enumerator.h"
#include "molecule/molecule.h"
#include "molecule/query_molecule.h"
#include "molecule/elements.h"

using namespace indigo;

//
// AromatizerBase
// 

IMPL_ERROR(AromatizerBase, "aromatizer");

CP_DEF(AromatizerBase);

AromatizerBase::AromatizerBase (BaseMolecule &molecule) : _basemol(molecule),
   CP_INIT,
   TL_CP_GET(_bonds_arom),
   TL_CP_GET(_bonds_arom_count),
   TL_CP_GET(_unsure_cycles),
   TL_CP_GET(_cycle_atoms)
{
   _bonds_arom.resize(bitGetSize(molecule.edgeEnd()));
   _bonds_arom_count.resize(molecule.edgeEnd());

   _cycle_atoms.clear_resize(_basemol.vertexEnd());

   reset();
}

AromatizerBase::~AromatizerBase ()
{
}

bool AromatizerBase::_checkDoubleBonds (const int *cycle, int cycle_len)
{
   int j;

   for (j = 0; j < cycle_len; j++)
   {
      int v_left_idx = cycle[j];
      int v_center_idx = cycle[(j + 1) % cycle_len];
      int v_right_idx = cycle[(j + 2) % cycle_len];

      const Vertex &vertex = _basemol.getVertex(v_center_idx);
      int i;

      int internal_double_bond_count = 0;
      for (i = vertex.neiBegin(); i != vertex.neiEnd(); i = vertex.neiNext(i))
      {
         int nei_idx = vertex.neiVertex(i);

         int e_idx = vertex.neiEdge(i);
         int type = _basemol.getBondOrder(e_idx);
         if (type == BOND_DOUBLE && !isBondAromatic(e_idx))
         {
            if (nei_idx != v_left_idx && nei_idx != v_right_idx)
            {
               // Double bond going outside 
               if (!_acceptOutgoingDoubleBond(v_center_idx, e_idx))
                  return false;
            }
            else if (nei_idx == v_left_idx || nei_idx == v_right_idx)
               internal_double_bond_count++;
         }
      }
      if (internal_double_bond_count >= 2)
         return false;
   }
   return true;
}

void AromatizerBase::_aromatizeCycle (const int *cycle, int cycle_len)
{
   for (int i = 0; i < cycle_len; i++)
   {
      int a = cycle[i], b = cycle[(i + 1) % cycle_len];
      int e_idx = _basemol.findEdgeIndex(a, b);
      _bonds_arom_count[e_idx]++;
      bitSetBit(_bonds_arom.ptr(), e_idx, 1);
   }

   // Marks all single bonds that are inside this cycle like in CC1=CC2=CNC=CC2=N1 as aromatic
   _cycle_atoms_mark++;
   for (int i = 0; i < cycle_len; i++)
      _cycle_atoms[cycle[i]] = _cycle_atoms_mark;

   for (int i = 0; i < cycle_len; i++)
   {
      const Vertex &v = _basemol.getVertex(cycle[i]);
      for (int nei : v.neighbors())
      {
         int nei_index = v.neiVertex(nei);
         // Check that the end is in the cycle
         if (_cycle_atoms[nei_index] != _cycle_atoms_mark)
            continue;

         // Check if the bond has already been marked as aromatic
         int nei_edge = v.neiEdge(nei);
         if (_bonds_arom_count[nei_edge] != 0)
            continue;

         // Check that the bond is single
         if (_basemol.getBondOrder(nei_edge) == BOND_SINGLE)
         {
            bitSetBit(_bonds_arom.ptr(), nei_edge, 1);
            _bonds_arom_count[nei_edge]++;
         }
      }
   }

   _handleAromaticCycle(cycle, cycle_len);
}

void AromatizerBase::_handleCycle (const Array<int> &path)
{
   // Check Huckel's rule
   if (!_isCycleAromatic(path.ptr(), path.size()))
      return;
   addAromaticCycle(-1, path.ptr(), path.size());
}

bool AromatizerBase::handleUnsureCycles ()
{
   bool changed = true;
   bool is_all_aromatic = true;

   while (changed)
   {
      changed = false;

      for (int i = 0; i < _unsure_cycles.size(); i++)
      {
         if (_unsure_cycles[i].is_empty)
            continue;

         if (_checkDoubleBonds(_unsure_cycles[i].cycle, _unsure_cycles[i].length))
         {
            _aromatizeCycle(_unsure_cycles[i].cycle, _unsure_cycles[i].length);
            _unsure_cycles[i].is_empty = true;
            changed = true;
         }
         else 
            is_all_aromatic = false;
      }
   }
   return is_all_aromatic;
}

bool AromatizerBase::_cb_check_vertex (Graph &graph, int v_idx, void *context)
{
   AromatizerBase *arom = (AromatizerBase *)context;
   return arom->_checkVertex(v_idx);
}

bool AromatizerBase::_cb_handle_cycle (Graph &graph, const Array<int> &vertices, const Array<int> &edges, void *context)
{
   AromatizerBase *arom = (AromatizerBase *)context;
   arom->_handleCycle(vertices);
   return true;
}

void AromatizerBase::aromatize ()
{
   CycleEnumerator cycle_enumerator(_basemol);

   cycle_enumerator.cb_check_vertex = _cb_check_vertex;
   cycle_enumerator.cb_handle_cycle = _cb_handle_cycle;
   cycle_enumerator.max_length = MAX_CYCLE_LEN;
   cycle_enumerator.context = this;
   cycle_enumerator.process();

   handleUnsureCycles();
}

bool AromatizerBase::isBondAromatic (int e_idx)
{
   return _bonds_arom_count[e_idx] != 0;
}

const byte* AromatizerBase::isBondAromaticArray (void)
{
   return _bonds_arom.ptr();
}

void AromatizerBase::addAromaticCycle (int id, const int *cycle, int cycle_len)
{
   if (!_checkDoubleBonds(cycle, cycle_len))
   {
      int empty_idx;
      if (_unsureCyclesCount == _unsure_cycles.size())
      {
         empty_idx = _unsure_cycles.size();
         _unsure_cycles.push();
      }
      else
      {
         // Find first empty space
         empty_idx = -1;
         for (int i = 0; i < _unsure_cycles.size(); i++)
            if (_unsure_cycles[i].is_empty)
            {
               empty_idx = i;
               break;
            }
         if (empty_idx == -1)
            throw Exception("AromatizerBase::addAromaticCycle: internal logic error");
      }

      CycleDef &cycleDef = _unsure_cycles[empty_idx];
      cycleDef.id = id;
      cycleDef.is_empty = false;
      cycleDef.length = cycle_len;

      memcpy(cycleDef.cycle, cycle, cycle_len * sizeof(int));

      _unsureCyclesCount++;
   }
   else
      _aromatizeCycle(cycle, cycle_len);
}

void AromatizerBase::removeAromaticCycle (int id, const int *cycle, int cycle_len)
{
   // Find id in unsure cycles
   for (int i = 0; i < _unsure_cycles.size(); i++)
      if (!_unsure_cycles[i].is_empty && _unsure_cycles[i].id == id)
      {
         _unsure_cycles[i].is_empty = true;
         return;
      }

   // Just decrease bond marks
   for (int i = 0; i < cycle_len; i++)
   {
      int a = cycle[i], b = cycle[(i + 1) % cycle_len];
      int e_idx = _basemol.findEdgeIndex(a, b);
      _bonds_arom_count[e_idx]--;
      if (_bonds_arom_count[e_idx] == 0)
         bitSetBit(_bonds_arom.ptr(), e_idx, 0);
   }
}

bool AromatizerBase::_checkVertex (int v_idx)
{
   return true;
}

void AromatizerBase::_handleAromaticCycle (const int *cycle, int cycle_len)
{
}

void AromatizerBase::reset (void)
{
   _unsure_cycles.clear();
   _bonds_arom.zerofill();
   _bonds_arom_count.zerofill();

   _cycle_atoms.zerofill();
   _cycle_atoms_mark = 1;

   _cyclesHandled = 0;
   _unsureCyclesCount = 0;
}

void AromatizerBase::setBondAromaticCount (int e_idx, int count)
{
   _bonds_arom_count[e_idx] = count;
   bitSetBit(_bonds_arom.ptr(), e_idx, count != 0);
}

//
// MoleculeAromatizer
// 

CP_DEF(MoleculeAromatizer);

MoleculeAromatizer::MoleculeAromatizer (Molecule &molecule, const AromaticityOptions &options) : AromatizerBase(molecule),
   CP_INIT,
   TL_CP_GET(_pi_labels)
{
   _pi_labels.clear_resize(molecule.vertexEnd());
   _options = options;
}

int MoleculeAromatizer::_getPiLabel (int v_idx)
{
   if (!_basemol.vertexInRing(v_idx))
      return -1;

   const Vertex &vertex = _basemol.getVertex(v_idx);
  
   if (_basemol.isPseudoAtom(v_idx))
      return -1;

   if (_basemol.isTemplateAtom(v_idx))
      return -1;

   if (_basemol.isRSite(v_idx))
      return -1;

   if (!Element::canBeAromatic(_basemol.getAtomNumber(v_idx)))
      return -1;

   Molecule &mol = (Molecule &)_basemol;

   int non_arom_conn = 0, arom_bonds = 0;
   int n_double_ext = 0, n_double_ring = 0;
   for (int i = vertex.neiBegin(); i != vertex.neiEnd(); i = vertex.neiNext(i))
   {
      int bond_idx = vertex.neiEdge(i);
      int type = _basemol.getBondOrder(bond_idx);
      if (type == BOND_DOUBLE)
      {
         if (_basemol.getBondTopology(bond_idx) == TOPOLOGY_RING)
            n_double_ring++;
         else
         {
            if (!_acceptOutgoingDoubleBond(v_idx, bond_idx))
               return -1;
            n_double_ext++;
         }
      }
      if (type == BOND_TRIPLE)
         return -1;
      if (type == BOND_AROMATIC)
         arom_bonds++;
      else
         non_arom_conn++;
   }

   if (arom_bonds == 0)
   {
      // Verify that this atom has valid valence
      if (mol.getImplicitH_NoThrow(v_idx, -1) == -1)
         return -1;
   }

   if (n_double_ring > 0)
      return 1;

   if (n_double_ext > 1)
      return -1;
   else if (n_double_ext == 1)
   {
      // Only a single external double bond that was accepted in _acceptOutgoingDoubleBond
      // It means that it is C=S, C=O, or C=N, like in O=C1NC=CC(=O)N1
      int atom_number = _basemol.getAtomNumber(v_idx);
      if (atom_number == ELEM_S)
         return 2;
      return 0;
   }

   int conn = mol.getAtomConnectivity_NoThrow(v_idx, -1);
   if (conn == -1)
      return -1;

   // Atom is already aromatic and in general number of hydrogens 
   // cannot be deduced. But if atom can have one single or onle 
   // double bond while being aromatic then pi label can be calculated
   if (arom_bonds != 0)
   {
      int single_bonds_conn = non_arom_conn + arom_bonds;
      int h_with_single = mol.calcImplicitHForConnectivity(v_idx, single_bonds_conn);

      bool can_have_single_bonds = false;
      if (h_with_single >= 0 && _getPiLabelByConn(v_idx, single_bonds_conn) >= 0)
      {
         can_have_single_bonds = true;
         conn = single_bonds_conn;
      }

      bool can_have_one_double_bond = 
         (mol.calcImplicitHForConnectivity(v_idx, single_bonds_conn + 1) >= 0);

      bool can_have_more_double_bonds = false;
      for (int i = 2; i < arom_bonds; i++)
      {
         int h_with_double = mol.calcImplicitHForConnectivity(v_idx, single_bonds_conn + i);
         if (h_with_double >= 0)
            can_have_more_double_bonds = true;
      }

      if (!can_have_single_bonds && can_have_one_double_bond && !can_have_more_double_bonds)
         return 1; // This atom must have double bond
      if (can_have_single_bonds && !can_have_one_double_bond && !can_have_more_double_bonds)
         ; // This atom must have only single bonds as aromatic ones
      else
         return -1; // This case is ambiguous. Treat as nonaromatic.
   }

   return _getPiLabelByConn(v_idx, conn);
}

int MoleculeAromatizer::_getPiLabelByConn (int v_idx, int conn)
{
   Molecule &mol = (Molecule &)_basemol;
   int radical = _basemol.getAtomRadical(v_idx);
   if (radical > 0)
      return 1;

   int lonepairs = 0;
   if (mol.getVacantPiOrbitals(v_idx, conn, &lonepairs) > 0)
      return 0;

   if (lonepairs > 0)
      return 2;

   return -1;
}

void MoleculeAromatizer::precalculatePiLabels ()
{
   for (int v_idx = _basemol.vertexBegin(); 
         v_idx < _basemol.vertexEnd(); 
         v_idx = _basemol.vertexNext(v_idx))
      _pi_labels[v_idx] = _getPiLabel(v_idx);
}

bool MoleculeAromatizer::_checkVertex (int v_idx)
{
   return _pi_labels[v_idx] != -1;
}

bool MoleculeAromatizer::_isCycleAromatic (const int *cycle, int cycle_len)
{
   int count = 0;
   // Check Huckel's rule
   for (int i = 0; i < cycle_len; i++)
      count += _pi_labels[cycle[i]];

   if (((count - 2) % 4) != 0) 
      return false;
   return true;
}

bool MoleculeAromatizer::_acceptOutgoingDoubleBond (int atom, int bond)
{
   if (_options.method == AromaticityOptions::GENERIC)
   {
      // Note: this method should be in sync with QueryMoleculeAromatizer::_acceptOutgoingDoubleBond

      // CC1=CC=CC=[N]1=C
      int atom_number = _basemol.getAtomNumber(atom);
      if (atom_number == ELEM_C || atom_number == ELEM_S)
      {
         int end = _basemol.getEdgeEnd(atom, bond);
         int end_number = _basemol.getAtomNumber(end);
         if (atom_number == ELEM_C)
         {
            // [O-][N+](=O)C1=CNC=C(Cl)C1=O (see CID 11850826)
            // CN1SC(=N)N(C)C1=S (see CID 11949795)
            if (end_number == ELEM_N || end_number == ELEM_O || end_number == ELEM_S)
               // Corresponding pi label is 0
               return true;
         }
         if (atom_number == ELEM_S)
         {
            // O=S1N=CC=N1
            if (end_number == ELEM_O)
               // Corresponding pi label is 0
               return true;
         }
      }
   }

   Molecule &mol = _basemol.asMolecule();
   if (mol.isNitrogenV5(atom))
      return true;

   return false;
}

bool MoleculeAromatizer::aromatizeBonds (Molecule &mol, const AromaticityOptions &options)
{
   MoleculeAromatizer aromatizer(mol, options);

   aromatizer.precalculatePiLabels();
   aromatizer.aromatize();

   bool aromatic_bond_found = false;
   for (int e_idx = mol.edgeBegin(); e_idx < mol.edgeEnd(); e_idx = mol.edgeNext(e_idx))
      if (aromatizer.isBondAromatic(e_idx))
      {
         mol.setBondOrder(e_idx, BOND_AROMATIC, true);
         aromatic_bond_found = true;
      }

   // Aromatize RGroups
   int n_rgroups = mol.rgroups.getRGroupCount();
   for (int i = 1; i <= n_rgroups; i++)
   {
      PtrPool<BaseMolecule> &frags = mol.rgroups.getRGroup(i).fragments;

      for (int j = frags.begin(); j != frags.end(); j = frags.next(j))
      {
         Molecule &fragment = frags[j]->asMolecule();
         aromatic_bond_found |= MoleculeAromatizer::aromatizeBonds(fragment, options);
      }
   }

   return aromatic_bond_found;
}

//
// QueryMoleculeAromatizer
//

CP_DEF(QueryMoleculeAromatizer);

QueryMoleculeAromatizer::QueryMoleculeAromatizer (QueryMolecule &molecule, const AromaticityOptions &options) : 
   AromatizerBase(molecule), 
   CP_INIT,
   TL_CP_GET(_pi_labels),
   TL_CP_GET(_aromatic_cycles)
{
   _pi_labels.clear_resize(molecule.vertexEnd());
   _aromatic_cycles.clear();
   _aromatic_cycles.reserve(100);
   _mode = FUZZY;
   _collecting = false;
   _options = options;
}

void QueryMoleculeAromatizer::precalculatePiLabels ()
{
   for (int v_idx = _basemol.vertexBegin(); 
            v_idx < _basemol.vertexEnd(); 
            v_idx = _basemol.vertexNext(v_idx))
      _pi_labels[v_idx] = _getPiLabel(v_idx);
}

bool QueryMoleculeAromatizer::_checkVertex (int v_idx)
{
   return _pi_labels[v_idx].canBeAromatic();
}

bool QueryMoleculeAromatizer::_isCycleAromatic (const int *cycle, int cycle_len)
{
   QueryMolecule &query = (QueryMolecule &)_basemol;
   // Single/double bond can't be aromatic and Check if cycle wasn't aromatic
   bool all_aromatic = true;
   for (int i = 0; i < cycle_len; i++)
   {
      int a = cycle[i], b = cycle[(i + 1) % cycle_len];
      int e_idx = _basemol.findEdgeIndex(a, b);
      if (!query.possibleBondOrder(e_idx, BOND_AROMATIC))
         all_aromatic = false;
   }
   if (all_aromatic)
      return false;

   PiValue cycle_sum(0, 0);
   // Check Huckel's rule
   for (int i = 0; i < cycle_len; i++)
   {
      PiValue &cur = _pi_labels[cycle[i]];
      if (cur.min == -1 || cur.max == -1)
         throw Error("interal error in _isCycleAromatic");

      cycle_sum.max += cur.max;
      cycle_sum.min += cur.min;
   }

   // Check Huckel's rule
   if (_mode == EXACT)
   {
      if (cycle_sum.min != cycle_sum.max)
         return false;

      int sum = cycle_sum.min;
      // Check if cycle have pi-lables sum 4n+2 for drawn query
      if (sum % 4 != 2)
         return false;
      return true;
   }

   //
   // Fuzzy mode: check if circle can have 4n-2 value
   //

   if (cycle_sum.max - cycle_sum.min > 3)
      return true;

   int residue_min = (cycle_sum.min + 2) % 4;
   int residue_max = (cycle_sum.max + 2) % 4;

   if (residue_min == 0 || residue_min > residue_max) 
      return true;
   return false;
}

QueryMoleculeAromatizer::PiValue QueryMoleculeAromatizer::_getPiLabel (int v_idx)
{
   int exact_double_bonds = 0;
   bool has_query_bond = false;

   QueryMolecule &query = (QueryMolecule &)_basemol;

   // Check double bonds
   const Vertex &vertex = _basemol.getVertex(v_idx);
   int min_conn = vertex.degree();
   for (int i = vertex.neiBegin(); i != vertex.neiEnd(); i = vertex.neiNext(i))
   {
      int bond_type = query.getBondOrder(vertex.neiEdge(i));

      switch (bond_type)
      {
      case BOND_DOUBLE:
         exact_double_bonds++;
         min_conn++;
         break;
      case BOND_TRIPLE:
         // Triple bonds can't be attached to atoms in aromatic rings
         return PiValue(-1, -1);
      case -1:
      case BOND_AROMATIC:
         has_query_bond = true;
         break;
      }
   }

   if (query.isRSite(v_idx))
   {
      if (vertex.degree() == 1)
      {
         // R-Group with single attachment point cannot be in aromatic ring
         return PiValue(-1, -1);
      }
      else
      {
         // R-Group with two attachment points
         // Here can be chain of atoms with different summary pi-labels
         return PiValue(0, 4);
      }
   }

   if (exact_double_bonds > 1)
   {
      if (_options.method == AromaticityOptions::BASIC)
      {
         if (!query.possibleNitrogenV5(v_idx))
            return PiValue(-1, -1);
      }
      else
      {
         bool possible_c = _basemol.possibleAtomNumber(v_idx, ELEM_C);
         bool possible_s = _basemol.possibleAtomNumber(v_idx, ELEM_S);
         if (possible_s && possible_c)
            return PiValue(0, 2);
         else if (possible_s)
            return PiValue(2, 2);
         else
            return PiValue(0, 0);
      }
   }

   if (has_query_bond)
   {
      if (_mode == EXACT)
         return PiValue(-1, -1);
      else
      {
         if (_options.method == AromaticityOptions::BASIC)
            if (exact_double_bonds > 0)
               return PiValue(1, 1);

         return PiValue(0, 2); // TODO: check different cases 
      }
   }

   // For aromaticity treat atoms without constrains as having default constraint.
   // For example if charge not specified then treat as charge is zero
   int number = query.getAtomNumber(v_idx);

   QueryMolecule::Atom &atom = query.getAtom(v_idx);
   //if (atom.hasConstraint(QueryMolecule::ATOM_FRAGMENT))
   //   throw Error("not implemented yet");

   if (number == -1)
      return PiValue(0, 2); // TODO: check different cases 

   if (!Element::canBeAromatic(number))
      return PiValue(-1, -1);

   int radical = query.getAtomRadical(v_idx);
   if (radical == -1)
   {
      if (atom.hasConstraint(QueryMolecule::ATOM_RADICAL))
         return PiValue(0, 2); // TODO: check different cases 
      radical = 0;
   }

   int charge = query.getAtomCharge(v_idx);
   if (charge == CHARGE_UNKNOWN)
   {
      if (atom.hasConstraint(QueryMolecule::ATOM_CHARGE))
         return PiValue(0, 2); // TODO: check different cases 
      charge = 0;
   }

   if (radical > 0)
      return PiValue(1, 1);


   int valence, implicit_h;

   if (!Element::calcValence(number, charge, radical, min_conn, valence, implicit_h, false) &&
       !query.possibleNitrogenV5(v_idx))
      return PiValue(-1, -1);

   if (_basemol.possibleAtomNumber(v_idx, ELEM_C) && query.getExplicitValence(v_idx) == 5)
      return PiValue(-1, -1);

   if (exact_double_bonds >= 1)
   {
      if (_options.method == AromaticityOptions::BASIC)
      {
         if (exact_double_bonds > 0)
            return PiValue(1, 1);
      }
      else
      {
         for (int i = vertex.neiBegin(); i != vertex.neiEnd(); i = vertex.neiNext(i))
         {
            int edge = vertex.neiEdge(i);
            if (query.possibleBondOrder(edge, BOND_DOUBLE))
            {
               if (_acceptOutgoingDoubleBond(v_idx, edge))
               {
                  bool possible_c = _basemol.possibleAtomNumber(v_idx, ELEM_C);
                  bool possible_s = _basemol.possibleAtomNumber(v_idx, ELEM_S);
                  if (possible_s && possible_c)
                     return PiValue(1, 2);
                  else if (possible_s)
                     return PiValue(1, 2);
                  else
                     return PiValue(0, 1);
               }
            }
         }
      }
      return PiValue(1, 1);
   }

   int pi_label = -1;
   int lonepairs = 0;

   int group = Element::group(number);
   if (BaseMolecule::getVacantPiOrbitals(group, charge, radical, min_conn + implicit_h, &lonepairs) > 0)
      pi_label = 0;
   else if (lonepairs > 0)
      pi_label = 2;

   return PiValue(pi_label, pi_label);
}

void QueryMoleculeAromatizer::_handleAromaticCycle (const int *cycle, int cycle_len)
{
   if (!_collecting)
      return;
   // Add cycle to storage      
   _aromatic_cycles.push();
   CycleDef &def = _aromatic_cycles[_aromatic_cycles.size() - 1];
   def.id = _aromatic_cycles.size() - 1;
   def.is_empty = false;
   def.length = cycle_len;
   memcpy(def.cycle, cycle, cycle_len * sizeof(int));

   AromatizerBase::_handleAromaticCycle(cycle, cycle_len);
}

bool QueryMoleculeAromatizer::_acceptOutgoingDoubleBond (int atom, int bond)
{
   if (_mode == EXACT)
      return false;

   if (_options.method == AromaticityOptions::GENERIC)
   {
      // Note: this method should be in sync with MoleculeAromatizer::_acceptOutgoingDoubleBond

      // CC1=CC=CC=[N]1=C
      bool possible_c = _basemol.possibleAtomNumber(atom, ELEM_C);
      bool possible_s = _basemol.possibleAtomNumber(atom, ELEM_S);
      if (possible_c || possible_s)
      {
         int end = _basemol.getEdgeEnd(atom, bond);
         int end_number = _basemol.getAtomNumber(end);
         if (possible_c)
         {
            // [O-][N+](=O)C1=CNC=C(Cl)C1=O (see CID 11850826)
            // CN1SC(=N)N(C)C1=S (see CID 11949795)
            if (_basemol.possibleAtomNumber(end, ELEM_N) || 
                  _basemol.possibleAtomNumber(end, ELEM_O) || _basemol.possibleAtomNumber(end, ELEM_S))
               // Corresponding pi label is 0
               return true;
         }
         if (possible_s)
         {
            // O=S1N=CC=N1
            if (_basemol.possibleAtomNumber(end, ELEM_O))
               // Corresponding pi label is 0
               return true;
         }
      }
   }

   QueryMolecule &qmol = _basemol.asQueryMolecule();
   if (qmol.possibleNitrogenV5(atom))
      return true;

   return false;
}

void QueryMoleculeAromatizer::setMode (int mode)
{
   _mode = mode;
}

bool QueryMoleculeAromatizer::aromatizeBonds (QueryMolecule &mol, const AromaticityOptions &options)
{
   return _aromatizeBonds(mol, -1, options);
}

bool QueryMoleculeAromatizer::_aromatizeBonds (QueryMolecule &mol, int additional_atom, const AromaticityOptions &options)
{
   bool aromatized = false;
   // Mark edges that can be aromatic in some matching
   aromatized |= _aromatizeBondsFuzzy(mol, options);
   // Aromatize all aromatic cycles
   aromatized |= _aromatizeBondsExact(mol, options);

   MoleculeRGroups &rgroups = mol.rgroups;
   int n_rgroups = rgroups.getRGroupCount();

   // Check if r-groups are attached with single bonds
   QS_DEF(Array<bool>, rgroups_attached_single);
   rgroups_attached_single.clear();
   for (int v = mol.vertexBegin(); v != mol.vertexEnd(); v = mol.vertexNext(v))
   {
      if (v == additional_atom)
         continue;
      if (mol.isRSite(v))
      {
         // Check if neighbor bonds are single
         const Vertex &vertex = mol.getVertex(v);
         for (int nei = vertex.neiBegin(); nei != vertex.neiEnd(); nei = vertex.neiNext(nei))
         {
            int edge = vertex.neiEdge(nei);
            QueryMolecule::Bond &bond = mol.getBond(edge);

            // DP TODO: implement smth. like Node::possibleOtherValueExcept() ...

            bool can_be_double = bond.possibleValue(QueryMolecule::BOND_ORDER, BOND_DOUBLE);
            bool can_be_triple = bond.possibleValue(QueryMolecule::BOND_ORDER, BOND_TRIPLE);
            bool can_be_arom = bond.possibleValue(QueryMolecule::BOND_ORDER, BOND_AROMATIC);
            if (can_be_double || can_be_triple || can_be_arom)
            {
               QS_DEF(Array<int>, sites);

               mol.getAllowedRGroups(v, sites);
               for (int j = 0; j < sites.size(); j++)
               {
                  rgroups_attached_single.expandFill(sites[j] + 1, true);
                  rgroups_attached_single[sites[j]] = false;
               }
            }
         }
      }
   }

   rgroups_attached_single.expandFill(n_rgroups + 1, true);
   for (int i = 1; i <= n_rgroups; i++)
   {
      PtrPool<BaseMolecule> &frags = rgroups.getRGroup(i).fragments;

      for (int j = frags.begin(); j != frags.end(); j = frags.next(j))
      {
         QueryMolecule &fragment = frags[j]->asQueryMolecule();

         aromatized |= _aromatizeRGroupFragment(fragment, rgroups_attached_single[i], options);
      }
   }
   return aromatized;
}

bool QueryMoleculeAromatizer::_aromatizeRGroupFragment (QueryMolecule &fragment, 
                                                        bool add_single_bonds, const AromaticityOptions &options)
{
   // Add additional atom to attachment points
   int additional_atom = fragment.addAtom(new QueryMolecule::Atom(QueryMolecule::ATOM_RSITE, 1));

   // Connect it with attachment points
   int maxOrder = fragment.attachmentPointCount();
   for (int i = 1; i <= maxOrder; i++)
   {
      int pointIndex = 0;
      int point;
      while (true)
      {
         point = fragment.getAttachmentPoint(i, pointIndex);
         if (point == -1)
            break;

         if (fragment.findEdgeIndex(point, additional_atom) == -1)
         {
            AutoPtr<QueryMolecule::Bond> bond;
            if (add_single_bonds)
               bond.reset(new QueryMolecule::Bond(QueryMolecule::BOND_ORDER, BOND_SINGLE));
            else
               bond.reset(new QueryMolecule::Bond());

            fragment.addBond(point, additional_atom, bond.release());
         }

         pointIndex++;
      }
   }

   bool aromatized = _aromatizeBonds(fragment, additional_atom, options);

   QS_DEF(Array<int>, indices);
   indices.clear();
   indices.push(additional_atom);

   fragment.removeAtoms(indices);
   return aromatized;
}

// Some cycles with query features can be aromatized
bool QueryMoleculeAromatizer::_aromatizeBondsExact (QueryMolecule &qmol, const AromaticityOptions &options)
{
   bool aromatized = false;
   QueryMoleculeAromatizer aromatizer(qmol, options);

   aromatizer.setMode(QueryMoleculeAromatizer::EXACT);
   aromatizer.precalculatePiLabels();
   aromatizer.aromatize();

   for (int e_idx = qmol.edgeBegin(); e_idx < qmol.edgeEnd(); e_idx = qmol.edgeNext(e_idx))
      if (aromatizer.isBondAromatic(e_idx))
      {
         AutoPtr<QueryMolecule::Bond> bond(qmol.releaseBond(e_idx));
         bond->removeConstraints(QueryMolecule::BOND_ORDER);

         AutoPtr<QueryMolecule::Bond> arom_bond(
            new QueryMolecule::Bond(QueryMolecule::BOND_ORDER, BOND_AROMATIC));

         qmol.resetBond(e_idx, QueryMolecule::Bond::und(bond.release(), arom_bond.release()));

         aromatized = true;
      }
   return aromatized;
}

bool QueryMoleculeAromatizer::_aromatizeBondsFuzzy (QueryMolecule &mol, const AromaticityOptions &options)
{
   bool aromatized = false;
   QueryMoleculeAromatizer aromatizer(mol, options);

   aromatizer.setMode(QueryMoleculeAromatizer::FUZZY);
   aromatizer.precalculatePiLabels();
   aromatizer.aromatize();

   mol.aromaticity.clear();
   for (int e_idx = mol.edgeBegin(); e_idx < mol.edgeEnd(); e_idx = mol.edgeNext(e_idx))
   {
      bool aromatic_constraint = 
         mol.getBond(e_idx).possibleValue(QueryMolecule::BOND_ORDER, BOND_AROMATIC);
      if (aromatic_constraint || aromatizer.isBondAromatic(e_idx))
      {
         mol.aromaticity.setCanBeAromatic(e_idx, true);
         aromatized = true;
      }
   }
   return aromatized;
}

void MoleculeAromatizer::findAromaticAtoms (BaseMolecule &mol, Array<int> *atoms, Array<int> *bonds, const AromaticityOptions &options)
{
   AutoPtr<BaseMolecule> clone;
   QS_DEF(Array<int>, mapping);

   clone.reset(mol.neu());
   mapping.clear();

   if (atoms != 0)
   {
      atoms->clear_resize(mol.vertexEnd());
      atoms->zerofill();
   }

   if (bonds != 0)
   {
      bonds->clear_resize(mol.edgeEnd());
      bonds->zerofill();
   }

   clone->clone(mol, &mapping, 0);

   clone->aromatize(options);

   for (int i = clone->edgeBegin(); i != clone->edgeEnd(); i = clone->edgeNext(i))
   {
      if (clone->getBondOrder(i) == BOND_AROMATIC)
      {
         const Edge &edge = clone->getEdge(i);

         if (atoms != 0)
         {
            atoms->at(mapping[edge.beg]) = 1;
            atoms->at(mapping[edge.end]) = 1;
         }

         if (bonds != 0)
            bonds->at(mol.findEdgeIndex(mapping[edge.beg], mapping[edge.end])) = 1;

      }
   }
}

//
// QueryMoleculeAromaticity
//

bool QueryMoleculeAromaticity::canBeAromatic (int edge_index) const
{
   if (edge_index >= can_bond_be_aromatic.size())
      return false;
   return can_bond_be_aromatic[edge_index];
}

void QueryMoleculeAromaticity::setCanBeAromatic (int edge_index, bool state)
{
   if (state == false && edge_index >= can_bond_be_aromatic.size())
      return;

   can_bond_be_aromatic.expandFill(edge_index + 1, false);
   can_bond_be_aromatic[edge_index] = state;
}

void QueryMoleculeAromaticity::clear()
{
   can_bond_be_aromatic.clear();
}
