/****************************************************************************
 * 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 "indigo_molecule.h"
#include "indigo_reaction.h"
#include "reaction/reaction.h"
#include "molecule/molecule_automorphism_search.h"
#include "molecule/molecule_exact_matcher.h"

CEXPORT int indigoStereocenterType (int atom)
{
   INDIGO_BEGIN
   {
      IndigoAtom &ia = IndigoAtom::cast(self.getObject(atom));

      if (ia.mol.allene_stereo.isCenter(ia.idx))
         return INDIGO_ALLENE;

      switch (ia.mol.stereocenters.getType(ia.idx))
      {
         case MoleculeStereocenters::ATOM_ABS: return INDIGO_ABS;
         case MoleculeStereocenters::ATOM_OR: return INDIGO_OR;
         case MoleculeStereocenters::ATOM_AND: return INDIGO_AND;
         case MoleculeStereocenters::ATOM_ANY: return INDIGO_EITHER;
         default: return 0;
      }
   }
   INDIGO_END(-1);
}

static int mapStereocenterType (int api_stereocenter_type)
{
   switch (api_stereocenter_type)
   {
      case INDIGO_ABS: return MoleculeStereocenters::ATOM_ABS;
      case INDIGO_OR: return MoleculeStereocenters::ATOM_OR;
      case INDIGO_AND: return MoleculeStereocenters::ATOM_AND;
      case INDIGO_EITHER: return MoleculeStereocenters::ATOM_ANY;
      default: throw IndigoError("Unknown stereocenter type");
   }
}

CEXPORT int indigoStereocenterGroup (int atom)
{
   INDIGO_BEGIN
   {
      IndigoAtom &ia = IndigoAtom::cast(self.getObject(atom));

      if (ia.mol.stereocenters.getType(ia.idx) == 0)
         throw IndigoError("Atom is not a stereocenter");

      return ia.mol.stereocenters.getGroup(ia.idx);
   }
   INDIGO_END(-1);
}

CEXPORT int indigoSetStereocenterGroup (int atom, int group)
{
   INDIGO_BEGIN
   {
      IndigoAtom &ia = IndigoAtom::cast(self.getObject(atom));

      if (ia.mol.stereocenters.getType(ia.idx) == 0)
         throw IndigoError("Atom is not a stereocenter");

      ia.mol.stereocenters.setGroup(ia.idx, group);
      return 0;
   }
   INDIGO_END(-1);
}

CEXPORT int indigoChangeStereocenterType (int atom, int type)
{
   INDIGO_BEGIN
   {
      IndigoAtom &ia = IndigoAtom::cast(self.getObject(atom));

      if (ia.mol.stereocenters.getType(ia.idx) == 0)
         throw IndigoError("Atom is not a stereocenter");

      int group = ia.mol.stereocenters.getGroup(ia.idx);
      ia.mol.stereocenters.setType(ia.idx, mapStereocenterType(type), group);
      if (ia.mol.have_xyz)
         ia.mol.stereocenters.markBond(ia.idx);

      return 0;
   }
   INDIGO_END(-1);
}

CEXPORT int indigoAddStereocenter (int atom, int type, int v1, int v2, int v3, int v4)
{
   INDIGO_BEGIN
   {
      IndigoAtom &ia = IndigoAtom::cast(self.getObject(atom));

      int core_type;
      switch (type)
      {
         case INDIGO_ABS: core_type = MoleculeStereocenters::ATOM_ABS; break;
         case INDIGO_OR: core_type = MoleculeStereocenters::ATOM_OR; break;
         case INDIGO_AND: core_type = MoleculeStereocenters::ATOM_AND; break;
         case INDIGO_EITHER: core_type = MoleculeStereocenters::ATOM_ANY; break;
         default: throw IndigoError("Unknown stereocenter type");
      }

      int pyramid[4] = { v1, v2, v3, v4 };
      ia.mol.stereocenters.add(ia.idx, core_type, 0, pyramid);
      return 1;
   }
   INDIGO_END(-1);
}

CEXPORT const int* indigoStereocenterPyramid (int atom)
{
   INDIGO_BEGIN
   {
      IndigoAtom &ia = IndigoAtom::cast(self.getObject(atom));
      int *pyramid = ia.mol.stereocenters.getPyramid(ia.idx);
      if (pyramid == 0)
         throw IndigoError("No stereocenter at the atom %d", atom);

      return ia.mol.stereocenters.getPyramid(ia.idx);
   }
   INDIGO_END(NULL);
}

CEXPORT int indigoCountStereocenters (int molecule)
{
   INDIGO_BEGIN
   {
      BaseMolecule &mol = self.getObject(molecule).getBaseMolecule();

      return mol.stereocenters.size();
   }
   INDIGO_END(-1)
}

CEXPORT int indigoClearAlleneCenters (int molecule)
{
   INDIGO_BEGIN
   {
      BaseMolecule &mol = self.getObject(molecule).getBaseMolecule();

      mol.allene_stereo.clear();
      return 1;
   }
   INDIGO_END(-1)
}

CEXPORT int indigoCountAlleneCenters (int molecule)
{
   INDIGO_BEGIN
   {
      BaseMolecule &mol = self.getObject(molecule).getBaseMolecule();

      return mol.allene_stereo.size();
   }
   INDIGO_END(-1)
}

CEXPORT int indigoBondStereo (int bond)
{
   INDIGO_BEGIN
   {
      IndigoBond &ib = IndigoBond::cast(self.getObject(bond));
      BaseMolecule &mol = ib.mol;

      int dir = mol.getBondDirection(ib.idx);

      if (dir == BOND_UP)
         return INDIGO_UP;
      if (dir == BOND_DOWN)
         return INDIGO_DOWN;
      if (dir == BOND_EITHER)
         return INDIGO_EITHER;

      int parity = mol.cis_trans.getParity(ib.idx);

      if (parity == MoleculeCisTrans::CIS)
         return INDIGO_CIS;
      if (parity == MoleculeCisTrans::TRANS)
         return INDIGO_TRANS;
      return 0;
   }
   INDIGO_END(-1);
}

CEXPORT int indigoInvertStereo (int item)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(item);
      if (IndigoAtom::is(obj))
      {
         IndigoAtom &ia = IndigoAtom::cast(self.getObject(item));

         if (ia.mol.stereocenters.getType(ia.idx) > 0)
         {
            int k, *pyramid = ia.mol.stereocenters.getPyramid(ia.idx);
            if (pyramid == 0)
               throw IndigoError("indigoInvertStereo: internal");
            __swap(pyramid[0], pyramid[1], k);
         }
         else if (ia.mol.allene_stereo.isCenter(ia.idx))
            ia.mol.allene_stereo.invert(ia.idx);
         else
            throw IndigoError("indigoInvertStereo: not a stereo atom");
      }
      else if (IndigoBond::is(obj))
      {
         IndigoBond &ib = IndigoBond::cast(self.getObject(item));

         int parity = ib.mol.cis_trans.getParity(ib.idx);
         if (parity == 0)
            throw IndigoError("indigoInvertStereo: not a stereobond");

         if (parity == MoleculeCisTrans::CIS)
            ib.mol.cis_trans.setParity(ib.idx, MoleculeCisTrans::TRANS);
         else
            ib.mol.cis_trans.setParity(ib.idx, MoleculeCisTrans::CIS);
      }
      else
         throw IndigoError("indigoInvertStereo(): %s given", obj.debugInfo());
      return 1;
   }
   INDIGO_END(-1)
}

CEXPORT int indigoResetStereo (int item)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(item);

      if (IndigoAtom::is(obj))
      {
         IndigoAtom &ia = IndigoAtom::cast(self.getObject(item));

         if (ia.mol.stereocenters.getType(ia.idx) != 0)
            ia.mol.stereocenters.remove(ia.idx);
         if (ia.mol.allene_stereo.isCenter(ia.idx))
            ia.mol.allene_stereo.reset(ia.idx);
      }
      else if (IndigoBond::is(obj))
      {
         IndigoBond &ib = IndigoBond::cast(self.getObject(item));

         ib.mol.setBondDirection(ib.idx, 0);
         ib.mol.cis_trans.setParity(ib.idx, 0);
      }
      else
         throw IndigoError("indigoResetStereo(): %s given", obj.debugInfo());
      return 1;
   }
   INDIGO_END(-1)
}


CEXPORT int indigoClearStereocenters (int object)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(object);

      if (IndigoBaseMolecule::is(obj))
      {
         obj.getBaseMolecule().stereocenters.clear();
         obj.getBaseMolecule().clearBondDirections();
      }
      else if (IndigoBaseReaction::is(obj))
      {
         BaseReaction &rxn = obj.getBaseReaction();
         int i;

         for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
         {
            rxn.getBaseMolecule(i).stereocenters.clear();
            rxn.getBaseMolecule(i).clearBondDirections();
         }
      }
      else
         throw IndigoError("only molecules and reactions have stereocenters");
      return 1;
   }
   INDIGO_END(-1)
}

CEXPORT int indigoClearCisTrans (int object)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(object);

      if (IndigoBaseMolecule::is(obj))
         obj.getBaseMolecule().cis_trans.clear();
      else if (IndigoBaseReaction::is(obj))
      {
         BaseReaction &rxn = obj.getBaseReaction();
         int i;

         for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
            rxn.getBaseMolecule(i).cis_trans.clear();
      }
      else
         throw IndigoError("only molecules and reactions have cis-trans");
      return 1;
   }
   INDIGO_END(-1)
}

static int _resetSymmetric (Molecule &mol, bool cistrans, bool stereo)
{
   MoleculeAutomorphismSearch am;
   int sum = 0;

   if (cistrans)
      am.detect_invalid_cistrans_bonds = true;
   if (stereo)
      am.detect_invalid_stereocenters = true;
   am.allow_undefined = true;
   am.process(mol);

   if (cistrans)
   {
      for (int i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
      {
         if (mol.cis_trans.getParity(i) == 0)
            continue;

         if (am.invalidCisTransBond(i))
         {
            mol.cis_trans.setParity(i, 0);
            sum++;
         }
      }
   }

   if (stereo)
   {
      QS_DEF(Array<int>, to_remove);
      to_remove.clear();
      for (int i = mol.stereocenters.begin(); i != mol.stereocenters.end(); i = mol.stereocenters.next(i))
      {
         int atom_index = mol.stereocenters.getAtomIndex(i);
         if (am.invalidStereocenter(atom_index))
         {
            to_remove.push(atom_index);
            sum++;
         }
      }
      for (int i = 0; i < to_remove.size(); i++)
         mol.stereocenters.remove(to_remove[i]);

      if (to_remove.size() > 0)
      {
         mol.clearBondDirections();
         mol.stereocenters.markBonds();
      }
   }
   return sum;
}

static int _markEitherCisTrans (Molecule &mol)
{
   MoleculeAutomorphismSearch am;
   int i, sum = 0;

   for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
   {
      int substituents[4];

      if (mol.cis_trans.getParity(i) != 0)
         continue;

      if (!MoleculeCisTrans::isGeomStereoBond(mol, i, substituents, false))
         continue;

      if (mol.getEdgeTopology(i) == TOPOLOGY_RING)
      {
         // Mark all bonds in large cycles
         if (mol.edgeSmallestRingSize(i) >= 8)
            mol.cis_trans.ignore(i);
         continue;
      }

      am.possible_cis_trans_to_check.push(i);
   }

   am.allow_undefined = true;
   am.process(mol);

   for (i = 0; i < am.possible_cis_trans_to_check.size(); i++)
   {
      int bond = am.possible_cis_trans_to_check[i];
      mol.cis_trans.ignore(bond);
      sum++;
   }

   return sum;
}

CEXPORT int indigoResetSymmetricCisTrans (int handle)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(handle);

      if (IndigoBaseMolecule::is(obj))
         return _resetSymmetric(obj.getMolecule(), true, false);
      else if (IndigoBaseReaction::is(obj))
      {
         Reaction &rxn = obj.getReaction();
         int i, sum = 0;

         for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
            sum += _resetSymmetric(rxn.getMolecule(i), true, false);
         return sum;
      }
      throw IndigoError("only molecules and reactions have cis-trans");
   }
   INDIGO_END(-1)
}

CEXPORT int indigoResetSymmetricStereocenters (int handle)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(handle);

      if (IndigoBaseMolecule::is(obj))
         return _resetSymmetric(obj.getMolecule(), false, true);
      else if (IndigoBaseReaction::is(obj))
      {
         Reaction &rxn = obj.getReaction();
         int i, sum = 0;

         for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
            sum += _resetSymmetric(rxn.getMolecule(i), false, true);
         return sum;
      }
      throw IndigoError("only molecules and reactions have cis-trans");
   }
   INDIGO_END(-1)
}

CEXPORT int indigoMarkEitherCisTrans (int handle)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(handle);

      if (IndigoBaseMolecule::is(obj))
         return _markEitherCisTrans(obj.getMolecule());
      else if (IndigoBaseReaction::is(obj))
      {
         Reaction &rxn = obj.getReaction();
         int i, sum = 0;

         for (i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
            sum += _markEitherCisTrans(rxn.getMolecule(i));
         return sum;
      }
      throw IndigoError("only molecules and reactions have cis-trans");
   }
   INDIGO_END(-1)
}

CEXPORT int indigoMarkStereobonds (int handle)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(handle);

      if (IndigoBaseMolecule::is(obj))
         obj.getMolecule().stereocenters.markBonds();
      else if (IndigoBaseReaction::is(obj))
      {
         Reaction &rxn = obj.getReaction();
         for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
            rxn.getMolecule(i).stereocenters.markBonds();
      }
      else
         throw IndigoError("only molecules and reactions have stereocenters");
      return 0;
   }
   INDIGO_END(-1)
}

static void _indigoValidateMoleculeChirality (Molecule &mol)
{
   if (mol.stereocenters.size() == 0)
      return;
   if (!mol.stereocenters.haveAbs())
      return;

   QS_DEF(Molecule, mirror);
   mirror.clone(mol, 0, 0);

   for (int s = mirror.stereocenters.begin();
      s != mirror.stereocenters.end();
      s = mirror.stereocenters.next(s))
   {
      int atom = mirror.stereocenters.getAtomIndex(s);
      if (mirror.stereocenters.getType(atom) == MoleculeStereocenters::ATOM_ABS)
         mirror.stereocenters.invertPyramid(atom);
   }

   // Check exact matching
   MoleculeExactMatcher matcher(mol, mirror);
   matcher.flags = MoleculeExactMatcher::CONDITION_ALL;

   if (!matcher.find())
      return;
         
   for (int s = mol.stereocenters.begin();
      s != mol.stereocenters.end();
      s = mol.stereocenters.next(s))
   {
      int atom = mol.stereocenters.getAtomIndex(s);
      if (mol.stereocenters.getType(atom) == MoleculeStereocenters::ATOM_ABS)
         mol.stereocenters.setType(atom, MoleculeStereocenters::ATOM_AND);
   }
}

CEXPORT int indigoValidateChirality (int handle)
{
   INDIGO_BEGIN
   {
      IndigoObject &obj = self.getObject(handle);

      if (IndigoBaseMolecule::is(obj))
      {
         Molecule &mol = obj.getMolecule();
         _indigoValidateMoleculeChirality(mol);
      }
      else if (IndigoBaseReaction::is(obj))
      {
         Reaction &rxn = obj.getReaction();
         for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
            _indigoValidateMoleculeChirality(rxn.getMolecule(i));
      }
      else
         throw IndigoError("only molecules and reactions have stereocenters");
      return 0;
   }
   INDIGO_END(-1)
}