/****************************************************************************
 * 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_chain_fingerprints.h"
#include "molecule/molecule.h"
#include "graph/graph_subchain_enumerator.h"
#include "base_cpp/crc32.h"
#include "molecule/molecule_fingerprint.h"
#include "molecule/elements.h"

using namespace indigo;

IMPL_ERROR(MoleculeChainFingerprintBuilder, "chain fingerprint builder");

CP_DEF(MoleculeChainFingerprintBuilder);

MoleculeChainFingerprintBuilder::MoleculeChainFingerprintBuilder
        (Molecule &mol, const MoleculeChainFingerprintParameters &parameters) :
_mol(mol), _parameters(parameters),
CP_INIT, TL_CP_GET(_fingerprint)
{
}

void MoleculeChainFingerprintBuilder::process ()
{
   QS_DEF(Molecule, copy_without_h);
   QS_DEF(Array<int>, vertices);
   int i;

   vertices.clear();

   // remove hydrogens
   for (i = _mol.vertexBegin(); i < _mol.vertexEnd(); i = _mol.vertexNext(i))
      if (_mol.getAtomNumber(i) != ELEM_H)
         vertices.push(i);

   copy_without_h.makeSubmolecule(_mol, vertices, 0);

   GraphSubchainEnumerator gse(copy_without_h, _parameters.min_edges,
                               _parameters.max_edges, _parameters.mode);

   gse.context = this;
   gse.cb_handle_chain = _handleChain;

   _fingerprint.clear_resize(_parameters.size_qwords * 8);

   _fingerprint.zerofill();
   gse.processChains();
}

void MoleculeChainFingerprintBuilder::_handleChain (Graph &graph, int size,
        const int *vertices, const int *edges, void *context)
{
   MoleculeChainFingerprintBuilder *self = (MoleculeChainFingerprintBuilder *)context;
   QS_DEF(Array<char>, str);
   QS_DEF(Array<char>, rev_str);
   int i;

   str.clear();
   rev_str.clear();
   for (i = 0; i <= size; i++)
   {
      int number = self->_mol.getAtomNumber(vertices[i]);

      str.push(number & 0xFF);

      if (i == size)
         break;

      int order = self->_mol.getBondOrder(edges[i]);

      switch (order)
      {
         case BOND_SINGLE: str.push('-'); break;
         case BOND_DOUBLE: str.push('='); break;
         case BOND_TRIPLE: str.push('#'); break;
         default: str.push(':');
      }
   }

   int len = str.size();

   for (i = 0; i < len; i++)
      rev_str.push(str[len - i - 1]);

   str.push(0);
   rev_str.push(0);

   unsigned seed;

   unsigned seed1 = CRC32::get(str.ptr());
   unsigned seed2 = CRC32::get(rev_str.ptr());

   seed = __min(seed1, seed2);

	for (int i = 0; i < self->_parameters.bits_per_chain; i++)
   {
      seed = seed * 0x8088405 + 1;

      int k = seed % (self->_fingerprint.size() * 8);
      int nbyte = k / 8;
      int nbit = k % 8;

		self->_fingerprint[nbyte] |= (1 << nbit);
	}
}

const byte * MoleculeChainFingerprintBuilder::get ()
{
   return _fingerprint.ptr();
}