/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. All rights reserved.
 *
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder 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.
 *
 *    MoleCuilder 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 MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * ExportGraph_ToFiles.cpp
 *
 *  Created on: 08.03.2012
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include "ExportGraph_ToFiles.hpp"

#include "CodePatterns/Info.hpp"
#include "CodePatterns/Log.hpp"

#include "Bond/bond.hpp"
#include "Element/element.hpp"
#include "Fragmentation/Graph.hpp"
#include "Fragmentation/KeySet.hpp"
#include "Fragmentation/SortIndex.hpp"
#include "Graph/ListOfLocalAtoms.hpp"
#include "molecule.hpp"
#include "MoleculeListClass.hpp"
#include "Parser/FormatParserStorage.hpp"
#include "World.hpp"

/** Constructor for class ExportGraph_ToFiles.
 *
 * @param _graph instance of Graph containing keyset of each fragment
 * @param _treatment whether to always add already present hydrogens or not
 * @param _saturation whether to saturate dangling bonds with hydrogen or not
 */
ExportGraph_ToFiles::ExportGraph_ToFiles(
    const Graph &_graph,
    const enum HydrogenTreatment _treatment,
    const enum HydrogenSaturation _saturation) :
		ExportGraph(_graph, _treatment, _saturation)
{}

/** Destructor of class ExportGraph_ToFiles.
 *
 * We free all created molecules again and also removed their copied atoms.
 */
ExportGraph_ToFiles::~ExportGraph_ToFiles()
{}

/** Actual implementation of the export to files function.
 */
void ExportGraph_ToFiles::operator()()
{
  ExportGraph::operator()();

  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
  LOG(1, "Writing " << BondFragments.ListOfMolecules.size() << " possible bond fragmentation configs");
  bool write_status = true;
  for (std::vector<std::string>::const_iterator iter = typelist.begin();
      iter != typelist.end();
      ++iter) {
    LOG(2, "INFO: Writing bond fragments for type " << (*iter) << ".");
    write_status = write_status
    && BondFragments.OutputConfigForListOfFragments(
        prefix,
        FormatParserStorage::getInstance().getTypeFromName(*iter));
  }
  if (write_status)
    LOG(1, "All configs written.");
  else
    LOG(1, "Some config writing failed.");

  // store force index reference file
  {
    SortIndex_t SortIndex;
    BondFragments.StoreForcesFile(prefix, SortIndex);
  }

  // store keysets file
  TotalGraph.StoreKeySetFile(prefix);

  // store Hydrogen saturation correction file
  BondFragments.AddHydrogenCorrection(prefix);

  // restore orbital and Stop values
  //CalculateOrbitals(*configuration);
}