source: src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp@ f5ea10

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2017 Frederik Heber. 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/>.
 */

/*
 * ChemicalSpaceEvaluator.cpp
 *
 *  Created on: Sep 26, 2017
 *      Author: heber
 */

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

//#include "CodePatterns/MemDebug.hpp"

#include <iostream>
#include <string>
#include <vector>

#include "CodePatterns/Log.hpp"

#include "Actions/GraphAction/ChemicalSpaceEvaluatorAction.hpp"

#include "Element/element.hpp"
#include "Graph/BoostGraphCreator.hpp"
#include "Fragmentation/Homology/HomologyContainer.hpp"
#include "FunctionApproximation/Extractors.hpp"
#include "World.hpp"

#include <boost/graph/adjacency_list.hpp>

using namespace MoleCuilder;

// and construct the stuff
#include "ChemicalSpaceEvaluatorAction.def"
#include "Action_impl_pre.hpp"
/** =========== define the function ====================== */
ActionState::ptr GraphChemicalSpaceEvaluatorAction::performCall() {
  // create boost::graph from graph6 string
  BoostGraphCreator BGC;
  BGC.createFromGraph6String(params.graph_string.get());

  BoostGraphCreator::UndirectedGraph graph = BGC.get();

  Extractors::index_map_t index_map = boost::get(boost::vertex_index, graph);
  LOG(2, "DEBUG: We have " << boost::num_vertices(graph) << " nodes in the fragment graph.");

  // associate type with a node index
  Extractors::type_index_lookup_t type_index_lookup;
  std::vector<unsigned int> elementnumbers;
  elementnumbers.reserve(params.graph_elements.get().size());
  for (std::vector<const element *>::const_iterator iter = params.graph_elements.get().begin();
      iter != params.graph_elements.get().end(); ++iter) {
    elementnumbers.push_back((*iter)->getAtomicNumber());
    type_index_lookup.left.insert(
        std::make_pair(
            std::distance(iter, params.graph_elements.get().begin()),
            Extractors::ParticleType_t(elementnumbers.back())));
  }

  // create all induced subgraphs
  const size_t nodes_in_graph = boost::num_vertices(graph);
  LOG(2, "DEBUG: There are " << nodes_in_graph << " nodes in the graph.");
  Extractors::set_of_nodes_t set_of_nodes;
  for (size_t nodeid = 0; nodeid < nodes_in_graph; ++nodeid) {
    const size_t &rootindex = nodeid;
    LOG(2, "DEBUG: Current root index is " << rootindex);

    /// 5a. from node in graph (with this index) perform BFS till n-1 (#nodes in binding model)
    std::vector<size_t> distances(boost::num_vertices(graph));
    boost::breadth_first_search(
        graph,
        boost::vertex(rootindex, graph),
        boost::visitor(Extractors::record_distance(&distances[0])));
    LOG(3, "DEBUG: BFS discovered the following distances " << distances);

    /// 5b. and store all node in map with distance to root as key
    Extractors::nodes_per_level_t nodes_per_level;
    for (size_t i=0;i<distances.size();++i) {
      nodes_per_level.insert( std::make_pair(Extractors::level_t(distances[i]), Extractors::node_t(i)) );
    }
    LOG(3, "DEBUG: Nodes per level are " << nodes_per_level);

    /// 6. construct all possible induced connected subgraphs with this map (see fragmentation)
    Extractors::nodes_t nodes;
    // rootindex is always contained
    nodes.insert( rootindex );
    Extractors::level_t level = 0;

    Extractors::generateAllInducedConnectedSubgraphs(
        nodes_in_graph-1, level, nodes, set_of_nodes, nodes_per_level, graph, distances, index_map);
    LOG(2, "DEBUG: We have found " << set_of_nodes.size() << " unique induced, connected subgraphs.");
  }

  const HomologyContainer &container = World::getInstance().getHomologies();
  /// go through each induced, connected subgraph
  for (Extractors::set_of_nodes_t::const_iterator nodesiter = set_of_nodes.begin();
      nodesiter != set_of_nodes.end(); ++nodesiter) {
    /// convert its nodes into a HomologyGraph using the graph and elements (types for index)
    const Extractors::nodes_t &nodes = *nodesiter;
    const HomologyGraph nodes_graph =
        Extractors::createHomologyGraphFromNodes(nodes, type_index_lookup, graph, index_map);

    /// Query HomologyContainer for this HomologyGraph.
    HomologyContainer::range_t range = container.getHomologousGraphs(nodes_graph);

    if (range.first == range.second) {
      // range is empty, the fragment is unknown
      ELOG(1, "Cannot find fragment graph " << nodes_graph << " to graph " << elementnumbers);
    } else {
      // list first energy
      LOG(1, "Fragment graph " << nodes_graph << " has energy " << range.first->second.energy);
    }
  }

  return Action::success;
}

ActionState::ptr GraphChemicalSpaceEvaluatorAction::performUndo(ActionState::ptr _state) {
  return Action::success;
}

ActionState::ptr GraphChemicalSpaceEvaluatorAction::performRedo(ActionState::ptr _state){
  return Action::success;
}

bool GraphChemicalSpaceEvaluatorAction::canUndo() {
  return true;
}

bool GraphChemicalSpaceEvaluatorAction::shouldUndo() {
  return true;
}
/** =========== end of function ====================== */