source: src/Fragmentation/Homology/HomologyGraph.hpp@ 91c409

/*
 * HomologyGraph.hpp
 *
 *  Created on: Sep 24, 2012
 *      Author: heber
 */

#ifndef HOMOLOGYGRAPH_HPP_
#define HOMOLOGYGRAPH_HPP_


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

#include <boost/serialization/export.hpp>
#include <boost/serialization/map.hpp>

#include <map>
#include <iosfwd>

#include "AtomIdSet.hpp"
#include "Fragmentation/Homology/FragmentEdge.hpp"
#include "Fragmentation/Homology/FragmentNode.hpp"

class IndexSet;
class KeySet;

/** This class contains the representation of a molecular fragment as a graph.
 *
 * Only, we do not store the full graph in here. We have to include symmetries
 * such that two hydrogens may switch places. Eventually, we only look for the
 * set of distances of a fragment. If two hydrogens switch places, then also in
 * the set of distances some distances are interchanged but the whole fragment
 * remains the same. Hence, we have to store the bond graph representation in
 * such a way as to automatically include these symmetries.
 *
 * To this end, we use FragmentNode and FragmentEdge to store the vital
 * information.
 *
 */
class HomologyGraph
{
  //!> grant output operator access to internals
  friend std::ostream& operator<<(std::ostream& ost, const HomologyGraph &graph);
public:
  //!> typedef for a set of nodes representing node information
  typedef std::map<FragmentNode, size_t> nodes_t;
  //!> typedef for a set of nodes representing edge information
  typedef std::map<FragmentEdge, size_t> edges_t;
public:
  /** Default constructor for class HomologyGraph.
   *
   * This is required to allow placement in STL containers
   *
   */
  HomologyGraph() {}

  /** Constructor for class HomologyGraph.
   *
   * @param _nodes information on nodes of this graph
   * @param _edges information on edges of this graph
   */
  HomologyGraph(const nodes_t &_nodes, const edges_t &_edges) :
    nodes(_nodes),
    edges(_edges)
  {}

  /** Constructor for class HomologyGraph from a keyset (i.e. from atoms in the World).
   *
   * @param keyset global ids of atoms to pick
   */
  explicit HomologyGraph(const KeySet &keyset);

  /** Constructor for class HomologyGraph from a IndexSet (i.e. from atoms in the World).
   *
   * @param index global ids of atoms to pick
   */
  explicit HomologyGraph(const IndexSet &index);

  /** Constructor for class HomologyGraph from a AtomIdSet (i.e. from atoms in the World).
   *
   * @param index global ids of atoms to pick
   */
  explicit HomologyGraph(const AtomIdSet::atomIdSet &index);

  /** Destructor for class HomologyGraph.
   *
   */
  ~HomologyGraph() {}

  // comparators (allows sorting and hence quicker finding in STL containers)
  bool operator<(const HomologyGraph &graph) const;
  bool operator>(const HomologyGraph &graph) const;
  bool operator==(const HomologyGraph &graph) const;
  bool operator!=(const HomologyGraph &graph) const {
    return (!(*this == graph));
  }

  /** Checks whether this graph contains a specific \a node.
   *
   * @param node node to look for
   * @param count how often this node must occur
   * @return true - graph contains this node at least once, false - else
   */
  bool hasNode(const FragmentNode &node, const size_t count = 1) const {
    nodes_t::const_iterator iter = nodes.find(node);
    if (iter == nodes.end())
      return count == 0;
    else
      return (iter->second == count);
  }

  /** Checks whether this graph contains a specific \a edge.
   *
   * @param edge edge to look for
   * @param count how often this edge must occur
   * @return true - graph contains this edge at least once, false - else
   */
  bool hasEdge(const FragmentEdge &edge, const size_t count = 1) const {
    edges_t::const_iterator iter = edges.find(edge);
    if (iter == edges.end())
      return count == 0;
    else
      return (iter->second == count);
  }

  /** Checks whether this graph contains the given \a graph.
   *
   * Every edge must be present in this graph.
   *
   * \return true - graph is contained, false - else
   */
  bool contains(const HomologyGraph &graph) const {
    for (edges_t::const_iterator iter = graph.edges.begin(); iter != graph.edges.end(); ++iter) {
      edges_t::const_iterator finditer = edges.find(iter->first);
      if (finditer == edges.end())
        return false;
      else if (finditer->second < iter->second)
        return false;
    }
    return true;
  }

  /** Checks whether this graph has \b exactly \a _times nodes with \a _number
   * atomic number.
   *
   * @param _number desired atomic number
   * @param _times number this must occur
   * @return true - graph has exactly \a _times nodes with \a _number, false - else
   */
  bool hasTimesAtomicNumber(const size_t _number, const size_t _times) const;

  /** Checks whether this graph has \b greater equal \a _times nodes with \a _number
   * atomic number.
   *
   * @param _number desired atomic number
   * @param _times number this must occur
   * @return true - graph has greater equal \a _times nodes with \a _number, false - else
   */
  bool hasGreaterEqualTimesAtomicNumber(const size_t _number, const size_t _times) const;

  /** Assignment operator for class HomologyGraph.
   *
   * This is required to allow placement in STL container as we need to
   * const_cast override our const member variables.
   *
   */
  HomologyGraph& operator=(const HomologyGraph &graph);

  /** Prints the nodes in the graph to stream \a ost.
   *
   * \param ost stream to print to
   */
  void printNodes(std::ostream& ost) const;

  /** Prints the edges in the graph to stream \a ost.
   *
   * \param ost stream to print to
   */
  void printEdges(std::ostream& ost) const;

  /** Getter for the nodes contained in this graph.
   *
   * \return const ref to vector of FragmentNode
   */
  const nodes_t &getNodes() const
  { return nodes; }

  /** Getter for the edges contained in this graph.
   *
   * \return const ref to vector of FragmentEdge
   */
  const edges_t &getEdges() const
  { return edges; }

private:
  //!> information on the nodes of the graph
  const nodes_t nodes;
  //!> information on the edges of the graph
  const edges_t edges;

private:
  friend class boost::serialization::access;
  // serialization
  template <typename Archive>
  void serialize(Archive& ar, const unsigned int version)
  {
    ar & const_cast<nodes_t &>(nodes);
    ar & const_cast<edges_t &>(edges);
  }
};

std::ostream& operator<<(std::ostream& ost, const HomologyGraph &graph);

// we need to give this class a unique key for serialization
BOOST_CLASS_EXPORT_KEY(HomologyGraph)

// define some helpers outside to allow for light-weight unit testing
namespace detail {
  const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset);
  const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset);
  const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset);
  const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset);
  const HomologyGraph::nodes_t getNodesFromAtomIds(const AtomIdSet::atomIdSet &keyset);
  const HomologyGraph::edges_t getEdgesFromAtomIds(const AtomIdSet::atomIdSet &keyset);
};


#endif /* HOMOLOGYGRAPH_HPP_ */