[7b6b21f] | 1 | /*
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| 2 | * HomologyGraph.hpp
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| 3 | *
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| 4 | * Created on: Sep 24, 2012
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef HOMOLOGYGRAPH_HPP_
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| 9 | #define HOMOLOGYGRAPH_HPP_
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| 10 |
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| 11 |
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| 12 | // include config.h
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| 13 | #ifdef HAVE_CONFIG_H
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| 14 | #include <config.h>
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| 15 | #endif
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| 16 |
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[67db80] | 17 | #include <boost/serialization/export.hpp>
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[28e203] | 18 | #include <boost/serialization/map.hpp>
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[67db80] | 19 |
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[28e203] | 20 | #include <map>
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[54a561] | 21 | #include <iosfwd>
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[7b6b21f] | 22 |
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| 23 | #include "Fragmentation/Homology/FragmentEdge.hpp"
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| 24 | #include "Fragmentation/Homology/FragmentNode.hpp"
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| 25 |
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[372c912] | 26 | class IndexSet;
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[77b350] | 27 | class KeySet;
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| 28 |
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[7b6b21f] | 29 | /** This class contains the representation of a molecular fragment as a graph.
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| 30 | *
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| 31 | * Only, we do not store the full graph in here. We have to include symmetries
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| 32 | * such that two hydrogens may switch places. Eventually, we only look for the
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| 33 | * set of distances of a fragment. If two hydrogens switch places, then also in
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| 34 | * the set of distances some distances are interchanged but the whole fragment
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| 35 | * remains the same. Hence, we have to store the bond graph representation in
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| 36 | * such a way as to automatically include these symmetries.
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| 37 | *
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| 38 | * To this end, we use FragmentNode and FragmentEdge to store the vital
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| 39 | * information.
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| 40 | *
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| 41 | */
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| 42 | class HomologyGraph
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| 43 | {
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[54a561] | 44 | //!> grant output operator access to internals
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| 45 | friend std::ostream& operator<<(std::ostream& ost, const HomologyGraph &graph);
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[7b6b21f] | 46 | public:
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| 47 | //!> typedef for a set of nodes representing node information
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[28e203] | 48 | typedef std::map<FragmentNode, size_t> nodes_t;
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[7b6b21f] | 49 | //!> typedef for a set of nodes representing edge information
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[28e203] | 50 | typedef std::map<FragmentEdge, size_t> edges_t;
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[7b6b21f] | 51 | public:
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| 52 | /** Default constructor for class HomologyGraph.
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| 53 | *
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| 54 | * This is required to allow placement in STL containers
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| 55 | *
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| 56 | */
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| 57 | HomologyGraph() {}
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| 58 |
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| 59 | /** Constructor for class HomologyGraph.
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| 60 | *
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| 61 | * @param _nodes information on nodes of this graph
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| 62 | * @param _edges information on edges of this graph
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| 63 | */
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| 64 | HomologyGraph(const nodes_t &_nodes, const edges_t &_edges) :
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| 65 | nodes(_nodes),
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| 66 | edges(_edges)
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| 67 | {}
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| 68 |
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[77b350] | 69 | /** Constructor for class HomologyGraph from a keyset (i.e. from atoms in the World).
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| 70 | *
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| 71 | * @param keyset global ids of atoms to pick
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| 72 | */
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| 73 | HomologyGraph(const KeySet &keyset);
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| 74 |
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[372c912] | 75 | /** Constructor for class HomologyGraph from a IndexSet (i.e. from atoms in the World).
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| 76 | *
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| 77 | * @param index global ids of atoms to pick
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| 78 | */
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| 79 | HomologyGraph(const IndexSet &index);
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| 80 |
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[7b6b21f] | 81 | /** Destructor for class HomologyGraph.
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| 82 | *
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| 83 | */
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| 84 | ~HomologyGraph() {}
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| 85 |
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| 86 | // comparators (allows sorting and hence quicker finding in STL containers)
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| 87 | bool operator<(const HomologyGraph &graph) const;
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| 88 | bool operator>(const HomologyGraph &graph) const;
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| 89 | bool operator==(const HomologyGraph &graph) const;
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| 90 | bool operator!=(const HomologyGraph &graph) const {
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| 91 | return (!(*this == graph));
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| 92 | }
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| 93 |
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[28e203] | 94 | /** Checks whether this graph contains a specific \a node.
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| 95 | *
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| 96 | * @param node node to look for
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| 97 | * @param count how often this node must occur
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| 98 | * @return true - graph contains this node at least once, false - else
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| 99 | */
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| 100 | bool hasNode(const FragmentNode &node, const size_t count = 1) const {
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| 101 | nodes_t::const_iterator iter = nodes.find(node);
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| 102 | if (iter == nodes.end())
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| 103 | return count == 0;
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| 104 | else
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| 105 | return (iter->second == count);
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| 106 | }
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| 107 |
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| 108 | /** Checks whether this graph contains a specific \a edge.
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| 109 | *
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| 110 | * @param edge edge to look for
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| 111 | * @param count how often this edge must occur
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| 112 | * @return true - graph contains this edge at least once, false - else
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| 113 | */
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| 114 | bool hasEdge(const FragmentEdge &edge, const size_t count = 1) const {
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| 115 | edges_t::const_iterator iter = edges.find(edge);
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| 116 | if (iter == edges.end())
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| 117 | return count == 0;
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| 118 | else
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| 119 | return (iter->second == count);
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| 120 | }
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| 121 |
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[e920d3d] | 122 | /** Checks whether this graph has \b exactly \a _times nodes with \a _number
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| 123 | * atomic number.
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| 124 | *
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| 125 | * @param _number desired atomic number
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| 126 | * @param _times number this must occur
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| 127 | * @return true - graph has exactly \a _times nodes with \a _number, false - else
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| 128 | */
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| 129 | bool hasTimesAtomicNumber(const size_t _number, const size_t _times) const;
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| 130 |
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[7c1091] | 131 | /** Checks whether this graph has \b greater equal \a _times nodes with \a _number
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| 132 | * atomic number.
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| 133 | *
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| 134 | * @param _number desired atomic number
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| 135 | * @param _times number this must occur
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| 136 | * @return true - graph has greater equal \a _times nodes with \a _number, false - else
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| 137 | */
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| 138 | bool hasGreaterEqualTimesAtomicNumber(const size_t _number, const size_t _times) const;
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| 139 |
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[7b6b21f] | 140 | /** Assignment operator for class HomologyGraph.
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| 141 | *
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| 142 | * This is required to allow placement in STL container as we need to
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| 143 | * const_cast override our const member variables.
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| 144 | *
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| 145 | */
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| 146 | HomologyGraph& operator=(const HomologyGraph &graph);
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| 147 |
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[0afe00] | 148 | /** Prints the nodes in the graph to stream \a ost.
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| 149 | *
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| 150 | * \param ost stream to print to
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| 151 | */
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| 152 | void printNodes(std::ostream& ost) const;
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| 153 |
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| 154 | /** Prints the edges in the graph to stream \a ost.
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| 155 | *
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| 156 | * \param ost stream to print to
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| 157 | */
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| 158 | void printEdges(std::ostream& ost) const;
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| 159 |
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[7b6b21f] | 160 | private:
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| 161 | //!> information on the nodes of the graph
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| 162 | const nodes_t nodes;
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| 163 | //!> information on the edges of the graph
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| 164 | const edges_t edges;
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[67db80] | 165 |
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| 166 | private:
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| 167 | friend class boost::serialization::access;
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| 168 | // serialization
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| 169 | template <typename Archive>
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| 170 | void serialize(Archive& ar, const unsigned int version)
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| 171 | {
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| 172 | ar & const_cast<nodes_t &>(nodes);
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| 173 | ar & const_cast<edges_t &>(edges);
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| 174 | }
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[7b6b21f] | 175 | };
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| 176 |
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[54a561] | 177 | std::ostream& operator<<(std::ostream& ost, const HomologyGraph &graph);
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| 178 |
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[67db80] | 179 | // we need to give this class a unique key for serialization
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| 180 | BOOST_CLASS_EXPORT_KEY(HomologyGraph)
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| 181 |
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[77b350] | 182 | // define some helpers outside to allow for light-weight unit testing
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| 183 | namespace detail {
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| 184 | const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset);
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| 185 | const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset);
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[372c912] | 186 | const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset);
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| 187 | const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset);
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[77b350] | 188 | };
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| 189 |
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[7b6b21f] | 190 |
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| 191 | #endif /* HOMOLOGYGRAPH_HPP_ */
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