Changeset f5ea10 for src


Ignore:
Timestamp:
Jun 22, 2018, 7:26:09 AM (7 years ago)
Author:
Frederik Heber <frederik.heber@…>
Branches:
Candidate_v1.6.1, ChemicalSpaceEvaluator
Children:
99c705
Parents:
8d56a6
git-author:
Frederik Heber <frederik.heber@…> (09/26/17 22:30:01)
git-committer:
Frederik Heber <frederik.heber@…> (06/22/18 07:26:09)
Message:

Added Graph6Reader, extended BoostGraphCreator, added ChemicalSpaceEvaluatorAction.

  • added visible generateAllInducedSubgraphs to Extractors.
  • TESTS: due to new option "graph6" containing a digit we needed to modify moltest_check.py to also scan for digits and not just letters.
  • DOCU: Added evaluate-chemical-space to userguide.
Location:
src
Files:
5 added
7 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/GlobalListOfActions.hpp

    r8d56a6 rf5ea10  
    7575  (GeometryPositionToVector) \
    7676  (GeometryRemove) \
     77  (GraphChemicalSpaceEvaluator) \
    7778  (GraphUpdateMolecules) \
    7879  (GraphCorrectBondDegree) \

  • src/Actions/Makefile.am

    r8d56a6 rf5ea10  
    312312
    313313GRAPHACTIONSOURCE = \
     314  Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp \
    314315  Actions/GraphAction/CorrectBondDegreeAction.cpp \
    315316  Actions/GraphAction/CreateAdjacencyAction.cpp \
    … …  
    319320  Actions/GraphAction/UpdateMoleculesAction.cpp
    320321GRAPHACTIONHEADER = \
     322  Actions/GraphAction/ChemicalSpaceEvaluatorAction.hpp \
    321323  Actions/GraphAction/CorrectBondDegreeAction.hpp \
    322324  Actions/GraphAction/CreateAdjacencyAction.hpp \
    … …  
    326328  Actions/GraphAction/UpdateMoleculesAction.hpp
    327329GRAPHACTIONDEFS = \
     330  Actions/GraphAction/ChemicalSpaceEvaluatorAction.def \
    328331  Actions/GraphAction/CorrectBondDegreeAction.def \
    329332  Actions/GraphAction/CreateAdjacencyAction.def \

  • src/FunctionApproximation/Extractors.cpp

    r8d56a6 rf5ea10  
    3434#include <config.h>
    3535#endif
    36 
    37 #include <boost/graph/adjacency_list.hpp>
    38 #include <boost/graph/breadth_first_search.hpp>
    39 #include <boost/graph/subgraph.hpp>
    4036
    4137//#include "CodePatterns/MemDebug.hpp"
    … …  
    4844#include <vector>
    4945#include <boost/assign.hpp>
    50 #include <boost/bimap.hpp>
    51 #include <boost/bimap/set_of.hpp>
    52 #include <boost/bimap/multiset_of.hpp>
    5346#include <boost/bind.hpp>
    5447#include <boost/foreach.hpp>
    … …  
    6760
    6861using namespace boost::assign;
     62
     63using namespace Extractors;
    6964
    7065FunctionModel::arguments_t
    … …  
    186181}
    187182
    188 typedef size_t level_t;
    189 typedef size_t node_t;
    190 typedef std::multimap< level_t, node_t > nodes_per_level_t;
    191 typedef std::set<node_t> nodes_t;
    192 typedef std::set<nodes_t> set_of_nodes_t;
    193 typedef boost::property_map < boost::adjacency_list <>, boost::vertex_index_t >::type index_map_t;
    194 
    195 typedef boost::bimap<
    196     boost::bimaps::set_of< size_t >,
    197     boost::bimaps::multiset_of< Extractors::ParticleType_t >
    198 > type_index_lookup_t;
    199 
    200 typedef std::set<node_t> set_type;
    201 typedef std::set<set_type> powerset_type;
    202 
    203 typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
    204     boost::no_property, boost::no_property > UndirectedGraph;
    205 typedef boost::subgraph< UndirectedGraph > UndirectedSubgraph;
    206 
    207 typedef std::map< node_t, std::pair<Extractors::ParticleType_t, size_t> > node_FragmentNode_map_t;
    208 
    209 typedef std::map< argument_t::indices_t, size_t> argument_placement_map_t;
    210 
    211 typedef std::map<size_t, size_t> argindex_to_nodeindex_t;
    212 
    213183void insertIntoNodeFragmentMap(
    214184    node_FragmentNode_map_t &_node_FragmentNode_map,
    … …  
    334304 * \param index_map with indices per \a graph' vertex
    335305 */
    336 static void generateAllInducedConnectedSubgraphs(
     306void Extractors::generateAllInducedConnectedSubgraphs(
    337307    const size_t N,
    338308    const level_t level,
    … …  
    438408}
    439409
    440 static HomologyGraph createHomologyGraphFromNodes(
     410HomologyGraph Extractors::createHomologyGraphFromNodes(
    441411    const nodes_t &nodes,
    442412    const type_index_lookup_t &type_index_lookup,
    … …  
    501471
    502472  return HomologyGraph(graph_nodes, graph_edges);
    503 }
    504 
    505 /**
    506  * I have no idea why this is so complicated with BGL ...
    507  *
    508  * This is taken from the book "The Boost Graph Library: User Guide and Reference Manual, Portable Documents",
    509  * chapter "Basic Graph Algorithms", example on calculating the bacon number.
    510  */
    511 template <typename DistanceMap>
    512 class distance_recorder : public boost::default_bfs_visitor
    513 {
    514 public:
    515   distance_recorder(DistanceMap dist) : d(dist) {}
    516 
    517   template <typename Edge, typename Graph>
    518   void tree_edge(Edge e, const Graph &g) const {
    519     typename boost::graph_traits<Graph>::vertex_descriptor u = source(e,g), v = target(e,g);
    520     d[v] = d[u] + 1;
    521   }
    522 
    523 private:
    524   DistanceMap d;
    525 };
    526 
    527 template <typename DistanceMap>
    528 distance_recorder<DistanceMap> record_distance(DistanceMap d)
    529 {
    530   return distance_recorder<DistanceMap>(d);
    531473}
    532474

  • src/FunctionApproximation/Extractors.hpp

    r8d56a6 rf5ea10  
    1414#endif
    1515
     16#include <boost/bimap.hpp>
     17#include <boost/bimap/set_of.hpp>
     18#include <boost/bimap/multiset_of.hpp>
     19#include <boost/graph/adjacency_list.hpp>
     20#include <boost/graph/breadth_first_search.hpp>
     21#include <boost/graph/subgraph.hpp>
    1622#include <boost/function.hpp>
     23
     24#include <map>
     25#include <set>
    1726
    1827#include "Fragmentation/EdgesPerFragment.hpp"
    … …  
    5160  typedef std::vector<ParticleType_t> ParticleTypes_t;
    5261
     62  typedef size_t level_t;
     63  typedef size_t node_t;
     64  typedef std::multimap< level_t, node_t > nodes_per_level_t;
     65  typedef std::set<node_t> nodes_t;
     66  typedef std::set<nodes_t> set_of_nodes_t;
     67
     68  typedef boost::bimap<
     69      boost::bimaps::set_of< size_t >,
     70      boost::bimaps::multiset_of< Extractors::ParticleType_t >
     71  > type_index_lookup_t;
     72
     73  typedef std::set<node_t> set_type;
     74  typedef std::set<set_type> powerset_type;
     75
     76  typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
     77      boost::property<boost::vertex_name_t, atomId_t>,
     78      boost::property<boost::vertex_color_t, boost::default_color_type> /* needed for limited-depth DFS,
     79      otherwise the property_map gets full size of graph */
     80      > UndirectedGraph;
     81  typedef boost::subgraph< UndirectedGraph > UndirectedSubgraph;
     82
     83  typedef boost::property_map < UndirectedGraph, boost::vertex_index_t >::type index_map_t;
     84
     85  typedef std::map< node_t, std::pair<Extractors::ParticleType_t, size_t> > node_FragmentNode_map_t;
     86
     87  typedef std::map< argument_t::indices_t, size_t> argument_placement_map_t;
     88
     89  typedef std::map<size_t, size_t> argindex_to_nodeindex_t;
     90
     91  /**
     92   * I have no idea why this is so complicated with BGL ...
     93   *
     94   * This is taken from the book "The Boost Graph Library: User Guide and Reference Manual, Portable Documents",
     95   * chapter "Basic Graph Algorithms", example on calculating the bacon number.
     96   */
     97  template <typename DistanceMap>
     98  class distance_recorder : public boost::default_bfs_visitor
     99  {
     100  public:
     101    distance_recorder(DistanceMap dist) : d(dist) {}
     102
     103    template <typename Edge, typename Graph>
     104    void tree_edge(Edge e, const Graph &g) const {
     105      typename boost::graph_traits<Graph>::vertex_descriptor u = source(e,g), v = target(e,g);
     106      d[v] = d[u] + 1;
     107    }
     108
     109  private:
     110    DistanceMap d;
     111  };
     112
     113  template <typename DistanceMap>
     114  distance_recorder<DistanceMap> record_distance(DistanceMap d)
     115  {
     116    return distance_recorder<DistanceMap>(d);
     117  }
     118
     119  HomologyGraph createHomologyGraphFromNodes(
     120      const nodes_t &nodes,
     121      const type_index_lookup_t &type_index_lookup,
     122      const UndirectedGraph &graph,
     123      const index_map_t &index_map
     124      );
     125
     126  void generateAllInducedConnectedSubgraphs(
     127      const size_t N,
     128      const level_t level,
     129      const nodes_t &nodes,
     130      set_of_nodes_t &set_of_nodes,
     131      const nodes_per_level_t &nodes_per_level,
     132      const UndirectedGraph &graph,
     133      const std::vector<size_t> &_distance,
     134      const index_map_t &index_map);
     135
    53136  /** Namespace for some internal helper functions.
    54137   *

  • src/Graph/BoostGraphCreator.cpp

    r8d56a6 rf5ea10  
    4343
    4444#include "Atom/atom.hpp"
     45#include "Graph/Graph6Reader.hpp"
    4546#include "molecule.hpp"
    4647
    … …  
    9495}
    9596
     97void BoostGraphCreator::createFromGraph6String(
     98    const std::string &_graph_string)
     99{
     100  Graph6Reader reader;
     101  {
     102    std::stringstream inputstream(_graph_string);
     103    reader(inputstream);
     104  }
     105
     106  graph = UndirectedGraph();
     107
     108  // add nodes
     109  for(int numbers = 0; numbers < reader.get_num_nodes(); ++numbers) {
     110    const atomId_t atomid = numbers;
     111    Vertex v = boost::add_vertex(atomid, graph);
     112    const atomId_t vertexname = boost::get(boost::get(boost::vertex_name, graph), v);
     113    const nodeId_t vertexindex = boost::get(boost::get(boost::vertex_index, graph), v);
     114    LOG(2, "DEBUG: Adding node " << vertexindex << " associated to atom #" << vertexname);
     115    ASSERT( vertexname == atomid,
     116        "BoostGraphCreator::createFromRange() - atomid "+toString(atomid)
     117        +" is not name of vertex "+toString(vertexname)+".");
     118    atomids_nodeids.insert( std::make_pair(vertexname, vertexindex) );
     119  }
     120
     121  // add edges
     122  const Graph6Reader::edges_t &edges = reader.get_edges();
     123  for(Graph6Reader::edges_t::const_iterator iter = edges.begin();
     124      iter != edges.end(); ++iter) {
     125    // graph6 contains only upper triangle of adjacency matrix, hence add only once
     126    const nodeId_t leftnodeid = iter->first;
     127    const nodeId_t rightnodeid = iter->second;
     128    boost::add_edge(leftnodeid, rightnodeid, graph);
     129  }
     130}
     131
    96132BoostGraphCreator::nodeId_t BoostGraphCreator::getNodeId(
    97133    const atomId_t &_atomid) const

  • src/Graph/BoostGraphCreator.hpp

    r8d56a6 rf5ea10  
    9090      const predicate_t &_pred);
    9191
     92  /** Creates the boost::graph from the defining graph6 string where the atom
     93   * nodes map is simply the identity.
     94   *
     95   * \param _graph_string graph6 string defining the graph
     96   */
     97  void createFromGraph6String(
     98      const std::string &_graph_string);
     99
    92100  /** Getter for the created graph.
    93101   *

  • src/Graph/Makefile.am

    r8d56a6 rf5ea10  
    1010        Graph/ConnectedSubgraph.cpp \
    1111        Graph/CyclicStructureAnalysis.cpp \
    12         Graph/DepthFirstSearchAnalysis.cpp
    13                                  
     12        Graph/DepthFirstSearchAnalysis.cpp \
     13        Graph/Graph6Reader.cpp
     14
    1415GRAPHHEADER = \
    1516        Graph/AdjacencyList.hpp \
    … …  
    2324        Graph/CyclicStructureAnalysis.hpp \
    2425        Graph/DepthFirstSearchAnalysis.hpp \
     26        Graph/Graph6Reader.hpp \
    2527        Graph/ListOfLocalAtoms.hpp
    2628
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