Changeset d83d64 for src

Timestamp:

Jun 21, 2018, 9:12:08 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Children:

a951f3

Parents:

8d56a6

git-author:

Frederik Heber <frederik.heber@…> (09/26/17 22:30:01)

git-committer:

Frederik Heber <frederik.heber@…> (06/21/18 09:12:08)

Message:

Added Graph6Reader, extended BoostGraphCreator, added ChemicalSpaceEvaluatorAction.

• 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.

Location:

src

Files:

• Actions/GlobalListOfActions.hpp (modified) (1 diff)
• Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (added)
• Actions/GraphAction/ChemicalSpaceEvaluatorAction.def (added)
• Actions/GraphAction/ChemicalSpaceEvaluatorAction.hpp (added)
• Actions/Makefile.am (modified) (3 diffs)
• FunctionApproximation/Extractors.cpp (modified) (5 diffs)
• FunctionApproximation/Extractors.hpp (modified) (1 diff)
• Graph/BoostGraphCreator.cpp (modified) (2 diffs)
• Graph/BoostGraphCreator.hpp (modified) (1 diff)
• Graph/Graph6Reader.cpp (added)
• Graph/Graph6Reader.hpp (added)
• Graph/Makefile.am (modified) (2 diffs)

src/Actions/GlobalListOfActions.hpp

@@ -75 +75 @@
   (GeometryPositionToVector) \
   (GeometryRemove) \
+  (GraphChemicalSpaceEvaluator) \
   (GraphUpdateMolecules) \
   (GraphCorrectBondDegree) \

src/Actions/Makefile.am

@@ -312 +312 @@
 
 GRAPHACTIONSOURCE = \
+  Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp \
   Actions/GraphAction/CorrectBondDegreeAction.cpp \
   Actions/GraphAction/CreateAdjacencyAction.cpp \
@@ -319 +320 @@
   Actions/GraphAction/UpdateMoleculesAction.cpp
 GRAPHACTIONHEADER = \
+  Actions/GraphAction/ChemicalSpaceEvaluatorAction.hpp \
   Actions/GraphAction/CorrectBondDegreeAction.hpp \
   Actions/GraphAction/CreateAdjacencyAction.hpp \
@@ -326 +328 @@
   Actions/GraphAction/UpdateMoleculesAction.hpp
 GRAPHACTIONDEFS = \
+  Actions/GraphAction/ChemicalSpaceEvaluatorAction.def \
   Actions/GraphAction/CorrectBondDegreeAction.def \
   Actions/GraphAction/CreateAdjacencyAction.def \

src/FunctionApproximation/Extractors.cpp

@@ -67 +67 @@
 
 using namespace boost::assign;
+
+using namespace Extractors;
 
 FunctionModel::arguments_t
@@ -186 +188 @@
 }
 
-typedef size_t level_t;
-typedef size_t node_t;
-typedef std::multimap< level_t, node_t > nodes_per_level_t;
-typedef std::set<node_t> nodes_t;
-typedef std::set<nodes_t> set_of_nodes_t;
-typedef boost::property_map < boost::adjacency_list <>, boost::vertex_index_t >::type index_map_t;
-
-typedef boost::bimap<
-    boost::bimaps::set_of< size_t >,
-    boost::bimaps::multiset_of< Extractors::ParticleType_t >
-> type_index_lookup_t;
-
-typedef std::set<node_t> set_type;
-typedef std::set<set_type> powerset_type;
-
-typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
-    boost::no_property, boost::no_property > UndirectedGraph;
-typedef boost::subgraph< UndirectedGraph > UndirectedSubgraph;
-
-typedef std::map< node_t, std::pair<Extractors::ParticleType_t, size_t> > node_FragmentNode_map_t;
-
-typedef std::map< argument_t::indices_t, size_t> argument_placement_map_t;
-
-typedef std::map<size_t, size_t> argindex_to_nodeindex_t;
-
 void insertIntoNodeFragmentMap(
     node_FragmentNode_map_t &_node_FragmentNode_map,
@@ -334 +311 @@
  * \param index_map with indices per \a graph' vertex
  */
-static void generateAllInducedConnectedSubgraphs(
+void generateAllInducedConnectedSubgraphs(
     const size_t N,
     const level_t level,
@@ -438 +415 @@
 }
 
-static HomologyGraph createHomologyGraphFromNodes(
+HomologyGraph createHomologyGraphFromNodes(
     const nodes_t &nodes,
     const type_index_lookup_t &type_index_lookup,
@@ -501 +478 @@
 
   return HomologyGraph(graph_nodes, graph_edges);
-}
-
-/**
- * I have no idea why this is so complicated with BGL ...
- *
- * This is taken from the book "The Boost Graph Library: User Guide and Reference Manual, Portable Documents",
- * chapter "Basic Graph Algorithms", example on calculating the bacon number.
- */
-template <typename DistanceMap>
-class distance_recorder : public boost::default_bfs_visitor
-{
-public:
-  distance_recorder(DistanceMap dist) : d(dist) {}
-
-  template <typename Edge, typename Graph>
-  void tree_edge(Edge e, const Graph &g) const {
-    typename boost::graph_traits<Graph>::vertex_descriptor u = source(e,g), v = target(e,g);
-    d[v] = d[u] + 1;
-  }
-
-private:
-  DistanceMap d;
-};
-
-template <typename DistanceMap>
-distance_recorder<DistanceMap> record_distance(DistanceMap d)
-{
-  return distance_recorder<DistanceMap>(d);
 }
 

src/FunctionApproximation/Extractors.hpp

@@ -51 +51 @@
   typedef std::vector<ParticleType_t> ParticleTypes_t;
 
+  typedef size_t level_t;
+  typedef size_t node_t;
+  typedef std::multimap< level_t, node_t > nodes_per_level_t;
+  typedef std::set<node_t> nodes_t;
+  typedef std::set<nodes_t> set_of_nodes_t;
+  typedef boost::property_map < boost::adjacency_list <>, boost::vertex_index_t >::type index_map_t;
+
+  typedef boost::bimap<
+      boost::bimaps::set_of< size_t >,
+      boost::bimaps::multiset_of< Extractors::ParticleType_t >
+  > type_index_lookup_t;
+
+  typedef std::set<node_t> set_type;
+  typedef std::set<set_type> powerset_type;
+
+  typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
+      boost::no_property, boost::no_property > UndirectedGraph;
+  typedef boost::subgraph< UndirectedGraph > UndirectedSubgraph;
+
+  typedef std::map< node_t, std::pair<Extractors::ParticleType_t, size_t> > node_FragmentNode_map_t;
+
+  typedef std::map< argument_t::indices_t, size_t> argument_placement_map_t;
+
+  typedef std::map<size_t, size_t> argindex_to_nodeindex_t;
+
+  /**
+   * I have no idea why this is so complicated with BGL ...
+   *
+   * This is taken from the book "The Boost Graph Library: User Guide and Reference Manual, Portable Documents",
+   * chapter "Basic Graph Algorithms", example on calculating the bacon number.
+   */
+  template <typename DistanceMap>
+  class distance_recorder : public boost::default_bfs_visitor
+  {
+  public:
+    distance_recorder(DistanceMap dist) : d(dist) {}
+
+    template <typename Edge, typename Graph>
+    void tree_edge(Edge e, const Graph &g) const {
+      typename boost::graph_traits<Graph>::vertex_descriptor u = source(e,g), v = target(e,g);
+      d[v] = d[u] + 1;
+    }
+
+  private:
+    DistanceMap d;
+  };
+
+  template <typename DistanceMap>
+  distance_recorder<DistanceMap> record_distance(DistanceMap d)
+  {
+    return distance_recorder<DistanceMap>(d);
+  }
+
+  HomologyGraph createHomologyGraphFromNodes(
+      const nodes_t &nodes,
+      const type_index_lookup_t &type_index_lookup,
+      const UndirectedGraph &graph,
+      const index_map_t &index_map
+      );
+
+  void generateAllInducedConnectedSubgraphs(
+      const size_t N,
+      const level_t level,
+      const nodes_t &nodes,
+      set_of_nodes_t &set_of_nodes,
+      const nodes_per_level_t &nodes_per_level,
+      const UndirectedGraph &graph,
+      const std::vector<size_t> &_distance,
+      const index_map_t &index_map);
+
   /** Namespace for some internal helper functions.
    *

src/Graph/BoostGraphCreator.cpp

@@ -43 +43 @@
 
 #include "Atom/atom.hpp"
+#include "Graph/Graph6Reader.hpp"
 #include "molecule.hpp"
 
@@ -94 +95 @@
 }
 
+void BoostGraphCreator::createFromGraph6String(
+    const std::string &_graph_string)
+{
+  Graph6Reader reader;
+  {
+    std::stringstream inputstream(_graph_string);
+    reader(inputstream);
+  }
+
+  graph = UndirectedGraph();
+
+  // add nodes
+  for(int numbers = 0; numbers < reader.get_num_nodes(); ++numbers) {
+    const atomId_t atomid = numbers;
+    Vertex v = boost::add_vertex(atomid, graph);
+    const atomId_t vertexname = boost::get(boost::get(boost::vertex_name, graph), v);
+    const nodeId_t vertexindex = boost::get(boost::get(boost::vertex_index, graph), v);
+    LOG(2, "DEBUG: Adding node " << vertexindex << " associated to atom #" << vertexname);
+    ASSERT( vertexname == atomid,
+        "BoostGraphCreator::createFromRange() - atomid "+toString(atomid)
+        +" is not name of vertex "+toString(vertexname)+".");
+    atomids_nodeids.insert( std::make_pair(vertexname, vertexindex) );
+  }
+
+  // add edges
+  const Graph6Reader::edges_t &edges = reader.get_edges();
+  for(Graph6Reader::edges_t::const_iterator iter = edges.begin();
+      iter != edges.end(); ++iter) {
+    // graph6 contains only upper triangle of adjacency matrix, hence add only once
+    const nodeId_t leftnodeid = iter->first;
+    const nodeId_t rightnodeid = iter->second;
+    boost::add_edge(leftnodeid, rightnodeid, graph);
+  }
+}
+
 BoostGraphCreator::nodeId_t BoostGraphCreator::getNodeId(
     const atomId_t &_atomid) const

src/Graph/BoostGraphCreator.hpp

@@ -90 +90 @@
       const predicate_t &_pred);
 
+  /** Creates the boost::graph from the defining graph6 string where the atom
+   * nodes map is simply the identity.
+   *
+   * \param _graph_string graph6 string defining the graph
+   */
+  void createFromGraph6String(
+      const std::string &_graph_string);
+
   /** Getter for the created graph.
    *

src/Graph/Makefile.am

@@ -10 +10 @@
         Graph/ConnectedSubgraph.cpp \
         Graph/CyclicStructureAnalysis.cpp \
-        Graph/DepthFirstSearchAnalysis.cpp
-                                  
+        Graph/DepthFirstSearchAnalysis.cpp \
+        Graph/Graph6Reader.cpp
+
 GRAPHHEADER = \
         Graph/AdjacencyList.hpp \
@@ -23 +24 @@
         Graph/CyclicStructureAnalysis.hpp \
         Graph/DepthFirstSearchAnalysis.hpp \
+        Graph/Graph6Reader.hpp \
         Graph/ListOfLocalAtoms.hpp