Changeset f5ea10 for src/Graph

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/Graph

Files:

• BoostGraphCreator.cpp (modified) (2 diffs)
• BoostGraphCreator.hpp (modified) (1 diff)
• Graph6Reader.cpp (added)
• Graph6Reader.hpp (added)
• Makefile.am (modified) (2 diffs)

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