Changeset 1be100

Timestamp:

Apr 23, 2021, 8:51:43 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

9171d8

Parents:

d951a5

git-author:

Frederik Heber <frederik.heber@…> (03/27/21 16:54:08)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:51:43)

Message:

FIX: Several small errors in Graph6Reader.

• off-by-one error with encoding starts at 63 (0), not 64.
• cur_byte needs to exist outside of scope of next_edge().
• need a mapping from edges_by_vertices in the subgraph (with indices from the subgraph vertices) to the edge index used in th degrees array to properly calculate the bond degrees.
• TESTS: Added a chemical space evaluator test case with 3 nodes.

Files:

• src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) (10 diffs)
• src/Graph/Graph6Reader.cpp (modified) (4 diffs)
• src/Graph/Graph6Reader.hpp (modified) (2 diffs)
• tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at (modified) (1 diff)

src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp

@@ -142 +142 @@
 {
   const BoostGraphCreator::Vertex u = source(e, graph);
-  const BoostGraphCreator::Vertex v = source(e, graph);
+  const BoostGraphCreator::Vertex v = target(e, graph);
   return getEdgeByVertices(u,v);
 }
@@ -204 +204 @@
     for (boost::tie(i, end) = boost::out_edges(v, graph); i != end; ++i) {
       const BoostGraphCreator::Edge &e = *i;
-      const BoostGraphCreator::Vertex e1 = source(e, graph);
-      const BoostGraphCreator::Vertex e2 = target(e, graph);
-      const edge_by_vertices_t edge_by_vertices = getEdgeByVertices(e1,e2);
+      const edge_by_vertices_t edge_by_vertices = getEdgeVerticesByEdge(e, graph);
       LOG(3, "DEBUG: Current edge is (" << edge_by_vertices << ")");
       const size_t index = getElementFromMap<edge_index_t, edge_by_vertices_t>(
@@ -231 +229 @@
       std::pair<BoostGraphCreator::Edge, bool> edge_inserter =
           boost::add_edge(v, h, newgraph.saturated_graph);
+      ASSERT( edge_inserter.second,
+          "Failed to insert hydrogen into saturation graph.");
     }
     LOG(2, "DEBUG: Added " << (max_valence - total_valence)
@@ -242 +242 @@
 BoostGraphCreator::UndirectedGraph extractSubgraph(
     const graph_t &_graph,
-    const Extractors::nodes_t &nodes)
+    const Extractors::nodes_t &nodes,
+    const edge_index_t &_edge_index,
+    edge_index_t &_subgraph_edge_index)
 {
   BoostGraphCreator::UndirectedGraph subgraph;
   const Extractors::index_map_t index_map = boost::get(boost::vertex_index, _graph);
+  typedef std::map<Extractors::node_t, BoostGraphCreator::Vertex> graph_index_to_subgraph_vertex_t;
+  graph_index_to_subgraph_vertex_t graph_index_to_subgraph_vertex;
 
   // add nodes
   BoostGraphCreator::vertex_iter viter, vend;
   for (boost::tie(viter, vend) = boost::vertices(_graph); viter != vend; ++viter) {
-    const size_t nodeid = boost::get(index_map, *viter);
+    const Extractors::node_t nodeid = boost::get(index_map, *viter);
     if (nodes.find(nodeid) != nodes.end()) {
-      boost::add_vertex(*viter, subgraph);
+      const BoostGraphCreator::Vertex vnew = boost::add_vertex(*viter, subgraph);
+      graph_index_to_subgraph_vertex.insert( std::make_pair(nodeid, vnew) );
       LOG(4, "DEBUG: Adding node " << *viter << " to subgraph.");
     }
   }
+  const Extractors::index_map_t subgraph_index_map = boost::get(boost::vertex_index, subgraph);
 
   // add edges
@@ -264 +270 @@
       const Extractors::node_t sourceindex = boost::get(index_map, boost::source(*i, _graph));
       const Extractors::node_t targetindex = boost::get(index_map, boost::target(*i, _graph));
+      // we need to translate the vertex index from graph to subgraph
+      const Extractors::node_t subsourceindex = boost::get(
+          subgraph_index_map, graph_index_to_subgraph_vertex[sourceindex]);
+      const Extractors::node_t subtargetindex = boost::get(
+          subgraph_index_map, graph_index_to_subgraph_vertex[targetindex]);
       if ((nodes.find(sourceindex) != nodes.end()) && (nodes.find(targetindex) != nodes.end())
           && (sourceindex < targetindex)) {
-        boost::add_edge(sourceindex, targetindex, subgraph);
-        LOG(4, "DEBUG: Adding edge " << sourceindex << "<->" << targetindex << " to subgraph.");
+        // and we need to translate the edge index from the graph to the subgraph
+        const std::pair<BoostGraphCreator::Edge, bool> newedgeinserter =
+            boost::add_edge(subsourceindex, subtargetindex, subgraph);
+        ASSERT( newedgeinserter.second,
+            "extractSubgraph() - could not insert edge "+toString(subsourceindex)+"<->"
+            +toString(subtargetindex)+".");
+        const edge_by_vertices_t edge_by_vertices = getEdgeVerticesByEdge(*i, _graph);
+        const edge_index_t::const_iterator edgeiter = _edge_index.find(edge_by_vertices);
+        ASSERT( edgeiter != _edge_index.end(),
+            "extractSubgraph() - could not find edge "+toString(edge_by_vertices)+" in edge_index map." );
+        const edge_by_vertices_t subgraph_edge_by_vertices =
+            getEdgeVerticesByEdge(newedgeinserter.first, subgraph);
+        _subgraph_edge_index.insert( std::make_pair(subgraph_edge_by_vertices, edgeiter->second) );
+        LOG(4, "DEBUG: Adding edge " << sourceindex << "<->" << targetindex
+            << " in graph to subgraph as edge " << subsourceindex << "<->" << subtargetindex << ".");
       }
     }
@@ -412 +436 @@
   }
 
-  typedef std::vector<
-      std::pair<
-          BoostGraphCreator::UndirectedGraph,
-          degrees_t> > graphs_with_degrees_t;
-
   // 6. for every combination saturate fragments for lookup and energy contribution summation
+  size_t num_admissible = 0;
   const HomologyContainer &container = World::getInstance().getHomologies();
   for (list_of_edge_degrees_t::const_iterator degrees_iter = list_of_edge_degrees.begin();
@@ -436 +456 @@
       continue;
     } else {
+      ++num_admissible;
       LOG(2, "DEBUG: The degree combination is admissable.");
     }
@@ -452 +473 @@
 
       // create subgraph
-      Extractors::UndirectedGraph newgraph = extractSubgraph(graph, current_nodes);
+      edge_index_t subgraph_edge_index;
+      Extractors::UndirectedGraph newgraph = extractSubgraph(
+          graph, current_nodes, edge_index, subgraph_edge_index);
 
       const BoostGraphCreator::name_map_t new_name_map =
@@ -469 +492 @@
       SaturatedGraph fragmentgraph =
           saturateGraph(newgraph, new_name_map,
-              type_index_lookup, type_valence_map, edge_index,
+              type_index_lookup, type_valence_map, subgraph_edge_index,
               edges, current_degrees);
 
@@ -514 +537 @@
     LOG(1, "The graph with degrees " << current_degrees << " has a total BOSSANOVA energy of " << total_energy);
   }
+  LOG(1, "There have been " << num_admissible << " admissible degree combinations for the given graph.");
 
   return Action::success;

src/Graph/Graph6Reader.cpp

@@ -57 +57 @@
         if (*_it <126) {
                 //6-bit encoding
-                num_nodes = *_it-64;
+                num_nodes = *_it-63;
         } else if (*_it++ == 126) {
                 unsigned int packets = 3;
@@ -66 +66 @@
                 }
                 for(unsigned int i =0; i<packets*packet_size; ++i) {
-                        unsigned char packet = (*_it++) - 64;
+                        unsigned char packet = (*_it++) - 63;
                         ASSERT(packet<=(1<<(packet_size+1)),
                                         "The input is malformed. "
@@ -84 +84 @@
 void Graph6Reader::next_edge(std::istream_iterator<unsigned char> &_it) {
   unsigned int bit = 0;
-  int cur_byte = 0;
   while(!bit && !eos) {
     if (++row==column) {
@@ -95 +94 @@
     }
     if (bit_pos<0) {
-      ASSERT((*_it >= 63) && (*_it <= 126),
+      ASSERT(_it != std::istream_iterator<unsigned char>(),
+          "Graph6Reader::next_edge() - less characters than expected in string.");
+      ASSERT((*_it >= 64) && (*_it <= 126),
           "The input contains a non-printable ascii char in the matrix encoding");
       cur_byte = (*_it) - 63;

src/Graph/Graph6Reader.hpp

@@ -44 +44 @@
     eos(false),
     bit_pos(-1),
+    cur_byte(0),
     num_nodes(0)
   {}
@@ -66 +67 @@
   bool eos;
   int bit_pos;
+  int cur_byte;
   static const int packet_size;
 

tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at

@@ -26 +26 @@
 AT_CHECK([../../molecuilder \
         --parse-homologies $file \
-        --evaluate-chemical-space --graph6 'B`' --elements C C], 0, [stdout], [stderr])
+        --evaluate-chemical-space --graph6 'A`' --elements C C], 0, [stdout], [stderr])
 AT_CHECK([fgrep "2 nodes in the fragment graph." stdout], 0, [ignore], [ignore])
 AT_CHECK([fgrep "Added 3 graph degree combinations" stdout], 0, [ignore], [ignore])
-AT_CHECK([fgrep "The graph with degrees ( 1; ) has a total energy of -78.9805" stdout], 0, [ignore], [ignore])
-AT_CHECK([fgrep "The graph with degrees ( 2; ) has a total energy of -77.7951" stdout], 0, [ignore], [ignore])
-AT_CHECK([fgrep "The graph with degrees ( 3; ) has a total energy of -38.1564" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 1; ) has a total BOSSANOVA energy of -78.9805" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 2; ) has a total BOSSANOVA energy of -77.7951" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 3; ) has a total BOSSANOVA energy of -38.1564" stdout], 0, [ignore], [ignore])
 
 AT_CLEANUP
 
+AT_SETUP([Graph - evaluate chemical space II])
+AT_KEYWORDS([graph evaluate-chemical-space graph6])
+
+file=homologies.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Graph/ChemicalSpaceEvaluator/pre/homologies_CC.dat $file], 0)
+AT_CHECK([chmod u+w $file], 0)
+AT_CHECK([../../molecuilder \
+        --parse-homologies $file \
+        --evaluate-chemical-space --graph6 'BW' --elements C C C], 0, [stdout], [stderr])
+AT_CHECK([fgrep "3 nodes in the fragment graph." stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "Added 9 graph degree combinations" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 1; 1; ) has a total BOSSANOVA energy of -117.884" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 1; 2; ) has a total BOSSANOVA energy of -116.699" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 1; 3; ) has a total BOSSANOVA energy of -77.0602" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 2; 1; ) has a total BOSSANOVA energy of -116.699" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 2; 2; ) has a total BOSSANOVA energy of -115.513" stdout], 0, [ignore], [ignore])
+AT_CHECK([fgrep "The graph with degrees ( 3; 1; ) has a total BOSSANOVA energy of -77.0602" stdout], 0, [ignore], [ignore])
+
+AT_CLEANUP