Changeset 6e5907 for src/Graph/BoostGraphCreator.cpp

Timestamp:

Jul 5, 2017, 7:40:48 PM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

ForceAnnealing_oldresults, IndependentFragmentGrids_IntegrationTest

Children:

89235ea

Parents:

6afd46

git-author:

Frederik Heber <frederik.heber@…> (05/18/17 17:45:47)

git-committer:

Frederik Heber <frederik.heber@…> (07/05/17 19:40:48)

Message:

Extracted extraction (subset of) nodes from BoostGraph into BreadthFirstSearchGatherer.

• also added helper namespace BoostGraphHelpers.
• we now treat the vertex indices and vertex names properly. Before that they had to coincide. Now, the name is the atomic id associated with the node and the index is the boost::graph internal index.

File:

• src/Graph/BoostGraphCreator.cpp (modified) (3 diffs)

src/Graph/BoostGraphCreator.cpp

@@ -85 +85 @@
       std::back_inserter(atomids), getAtomId);
   ASSERT( _atoms.size() == atomids.size(),
-      "BoostGraphCreator::createFromAtom() - atomids and atoms differ in size?");
+      "BoostGraphCreator::createFromAtom() - atomids "
+      +toString(atomids.size())+" and atoms "+toString(_atoms.size())
+      +" differ in size?");
   std::sort(atomids.begin(), atomids.end());
   const predicate_t predicate = boost::bind(inSetPredicate, boost::ref(atomids), _1);
@@ -95 +97 @@
 }
 
+BoostGraphCreator::nodeId_t BoostGraphCreator::getNodeId(
+    const atomId_t &_atomid) const
+{
+  atomids_nodeids_t::const_iterator iter =
+      atomids_nodeids.find(_atomid);
+  return (iter == atomids_nodeids.end()) ? (nodeId_t)-1 : iter->second;
+}
+
 template <typename iterator>
 void BoostGraphCreator::createFromRange(
@@ -101 +111 @@
     const size_t &_no_nodes,
     const predicate_t &_pred
-    ) {
-  // convert BondGraph into boost::graph
-  UndirectedGraph molgraph(_no_nodes);
+    )
+{
+  graph = UndirectedGraph();
+
+  // add vertices
   for(iterator iter = _begin; iter != _end; ++iter) {
-    LOG(2, "DEBUG: Looking at node " << (*iter)->getId());
+    const atomId_t atomid = (*iter)->getId();
+    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
+  for(iterator iter = _begin; iter != _end; ++iter) {
+    LOG(2, "DEBUG: Looking at atom " << (*iter)->getId());
     const BondList& ListOfBonds = (*iter)->getListOfBonds();
     for(BondList::const_iterator bonditer = ListOfBonds.begin();
         bonditer != ListOfBonds.end(); ++bonditer) {
+      LOG(2, "DEBUG: Looking at bond " << *(*bonditer));
       const atomId_t leftid = (*bonditer)->leftatom->getId();
+      const nodeId_t leftnodeid = getNodeId(leftid);
       const atomId_t rightid = (*bonditer)->rightatom->getId();
+      const nodeId_t rightnodeid = getNodeId(rightid);
       // only pick each bond once and evaluate predicate
       if ((leftid == (*iter)->getId())
           && (_pred(**bonditer))) {
-        LOG(3, "DEBUG: ADDING edge " << leftid << " <-> " << rightid);
-        boost::add_edge(leftid, rightid, graph);
+        LOG(3, "DEBUG: ADDING edge " << leftnodeid << " <-> " << rightnodeid);
+        boost::add_edge(leftnodeid, rightnodeid, graph);
       } else {
-        LOG(3, "DEBUG: Discarding edge " << leftid << " <-> " << rightid);
+        LOG(3, "DEBUG: Discarding edge " << leftnodeid << " <-> " << rightnodeid);
       }
     }