Changeset 8a2398

Timestamp:

Sep 1, 2016, 2:11:53 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Gui_Fixes

Children:

622f71

Parents:

85056e

Message:

FIX: HomologyGraph's getNodeFromSet() and getEdgesFromSet ignored saturation hydrogens.

• we need to add hydrogen bonds times bond degree for every non-member encountered in the bond list in both edges and hydrogens. Otherwise, we get HomologyGraphs such as "[Z6,E0]" instead of "4x[Z1,E1], 1x[Z6,E4]" for a CH4 fragment.
• this came up when we tried to fit a CH morse potential for the larger bio molecule 1KDF.

Location:

src

Files:

• Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (1 diff)
• Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -306 +306 @@
   const IndexSetContainer::Container_t &Indices = shortrangeresults.getContainer();
   const IndexSetContainer::Container_t &ForceIndices = ForceContainer->getContainer();
+  ASSERT( Indices.size() == ForceIndices.size(),
+      "appendToHomologies() - Indices ("+toString(Indices.size())
+      +") and ForceIndices ("+toString(ForceIndices.size())+") sizes differ.");
   IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
   IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -52 +52 @@
 // in all the cludder of World, atom, molecule, and so on ...
 
+template <typename S, typename U>
+void addNodeToMap(S &_map,  std::pair< U, size_t> _pair) {
+  std::pair<typename S::iterator,bool> inserter =
+      _map.insert( _pair );
+  if (!inserter.second)
+    inserter.first->second += _pair.second;
+}
+
 template <typename T>
 const HomologyGraph::nodes_t getNodesFromSet(const std::set<T> &keyset)
@@ -69 +77 @@
         if (keyset.count(OtherWalker->getId()))
           ++NoBonds;
+        else {
+          // add as many bonds as saturation hydrogens
+          NoBonds += (*bonditer)->getDegree();
+          // add a saturation node for each, too
+//          LOG(1, "DEBUG: Adding saturation node " << *Walker << ".");
+          addNodeToMap(nodes, std::make_pair(FragmentNode(1, 1), (size_t)1) );
+        }
       }
-//      LOG(2, "DEBUG: Adding node " << Walker->getId() << " with element "
+//      LOG(1, "DEBUG: Adding node " << *Walker << " with element "
 //          << Walker->getElementNo() << " and " << NoBonds << " bonds.");
-    std::pair<HomologyGraph::nodes_t::iterator,bool> inserter =
-        nodes.insert( std::make_pair(FragmentNode(Walker->getElementNo(), NoBonds), (size_t)1) );
-    if (!inserter.second)
-      inserter.first->second += (size_t)1;
+      addNodeToMap(nodes, std::make_pair(FragmentNode(Walker->getElementNo(), NoBonds), (size_t)1) );
     } else {
       ELOG(3, "Skipping id " << *iter << ", is not associated with any atom.");
@@ -97 +109 @@
           bonditer != ListOfBonds.end(); ++bonditer) {
         const atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker);
-//        LOG(2, "DEBUG: Neighbor is " << OtherWalker->getId() << ".");
-        if ((keyset.count(OtherWalker->getId())) && (Walker->getId() < OtherWalker->getId())) {
-//          LOG(1, "DEBUG: Adding edge " << Walker->getId() << " and " << OtherWalker->getId() << ".");
-          std::pair<HomologyGraph::edges_t::iterator,bool> inserter =
-              edges.insert( std::make_pair(FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()), (size_t)1) );
-          if (!inserter.second)
-            inserter.first->second += (size_t)1;
+//        LOG(1, "DEBUG: Neighbor is " << OtherWalker->getId() << ".");
+        if (keyset.count(OtherWalker->getId())) {
+          if (Walker->getId() < OtherWalker->getId()) {
+//            LOG(1, "DEBUG: Adding edge " << Walker->getId() << " and " << OtherWalker->getId() << ".");
+            addNodeToMap(edges, std::make_pair(FragmentEdge( Walker->getElementNo(), OtherWalker->getElementNo()), (size_t)1) );
+          }
+        } else { // also add edge for each saturation hydrogen
+          const size_t bonddegree = (*bonditer)->getDegree();
+//          LOG(1, "DEBUG: Adding " << bonddegree << " saturation edge(s) " << Walker->getId() << " and " << OtherWalker->getId() << ".");
+          addNodeToMap(edges, std::make_pair(FragmentEdge( Walker->getElementNo(), 1), bonddegree) );
         }
       }