Some add-ons for potential application in the PEX context

src/db/db/db.pro

@@ -23,6 +23,7 @@ SOURCES = \
   dbCommonReader.cc \
   dbCompoundOperation.cc \
   dbEdge.cc \
+  dbEdgeNeighborhood.cc \
   dbEdgePair.cc \
   dbEdgePairFilters.cc \
   dbEdgePairRelations.cc \
@@ -119,6 +120,7 @@ SOURCES = \
   gsiDeclDbCommonStreamOptions.cc \
   gsiDeclDbCompoundOperation.cc \
   gsiDeclDbEdge.cc \
+  gsiDeclDbEdgeNeighborhood.cc \
   gsiDeclDbEdgePair.cc \
   gsiDeclDbEdgePairs.cc \
   gsiDeclDbEdgeProcessor.cc \
@@ -249,6 +251,7 @@ HEADERS = \
   dbCommonReader.h \
   dbCompoundOperation.h \
   dbEdge.h \
+  dbEdgeNeighborhood.h \
   dbEdgePair.h \
   dbEdgePairFilters.h \
   dbEdgePairRelations.h \

src/db/db/dbCompoundOperation.h

@@ -266,6 +266,7 @@ class DB_PUBLIC CompoundRegionOperationNode
   virtual db::Coord computed_dist () const = 0;
 
   virtual std::string generated_description () const;
+  virtual bool wants_caching () const { return true; }
 
 private:
   std::string m_description;
@@ -276,23 +277,32 @@ class DB_PUBLIC CompoundRegionOperationNode
   {
     //  TODO: confine caching to those nodes which need it.
 
-    std::pair<bool, std::vector<std::unordered_set<TR> > *> cp = cache->get<TR> (this);
+    if (wants_caching ()) {
 
-    if (! cp.first) {
+      std::pair<bool, std::vector<std::unordered_set<TR> > *> cp = cache->get<TR> (this);
 
-      std::vector<std::unordered_set<TR> > uncached_results;
-      uncached_results.resize (results.size ());
+      if (! cp.first) {
 
-      do_compute_local (cache, layout, cell, interactions, uncached_results, proc);
+        std::vector<std::unordered_set<TR> > uncached_results;
+        uncached_results.resize (results.size ());
 
-      cp.second->swap (uncached_results);
+        do_compute_local (cache, layout, cell, interactions, uncached_results, proc);
 
-    }
+        cp.second->swap (uncached_results);
+
+      }
+
+      tl_assert (results.size () == cp.second->size ());
+      for (size_t r = 0; r < results.size (); ++r) {
+        results[r].insert ((*cp.second)[r].begin (), (*cp.second)[r].end ());
+      }
+
+    } else {
+
+      do_compute_local (cache, layout, cell, interactions, results, proc);
 
-    tl_assert (results.size () == cp.second->size ());
-    for (size_t r = 0; r < results.size (); ++r) {
-      results[r].insert ((*cp.second)[r].begin (), (*cp.second)[r].end ());
     }
+
   }
 };