Merge pull request #625 from jchodera/master

Don't add self exceptions to bond graph exceptions

parmed/openmm/topsystem.py

@@ -392,10 +392,12 @@ def _process_nonbonded(struct, force):
     bond_graph_exceptions = defaultdict(set)
     for atom in struct.atoms:
         for a2 in atom.bond_partners:
-            bond_graph_exceptions[atom].add(a2)
+            if atom is not a2:
+                bond_graph_exceptions[atom].add(a2)
             for a3 in a2.bond_partners:
                 if a3 is atom: continue
-                bond_graph_exceptions[atom].add(a3)
+                if atom is not a3:
+                    bond_graph_exceptions[atom].add(a3)
 
     # TODO should we compress exception types?
     for ii in range(force.getNumExceptions()):