Bugfixes in Residue bond accessors and ForceField.createSystem()

wrappers/python/simtk/openmm/app/forcefield.py

@@ -581,7 +581,7 @@ class ForceField(object):
                 if matches is None:
                     # No existing templates match.  Try any registered residue template generators.
                     for generator in self._templateGenerators:
-                        if generator(forcefield, res):
+                        if generator(self, res):
                             # This generator has registered a new residue template that should match.
                             [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
                             if matches is None:

wrappers/python/simtk/openmm/app/topology.py

@@ -373,17 +373,17 @@ class Residue(object):
 
     def bonds(self):
         """Iterate over all Bonds involving any atom in this residue."""
-        bonds = [ bond for bond in residue.chain.topology.bonds() if ((bond[0] in self._atoms) or (bond[1] in self._atoms)) ]
+        bonds = [ bond for bond in self.chain.topology.bonds() if ((bond[0] in self._atoms) or (bond[1] in self._atoms)) ]
         return iter(bonds)
 
     def internal_bonds(self):
         """Iterate over all internal Bonds."""
-        bonds = [ bond for bond in residue.chain.topology.bonds() if ((bond[0] in self._atoms) and (bond[1] in self._atoms)) ]
+        bonds = [ bond for bond in self.chain.topology.bonds() if ((bond[0] in self._atoms) and (bond[1] in self._atoms)) ]
         return iter(bonds)
 
     def external_bonds(self):
         """Iterate over all Bonds to external atoms."""
-        bonds = [ bond for bond in residue.chain.topology.bonds() if ((bond[0] in self._atoms) != (bond[1] in self._atoms)) ]
+        bonds = [ bond for bond in self.chain.topology.bonds() if ((bond[0] in self._atoms) != (bond[1] in self._atoms)) ]
         return iter(bonds)
 
     def __len__(self):