Fix up Residue assignment in CharmmPsfFile Topology

Also fixes the test case.  Everything should pass now.

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

@@ -612,13 +612,13 @@ class CharmmPsfFile(object):
         last_residue = None
         # Add each chain (separate 'system's) and residue
         for atom in self.atom_list:
+            resid = '%d%s' % (atom.residue.idx, atom.residue.inscode)
             if atom.system != last_chain:
                 chain = topology.addChain(atom.system)
                 last_chain = atom.system
-            if atom.residue.idx != last_residue:
-                last_residue = atom.residue.idx
-                residue = topology.addResidue(atom.residue.resname, chain,
-                                              str(atom.residue.idx))
+            if resid != last_residue:
+                last_residue = resid
+                residue = topology.addResidue(atom.residue.resname, chain, resid)
             if atom.type is not None:
                 # This is the most reliable way of determining the element
                 atomic_num = atom.type.atomic_number

wrappers/python/tests/TestCharmmFiles.py

@@ -120,7 +120,7 @@ class TestCharmmFiles(unittest.TestCase):
         psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf')
         self.assertEqual(len(list(psf.topology.atoms())), 66264)
         self.assertEqual(len(list(psf.topology.residues())), 20169)
-        self.assertEqual(len(list(psf.bonds())), 46634)
+        self.assertEqual(len(list(psf.topology.bonds())), 46634)
 
     def test_ImplicitSolventForces(self):
         """Compute forces for different implicit solvent types, and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""