Make sure the DCD file handle is closed -- do it the right way in the test.

Make sure files are appropriately closed by PDBFile()

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

@@ -75,9 +75,13 @@ class PDBFile(object):
             pdb = file
         else:
             inputfile = file
+            own_handle = False
             if isinstance(file, str):
                 inputfile = open(file)
+                own_handle = True
             pdb = PdbStructure(inputfile, load_all_models=True)
+            if own_handle:
+                inputfile.close()
         PDBFile._loadNameReplacementTables()
 
         # Build the topology

wrappers/python/tests/TestDcdFile.py

@@ -12,10 +12,10 @@ class TestDCDFile(unittest.TestCase):
         fname = tempfile.mktemp(suffix='.dcd')
         pdbfile = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
         natom = len(list(pdbfile.topology.atoms()))
-        dcd = app.DCDFile(open(fname, 'wb'), pdbfile.topology, 0.001)
-        for i in range(5):
-            dcd.writeModel([mm.Vec3(random(), random(), random()) for j in range(natom)]*unit.angstroms)
-        dcd._file.close()
+        with open(fname, 'wb') as f:
+            dcd = app.DCDFile(f, pdbfile.topology, 0.001)
+            for i in range(5):
+                dcd.writeModel([mm.Vec3(random(), random(), random()) for j in range(natom)]*unit.angstroms)
         os.remove(fname)
 
 if __name__ == '__main__':