Ensuring opened files are properly closed

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

@@ -133,7 +133,8 @@ class GromacsGroFile(object):
         xyz      = []
         ln       = 0
         frame    = 0
-        for line in open(file):
+        with open(file) as grofile:
+            for line in grofile:
                 if ln == 0:
                     comms.append(line.strip())
                 elif ln == 1:

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

@@ -75,6 +75,7 @@ class PDBxFile(object):
         reader = PdbxReader(inputFile)
         data = []
         reader.read(data)
+        inputFile.close()
         block = data[0]
 
         # Build the topology.

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -293,7 +293,8 @@ class TestAmberPrmtopFile(unittest.TestCase):
             context = Context(system, integrator, Platform.getPlatformByName("Reference"))
             context.setPositions(pdb.positions)
             state1 = context.getState(getForces=True)
-            state2 = XmlSerializer.deserialize(open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml').read())
+            with open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml') as infile:
+                state2 = XmlSerializer.deserialize(infile.read())
             for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                 diff = norm(f1-f2)
                 self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-4)

wrappers/python/tests/TestPdbFile.py

@@ -67,7 +67,8 @@ class TestPdbFile(unittest.TestCase):
 
     def test_BinaryStream(self):
         """Test reading a stream that was opened in binary mode."""
-        pdb = PDBFile(open('systems/triclinic.pdb', 'rb'))
+        with open('systems/triclinic.pdb', 'rb') as infile:
+            pdb = PDBFile(infile)
         self.assertEqual(len(pdb.positions), 8)
 
     def test_ExtraParticles(self):