Merge pull request #1536 from peastman/filewarning

Eliminated warnings about unclosed files

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

@@ -81,7 +81,7 @@ class CharmmCrdFile(object):
 
     def _parse(self, fname):
 
-        crdfile = open(fname, 'r')
+        with open(fname, 'r') as crdfile:
             line = crdfile.readline()
     
             while len(line.strip()) == 0:      # Skip whitespace, as a precaution

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

@@ -178,7 +178,7 @@ class CharmmPsfFile(object):
         if not os.path.exists(psf_name):
             raise IOError('Could not find PSF file %s' % psf_name)
         # Open the PSF and read the first line. It must start with "PSF"
-        psf = open(psf_name, 'r')
+        with open(psf_name, 'r') as psf:
             line = psf.readline()
             if not line.startswith('PSF'):
                 raise CharmmPSFError('Unrecognized PSF file. First line is %s' %

wrappers/python/tests/TestCharmmFiles.py

@@ -165,7 +165,8 @@ class TestCharmmFiles(unittest.TestCase):
             #out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
             #out.write(XmlSerializer.serialize(state1))
             #out.close()
-            state2 = XmlSerializer.deserialize(open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml').read())
+            with open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml') as xml:
+                state2 = XmlSerializer.deserialize(xml.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)