Merge pull request #722 from swails/fix_dcd

[WIP]Fix byte handling to work for both Py2 and Py3

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

@@ -73,7 +73,7 @@ class DCDFile(object):
         header = struct.pack('<i4c9if', 84, b'C', b'O', b'R', b'D', 0, firstStep, interval, 0, 0, 0, 0, 0, 0, dt)
         header += struct.pack('<13i', boxFlag, 0, 0, 0, 0, 0, 0, 0, 0, 24, 84, 164, 2)
         header += struct.pack('<80s', b'Created by OpenMM')
-        header += struct.pack('<80s', b'Created '+bytes(time.asctime(time.localtime(time.time())), 'ascii'))
+        header += struct.pack('<80s', b'Created '+time.asctime(time.localtime(time.time())).encode('ascii'))
         header += struct.pack('<4i', 164, 4, len(list(topology.atoms())), 4)
         file.write(header)
 

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

+import unittest
+import tempfile
+from simtk.openmm import app
+import simtk.openmm as mm
+from simtk import unit
+from random import random
+import os
+
+class TestDCDFile(unittest.TestCase):
+    def test_dcd(self):
+        """ Test the DCD file """
+        fname = tempfile.mktemp(suffix='.dcd')
+        pdbfile = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        natom = len(list(pdbfile.topology.atoms()))
+        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__':
+    unittest.main()