Enhance the test to ensure that the checkpoint can be loaded correctly

wrappers/python/tests/TestCheckpointReporter.py

 import unittest
 import tempfile
+import numpy as np
 from simtk.openmm import app
 import simtk.openmm as mm
 from simtk import unit
@@ -7,23 +8,31 @@ from simtk import unit
 
 class TestCheckpointReporter(unittest.TestCase):
     def setUp(self):
-        pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        with open('systems/alanine-dipeptide-implicit.pdb') as f:
+            pdb = app.PDBFile(f)
         forcefield = app.ForceField('amber99sbildn.xml')
-        system = forcefield.createSystem(pdb.topology, 
-            nonbondedMethod=app.CutoffNonPeriodic, nonbondedCutoff=1.0*unit.nanometers, 
+        system = forcefield.createSystem(pdb.topology,
+            nonbondedMethod=app.CutoffNonPeriodic, nonbondedCutoff=1.0*unit.nanometers,
             constraints=app.HBonds)
         self.simulation = app.Simulation(pdb.topology, system, mm.VerletIntegrator(0.002*unit.picoseconds))
         self.simulation.context.setPositions(pdb.positions)
-        
+
     def test_1(self):
         file = tempfile.NamedTemporaryFile()
         self.simulation.reporters.append(app.CheckpointReporter(file, 1))
         self.simulation.step(1)
-        
+
+        # get the current positions
+        positions = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)._value
+        # now set the positions into junk...
+        self.simulation.context.setPositions(np.random.random(positions.shape))
+        # then reload the right positions from the checkpoint
         with open(file.name, 'rb') as f:
             self.simulation.context.loadCheckpoint(f.read())
-
         file.close()
 
+        newPositions = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)._value
+        np.testing.assert_array_equal(positions, newPositions)
+
 if __name__ == '__main__':
     unittest.main()