Merge pull request #1086 from rmcgibbo/py3

Fix two tests for python3

wrappers/python/tests/TestGromacsTopFile.py

@@ -3,12 +3,16 @@ from validateConstraints import *
 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
+from simtk.openmm.app.gromacstopfile import _defaultGromacsIncludeDir
 import simtk.openmm.app.element as elem
 
+GROMACS_INCLUDE = _defaultGromacsIncludeDir()
+
+@unittest.skipIf(not os.path.exists(GROMACS_INCLUDE), 'GROMACS is not installed')
 class TestGromacsTopFile(unittest.TestCase):
 
     """Test the GromacsTopFile.createSystem() method."""
- 
+
     def setUp(self):
         """Set up the tests by loading the input files."""
 
@@ -20,15 +24,15 @@ class TestGromacsTopFile(unittest.TestCase):
     def test_NonbondedMethod(self):
         """Test all five options for the nonbondedMethod parameter."""
 
-        methodMap = {NoCutoff:NonbondedForce.NoCutoff, 
-                     CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic, 
-                     CutoffPeriodic:NonbondedForce.CutoffPeriodic, 
+        methodMap = {NoCutoff:NonbondedForce.NoCutoff,
+                     CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
+                     CutoffPeriodic:NonbondedForce.CutoffPeriodic,
                      Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
         for method in methodMap:
             system = self.top1.createSystem(nonbondedMethod=method)
             forces = system.getForces()
-            self.assertTrue(any(isinstance(f, NonbondedForce) and 
-                                f.getNonbondedMethod()==methodMap[method] 
+            self.assertTrue(any(isinstance(f, NonbondedForce) and
+                                f.getNonbondedMethod()==methodMap[method]
                                 for f in forces))
 
     def test_ff99SBILDN(self):
@@ -49,8 +53,8 @@ class TestGromacsTopFile(unittest.TestCase):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
         for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
-            system = self.top1.createSystem(nonbondedMethod=method, 
-                                               nonbondedCutoff=2*nanometer, 
+            system = self.top1.createSystem(nonbondedMethod=method,
+                                               nonbondedCutoff=2*nanometer,
                                                constraints=HBonds)
             cutoff_distance = 0.0*nanometer
             cutoff_check = 2.0*nanometer
@@ -63,8 +67,8 @@ class TestGromacsTopFile(unittest.TestCase):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
         for method in [Ewald, PME]:
-            system = self.top1.createSystem(nonbondedMethod=method, 
-                                               ewaldErrorTolerance=1e-6, 
+            system = self.top1.createSystem(nonbondedMethod=method,
+                                               ewaldErrorTolerance=1e-6,
                                                constraints=HBonds)
             tolerance = 0
             tolerance_check = 1e-6
@@ -86,9 +90,9 @@ class TestGromacsTopFile(unittest.TestCase):
         topology = self.top1.topology
         for constraints_value in [None, HBonds, AllBonds, HAngles]:
             for rigidWater_value in [True, False]:
-                system = self.top1.createSystem(constraints=constraints_value, 
+                system = self.top1.createSystem(constraints=constraints_value,
                                                    rigidWater=rigidWater_value)
-                validateConstraints(self, topology, system, 
+                validateConstraints(self, topology, system,
                                     constraints_value, rigidWater_value)
 
     def test_ImplicitSolvent(self):
@@ -102,8 +106,8 @@ class TestGromacsTopFile(unittest.TestCase):
         """Test that solventDielectric and soluteDielectric are passed correctly.
 
         """
-        system = self.top2.createSystem(implicitSolvent=OBC2, 
-                                           solventDielectric=50.0, 
+        system = self.top2.createSystem(implicitSolvent=OBC2,
+                                           solventDielectric=50.0,
                                            soluteDielectric = 0.9)
         found_matching_solvent_dielectric=False
         found_matching_solute_dielectric=False
@@ -115,12 +119,12 @@ class TestGromacsTopFile(unittest.TestCase):
                     found_matching_solute_dielectric = True
             if isinstance(force, NonbondedForce):
                 self.assertEqual(force.getReactionFieldDielectric(), 1.0)
-        self.assertTrue(found_matching_solvent_dielectric and 
+        self.assertTrue(found_matching_solvent_dielectric and
                         found_matching_solute_dielectric)
 
     def test_HydrogenMass(self):
         """Test that altering the mass of hydrogens works correctly."""
-        
+
         topology = self.top1.topology
         hydrogenMass = 4*amu
         system1 = self.top1.createSystem()

wrappers/python/tests/TestPdbFile.py

+import sys
 import unittest
 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
 import simtk.openmm.app.element as elem
-import cStringIO
+if sys.version_info >= (3, 0):
+    from io import StringIO
+else:
+    from cStringIO import StringIO
+
 
 class TestPdbFile(unittest.TestCase):
     """Test the PDB file parser"""
- 
+
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
         pdb = PDBFile('systems/triclinic.pdb')
@@ -43,9 +48,9 @@ class TestPdbFile(unittest.TestCase):
     def test_WriteFile(self):
         """Write a file, read it back, and make sure it matches the original."""
         pdb1 = PDBFile('systems/triclinic.pdb')
-        output = cStringIO.StringIO()
+        output = StringIO()
         PDBFile.writeFile(pdb1.topology, pdb1.positions, output)
-        input = cStringIO.StringIO(output.getvalue())
+        input = StringIO(output.getvalue())
         pdb2 = PDBFile(input)
         output.close();
         input.close();