Fix issue with simple ffxml StringIO in TestForceField.

wrappers/python/tests/TestForceField.py

@@ -293,22 +293,21 @@ class TestForceField(unittest.TestCase):
         # Define forcefield parameters used by simpleTemplateGenerator.
         # NOTE: This parameter definition file will currently only work for residues that either have
         # no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
-        simple_ffxml_contents = """\
+        simple_ffxml_contents = """
 <ForceField>
-<AtomTypes>
- <Type name="XXX" class="XXX" element="C" mass="12"/>
-</AtomTypes>
-<HarmonicBondForce>
+ <AtomTypes>
+  <Type name="XXX" class="XXX" element="C" mass="12.0"/>
+ </AtomTypes>
+ <HarmonicBondForce>
   <Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
-</HarmonicBondForce>
-<HarmonicAngleForce>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
   <Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
-</HarmonicAngleForce>
-<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
   <Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
-</NonbondedForce>
+ </NonbondedForce>
 </ForceField>"""
-        simple_ffxml = StringIO(simple_ffxml_contents)
 
         #
         # Test where we generate parameters for only a ligand.
@@ -317,7 +316,7 @@ class TestForceField(unittest.TestCase):
         # Load the PDB file.
         pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
-        forcefield = ForceField('amber99sb.xml', 'tip3p.xml', simple_ffxml)
+        forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
         # Add the residue template generator.
         forcefield.registerTemplateGenerator(simpleTemplateGenerator)
         # Parameterize system.
@@ -339,7 +338,7 @@ class TestForceField(unittest.TestCase):
             # Load the PDB file.
             pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
             # Create a ForceField object.
-            forcefield = ForceField(simple_ffxml)
+            forcefield = ForceField(StringIO(simple_ffxml_contents))
             # Add the residue template generator.
             forcefield.registerTemplateGenerator(simpleTemplateGenerator)
             # Parameterize system.
@@ -348,7 +347,7 @@ class TestForceField(unittest.TestCase):
 
         # Now test all systems with a single ForceField object.
         # Create a ForceField object.
-        forcefield = ForceField(simple_ffxml)
+        forcefield = ForceField(StringIO(simple_ffxml_contents))
         # Add the residue template generator.
         forcefield.registerTemplateGenerator(simpleTemplateGenerator)
         for test in tests: