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Commit 8190f59a authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Fix issue with simple ffxml StringIO in TestForceField.

parent 92cde5ca
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Showing with 16 additions and 17 deletions
wrappers/python/tests/TestForceField.py
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...@@ -293,22 +293,21 @@ class TestForceField(unittest.TestCase): ...@@ -293,22 +293,21 @@ class TestForceField(unittest.TestCase):
# Define forcefield parameters used by simpleTemplateGenerator. # Define forcefield parameters used by simpleTemplateGenerator.
# NOTE: This parameter definition file will currently only work for residues that either have # 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. # no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """\ simple_ffxml_contents = """
<ForceField> <ForceField>
<AtomTypes> <AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12"/> <Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes> </AtomTypes>
<HarmonicBondForce> <HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/> <Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce> </HarmonicBondForce>
<HarmonicAngleForce> <HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/> <Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce> </HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5"> <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/> <Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce> </NonbondedForce>
</ForceField>""" </ForceField>"""
simple_ffxml = StringIO(simple_ffxml_contents)
# #
# Test where we generate parameters for only a ligand. # Test where we generate parameters for only a ligand.
...@@ -317,7 +316,7 @@ class TestForceField(unittest.TestCase): ...@@ -317,7 +316,7 @@ class TestForceField(unittest.TestCase):
# Load the PDB file. # Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb')) pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object. # 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. # Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator) forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system. # Parameterize system.
...@@ -339,7 +338,7 @@ class TestForceField(unittest.TestCase): ...@@ -339,7 +338,7 @@ class TestForceField(unittest.TestCase):
# Load the PDB file. # Load the PDB file.
pdb = PDBFile(os.path.join('systems', test['pdb_filename'])) pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
# Create a ForceField object. # Create a ForceField object.
forcefield = ForceField(simple_ffxml) forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator. # Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator) forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system. # Parameterize system.
...@@ -348,7 +347,7 @@ class TestForceField(unittest.TestCase): ...@@ -348,7 +347,7 @@ class TestForceField(unittest.TestCase):
# Now test all systems with a single ForceField object. # Now test all systems with a single ForceField object.
# Create a ForceField object. # Create a ForceField object.
forcefield = ForceField(simple_ffxml) forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator. # Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator) forcefield.registerTemplateGenerator(simpleTemplateGenerator)
for test in tests: for test in tests:
......
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