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Commit 476e820b authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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add tests

parent 4e9b65cf
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wrappers/python/tests/TestForceField.py
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......@@ -534,6 +534,92 @@ class TestForceField(unittest.TestCase):
self.assertEqual(len(pertorsion2.proper), 110)
self.assertEqual(len(pertorsion2.improper), 42)
def test_ResidueTemplateUserChoice(self):
"""Test createSystem does not allow multiple matching templates, unless
user has specified which template to use via residueTemplates arg"""
ffxml = """<ForceField>
<AtomTypes>
<Type name="Fe2+" class="Fe2+" element="Fe" mass="55.85"/>
<Type name="Fe3+" class="Fe3+" element="Fe" mass="55.85"/>
</AtomTypes>
<Residues>
<Residue name="FE2">
<Atom name="FE2" type="Fe2+" charge="2.0"/>
</Residue>
<Residue name="FE">
<Atom name="FE" type="Fe3+" charge="3.0"/>
</Residue>
</Residues>
<NonbondedForce coulomb14scale="0.833333333333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom type="Fe2+" sigma="0.227535532613" epsilon="0.0150312292"/>
<Atom type="Fe3+" sigma="0.192790482606" epsilon="0.00046095128"/>
</NonbondedForce>
</ForceField>"""
pdb_string = "ATOM 1 FE FE A 1 20.956 27.448 -29.067 1.00 0.00 Fe"
ff = ForceField(StringIO(ffxml))
pdb = PDBFile(StringIO(pdb_string))
self.assertRaises(Exception, lambda: ff.createSystem(pdb.topology))
ff.createSystem(pdb.topology, residueTemplates={list(pdb.topology.residues())[0] : 'FE2'})
ff.createSystem(pdb.topology, residueTemplates={list(pdb.topology.residues())[0] : 'FE'})
def test_ResidueOverloading(self):
"""Test residue overloading via overload tag in the XML"""
ffxml1 = """<ForceField>
<AtomTypes>
<Type name="Fe2+_tip3p_HFE" class="Fe2+_tip3p_HFE" element="Fe" mass="55.85"/>
</AtomTypes>
<Residues>
<Residue name="FE2">
<Atom name="FE2" type="Fe2+_tip3p_HFE" charge="2.0"/>
</Residue>
</Residues>
<NonbondedForce coulomb14scale="0.833333333333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom type="Fe2+_tip3p_HFE" sigma="0.227535532613" epsilon="0.0150312292"/>
</NonbondedForce>
</ForceField>"""
ffxml2 = """<ForceField>
<AtomTypes>
<Type name="Fe2+_tip3p_standard" class="Fe2+_tip3p_standard" element="Fe" mass="55.85"/>
</AtomTypes>
<Residues>
<Residue name="FE2">
<Atom name="FE2" type="Fe2+_tip3p_standard" charge="2.0"/>
</Residue>
</Residues>
<NonbondedForce coulomb14scale="0.833333333333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom type="Fe2+_tip3p_standard" sigma="0.241077193129" epsilon="0.03940482832"/>
</NonbondedForce>
</ForceField>"""
ffxml3 = """<ForceField>
<AtomTypes>
<Type name="Fe2+_tip3p_standard" class="Fe2+_tip3p_standard" element="Fe" mass="55.85"/>
</AtomTypes>
<Residues>
<Residue name="FE2" overload="1">
<Atom name="FE2" type="Fe2+_tip3p_standard" charge="2.0"/>
</Residue>
</Residues>
<NonbondedForce coulomb14scale="0.833333333333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom type="Fe2+_tip3p_standard" sigma="0.241077193129" epsilon="0.03940482832"/>
</NonbondedForce>
</ForceField>"""
pdb_string = "ATOM 1 FE FE A 1 20.956 27.448 -29.067 1.00 0.00 Fe"
pdb = PDBFile(StringIO(pdb_string))
self.assertRaises(Exception, lambda: ForceField(StringIO(ffxml1), StringIO(ffxml2)))
ff = ForceField(StringIO(ffxml1), StringIO(ffxml3))
ff.createSystem(pdb.topology)
class AmoebaTestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method with the AMOEBA forcefield."""
......
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