def test_write_xml_parameters_amber_write_unused(self):
"""Test the write_unused argument in writing XML files"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB')))
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2178)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1646)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('atomic_ions.lib'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p')))
ffxml = StringIO()
warnings.filterwarnings('ignore', category=exceptions.ParameterWarning)
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 222)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 57)
def test_write_xml_parameters_amber_write_unused(self):
"""Test the write_unused argument in writing XML files"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB'))
)
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2178)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1646)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
ffxml = StringIO()
warnings.filterwarnings('ignore', category=exceptions.ParameterWarning)
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 222)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 57)
def test_write_xml_parameters_amber_write_unused(self):
""" Test writing XML parameters loaded from part of the ff14SB forcefield
files, using the write_unused argument"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB')))
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2178)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1646)
def test_write_xml_parameters_amber_write_unused(self):
""" Test writing XML parameters loaded from part of the ff14SB forcefield
files, using the write_unused argument"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn("amino12.lib"),
os.path.join(get_fn("parm"), "parm10.dat"),
os.path.join(get_fn("parm"), "frcmod.ff14SB"),
)
)
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2178)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1646)
def test_not_write_residues_with_same_templhash(self):
"""Test that no identical residues are written to XML, using the
templhasher function."""
# TODO add testing for multiatomic residues when support for those added
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib')))
new_residues = OrderedDict()
for name in ('K', 'K+', 'NA', 'Na+', 'CL', 'Cl-'):
new_residues[name] = params.residues[name]
params.residues = new_residues
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 16)
def test_not_write_residues_with_same_templhash(self):
"""Test that no identical residues are written to XML, using the
templhasher function."""
# TODO add testing for multiatomic residues when support for those added
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib'))
)
new_residues = OrderedDict()
for name in ('K', 'K+', 'NA', 'Na+', 'CL', 'Cl-'):
new_residues[name] = params.residues[name]
params.residues = new_residues
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 16)
def test_override_level(self):
"""Test correct support for the override_level attribute of
ResidueTemplates and correct writing to XML tag"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib')))
new_residues = OrderedDict()
new_residues['K'] = params.residues['K']
new_residues['NA'] = params.residues['NA']
new_residues['K'].override_level = 1
params.residues = new_residues
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
output_lines = ffxml.readlines()
control_line1 = ' <Residue name="K" override="1">\n'
control_line2 = ' <Residue name="NA">\n'
self.assertEqual(output_lines[5], control_line1)
self.assertEqual(output_lines[8], control_line2)
def test_overload_level(self):
"""Test correct support for the overload_level attribute of
ResidueTemplates and correct writing to XML tag"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib'))
)
new_residues = OrderedDict()
new_residues['K'] = params.residues['K']
new_residues['NA'] = params.residues['NA']
new_residues['K'].overload_level = 1
params.residues = new_residues
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
output_lines = ffxml.readlines()
control_line1 = ' <Residue name="K" overload="1">\n'
control_line2 = ' <Residue name="NA">\n'
self.assertEqual(output_lines[5], control_line1)
self.assertEqual(output_lines[8], control_line2)