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)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
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)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
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)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
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)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
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_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()), 2179)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1647)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
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, write_unused=True)
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)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
# Load TIP3P water box to ensure there are no duplicate ion parameters
pdbfile = app.PDBFile(get_fn('ionsjc.pdb'))
system = forcefield.createSystem(pdbfile.topology)
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()), 2179)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1647)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
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, write_unused=True)
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)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
# Load TIP3P water box to ensure there are no duplicate ion parameters
pdbfile = app.PDBFile(get_fn('ionsjc.pdb'))
system = forcefield.createSystem(pdbfile.topology)
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'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
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)
# TODO: Overhaul tests with lxml (xpath?) queries to eliminate dependence on file order
ffxml.seek(0)
nlines = len(ffxml.readlines())
self.assertEqual(nlines, 39, 'File contents:\n{}\nActual length: {} lines.'.format(ffxml.getvalue(), nlines))
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].strip(), control_line1.strip())
self.assertEqual(output_lines[8].strip(), control_line2.strip())
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'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
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)
# TODO: Overhaul tests with lxml (xpath?) queries to eliminate dependence on file order
ffxml.seek(0)
nlines = len(ffxml.readlines())
self.assertEqual(nlines, 39, 'File contents:\n{}\nActual length: {} lines.'.format(ffxml.getvalue(), nlines))
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].strip(), control_line1.strip())
self.assertEqual(output_lines[8].strip(), control_line2.strip())
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'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
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)
# TODO: Overhaul tests with lxml (xpath?) queries to eliminate dependence on file order
output_lines = ffxml.readlines()
control_line1 = ' <Residue name="K" override="1">\n'
control_line2 = ' <Residue name="NA">\n'
self.assertEqual(output_lines[16].strip(), control_line1.strip(), 'File contents:\n{}'.format(ffxml.getvalue()))
self.assertEqual(output_lines[19].strip(), control_line2.strip(), 'File contents:\n{}'.format(ffxml.getvalue()))
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'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
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)
# TODO: Overhaul tests with lxml (xpath?) queries to eliminate dependence on file order
output_lines = ffxml.readlines()
control_line1 = ' <Residue name="K" override="1">\n'
control_line2 = ' <Residue name="NA">\n'
self.assertEqual(output_lines[16].strip(), control_line1.strip(), 'File contents:\n{}'.format(ffxml.getvalue()))
self.assertEqual(output_lines[19].strip(), control_line2.strip(), 'File contents:\n{}'.format(ffxml.getvalue()))