def test_partial_bondorder(verbose=False):
"""Test setup of a molecule which activates partial bond order code."""
from openeye import oechem
mol = oechem.OEMol()
from openeye import oeiupac
oeiupac.OEParseIUPACName(mol, 'benzene')
positions = positions_from_oemol(mol)
oechem.OETriposAtomNames(mol)
topology = generateTopologyFromOEMol(mol)
# Load forcefield from above
ffxml = StringIO(ffxml_contents)
ff = ForceField(ffxml)
# Set up once using AM1BCC charges
system = ff.createSystem(topology, [mol],
chargeMethod='OECharges_AM1BCCSym',
verbose=verbose)
# Check that energy is what it ought to be -- the partial bond order
# for benzene makes the energy a bit higher than it would be without it
energy = get_energy(system, positions)
if energy < 7.50 or energy > 7.60:
raise Exception(
"Partial bond order code seems to have issues, as energy for benzene is outside of tolerance in tests."
)
# Set up once also without asking for charges
system = ff.createSystem(topology, [mol], verbose=verbose)
energy = get_energy(system, positions)
# Energy is lower with user supplied charges (which in this case are zero)
if energy < 4.00 or energy > 6.0:
raise Exception(
"Partial bond order code seems to have issues when run with user-provided charges, as energy for benzene is out of tolerance in tests."
)
def check_system_creation_from_molecule(forcefield,
mol,
chargeMethod=None,
verbose=False):
"""
Generate a System from the given OEMol and SMIRFF forcefield and check that its energy is finite.
Parameters
----------
forcefield : smarty.ForceField
SMIRFF forcefield
mol : oechem.OEMol
Molecule to test (need not have coordinates)
chargeMethod : str, optional, default=None
Charge method to use in creating system
"""
from smarty.forcefield import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
system = forcefield.createSystem(topology, [mol],
chargeMethod=chargeMethod,
verbose=verbose)
# Test energy computation.
positions = positions_from_oemol(mol)
check_energy_is_finite(system, positions)
def test_parameter_completeness_check(self):
"""Test that proper exceptions are raised if a force field fails to assign parameters to valence terms in a molecule."""
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'CCC')
oechem.OEAddExplicitHydrogens(mol)
oechem.OETriposAtomNames(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
topology = generateTopologyFromOEMol(mol)
# Test nonbonded error checking by wiping out required LJ parameter
params = ff.getParameter(paramID='n0001')
params['smirks'] = '[#136:1]'
ff.setParameter(paramID='n0001', params=params)
ff.setParameter(paramID='n0002', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
# Test bond error checking by wiping out a required bond parameter
params = ff.getParameter(paramID='b0001')
params['smirks'] = '[#136:1]~[*:2]'
ff.setParameter(paramID='b0001', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
# Test angle error checking by wiping out a required angle parameter
params = ff.getParameter(paramID='a0001')
params['smirks'] = '[#136:1]~[*:2]~[*:3]'
ff.setParameter(paramID='a0001', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
# Test torsion error checking by wiping out a required torsion parameter
params = ff.getParameter(paramID='t0001')
params['smirks'] = '[#136:1]~[*:2]~[*:3]~[*:4]'
ff.setParameter(paramID='t0001', params=params)
ff.setParameter(paramID='t0004', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
def test_change_parameters(verbose=False):
"""Test modification of forcefield parameters."""
from openeye import oechem
# Load simple OEMol
ifs = oechem.oemolistream(
get_data_filename('molecules/AlkEthOH_c100.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
# Load forcefield file
ffxml = get_data_filename('forcefield/Frosst_AlkEtOH.ffxml')
ff = ForceField(ffxml)
from smarty.forcefield import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Create initial system
system = ff.createSystem(topology, [mol], verbose=verbose)
# Get initial energy before parameter modification
positions = positions_from_oemol(mol)
old_energy = get_energy(system, positions)
# Get params for an angle
params = ff.getParameter(smirks='[a,A:1]-[#6X4:2]-[a,A:3]')
# Modify params
params['k'] = '0.0'
ff.setParameter(params, smirks='[a,A:1]-[#6X4:2]-[a,A:3]')
# Write params
ff.writeFile(tempfile.TemporaryFile(suffix='.ffxml'))
# Make sure params changed energy! (Test whether they get rebuilt on system creation)
system = ff.createSystem(topology, [mol], verbose=verbose)
energy = get_energy(system, positions)
if verbose:
print("New energy/old energy:", energy, old_energy)
if np.abs(energy - old_energy) < 0.1:
raise Exception("Error: Parameter modification did not change energy.")