def test_version(self):
"""Test version"""
for forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
generator = SMIRNOFFTemplateGenerator(forcefield=forcefield)
assert generator.forcefield == forcefield
assert generator.smirnoff_filename.endswith(forcefield + '.offxml')
assert os.path.exists(generator.smirnoff_filename)
def test_energies(self):
"""Test potential energies match between openforcefield and OpenMM ForceField"""
# DEBUG
from openforcefield.topology import Molecule
molecule = Molecule.from_smiles('C=O')
molecule.generate_conformers(n_conformers=1)
from simtk import unit
molecule.conformers[0][0, 0] += 0.1 * unit.angstroms
self.molecules.insert(0, molecule)
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
print(f'Testing energies for {small_molecule_forcefield}...')
# Create a generator that knows about a few molecules
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = SMIRNOFFTemplateGenerator(
molecules=self.molecules, forcefield=small_molecule_forcefield)
# Create a ForceField
import simtk
openmm_forcefield = simtk.openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Parameterize some molecules
for molecule in self.molecules:
# Create OpenMM System using OpenMM app
from simtk.openmm.app import NoCutoff
openmm_system = openmm_forcefield.createSystem(
molecule.to_topology().to_openmm(),
removeCMMotion=False,
onbondedMethod=NoCutoff)
# Retrieve System generated by the SMIRNOFF typing engine
smirnoff_system = generator.get_openmm_system(molecule)
# Compare energies and forces
self.compare_energies(molecule, openmm_system, smirnoff_system)
# Run some dynamics
molecule = self.propagate_dynamics(molecule, smirnoff_system)
# Compare energies again
self.compare_energies(molecule, openmm_system, smirnoff_system)
def test_partial_charges_are_none(self):
"""Test parameterizing a small molecule with `partial_charges=None` instead
of zeros (happens frequently in OFFTK>=0.7.0)"""
from openforcefield.topology import Molecule
molecule = Molecule.from_smiles('C=O')
molecule.generate_conformers(n_conformers=1)
#molecule._partial_charges = None
assert (molecule.partial_charges is None) or np.all(molecule.partial_charges / unit.elementary_charge == 0)
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
print(f'Testing energies for {small_molecule_forcefield}...')
# Create a generator that knows about a few molecules
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
generator = SMIRNOFFTemplateGenerator(molecules=[molecule], forcefield=small_molecule_forcefield)
# Create a ForceField
import simtk
openmm_forcefield = simtk.openmm.app.ForceField()
# Register the template generator
openmm_forcefield.registerTemplateGenerator(generator.generator)
# Create OpenMM System using OpenMM app
from simtk.openmm.app import NoCutoff
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, onbondedMethod=NoCutoff)
smirnoff_system = generator.get_openmm_system(molecule)