def test_parameterize(self):
"""Test parameterizing molecules with template generator for all supported force fields"""
# Test all supported small molecule force fields
for small_molecule_forcefield in self.TEMPLATE_GENERATOR.INSTALLED_FORCEFIELDS:
print(f'Testing {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 = self.TEMPLATE_GENERATOR(molecules=self.molecules, forcefield=small_molecule_forcefield)
# Check that we have loaded the right force field
assert generator.forcefield == small_molecule_forcefield
# Create a ForceField with the appropriate small molecule force field
from simtk.openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Parameterize some molecules
from simtk.openmm.app import NoCutoff
from openmmforcefields.utils import Timer
for molecule in self.molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as t1:
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
assert system.getNumParticles() == molecule.n_atoms
# Molecule should now be cached
with Timer() as t2:
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
assert system.getNumParticles() == molecule.n_atoms
assert (t2.interval() < t1.interval())
def test_parameterize_molecules_from_creation(self):
"""Test that SystemGenerator can parameterize pre-specified molecules in vacuum"""
from openmmforcefields.generators import SystemGenerator
for name, testsystem in self.testsystems.items():
print(testsystem)
molecules = testsystem['molecules']
for small_molecule_forcefield in SystemGenerator.SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator for this force field
generator = SystemGenerator(forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield,
molecules=molecules)
# Parameterize molecules
from openmmforcefields.utils import Timer
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as t1:
system = generator.create_system(openmm_topology)
assert system.getNumParticles() == molecule.n_atoms
# Molecule should now be cached
with Timer() as t2:
system = generator.create_system(openmm_topology)
assert system.getNumParticles() == molecule.n_atoms
assert (t2.interval() < t1.interval())
def test_add_molecules(self):
"""Test that Molecules can be added to SystemGenerator later"""
from openmmforcefields.generators import SystemGenerator
for small_molecule_forcefield in SystemGenerator.SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator for this force field
generator = SystemGenerator(forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield)
# Add molecules for each test system separately
for name, testsystem in self.testsystems.items():
molecules = testsystem['molecules']
# Add molecules
generator.add_molecules(molecules)
# Parameterize molecules
from openmmforcefields.utils import Timer
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as t1:
system = generator.create_system(openmm_topology)
assert system.getNumParticles() == molecule.n_atoms
# Molecule should now be cached
with Timer() as t2:
system = generator.create_system(openmm_topology)
assert system.getNumParticles() == molecule.n_atoms
assert (t2.interval() < t1.interval())
def test_cache(self):
"""Test that SystemGenerator correctly manages a cache"""
from openmmforcefields.generators import SystemGenerator
from openmmforcefields.utils import Timer
timing = dict(
) # timing[(small_molecule_forcefield, smiles)] is the time (in seconds) to parameterize molecule the first time
with tempfile.TemporaryDirectory() as tmpdirname:
# Create a single shared cache for all force fields
cache = os.path.join(tmpdirname, 'db.json')
# Test that we can parameterize all molecules for all test systems
SMALL_MOLECULE_FORCEFIELDS = SystemGenerator.SMALL_MOLECULE_FORCEFIELDS if not CI else [
'gaff-2.11', 'openff-1.1.0'
]
for small_molecule_forcefield in SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator
generator = SystemGenerator(
forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield,
cache=cache)
# Add molecules for each test system separately
for name, testsystem in self.testsystems.items():
molecules = testsystem['molecules']
# Add molecules
generator.add_molecules(molecules)
# Parameterize molecules
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as timer:
system = generator.create_system(openmm_topology)
assert system.getNumParticles() == molecule.n_atoms
# Record time
timing[(small_molecule_forcefield,
molecule.to_smiles())] = timer.interval()
# Molecules should now be cached; test timing is faster the second time
# Test that we can parameterize all molecules for all test systems
SMALL_MOLECULE_FORCEFIELDS = SystemGenerator.SMALL_MOLECULE_FORCEFIELDS if not CI else [
'gaff-2.11', 'openff-1.1.0'
]
for small_molecule_forcefield in SMALL_MOLECULE_FORCEFIELDS:
# Create a SystemGenerator
generator = SystemGenerator(
forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield,
cache=cache)
# Add molecules for each test system separately
for name, testsystem in self.testsystems.items():
molecules = testsystem['molecules']
# We don't need to add molecules that are already defined in the cache
# Parameterize molecules
for molecule in molecules:
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as timer:
system = generator.create_system(openmm_topology)
assert system.getNumParticles() == molecule.n_atoms