def test_unsupported_handler(self):
from openff.system.stubs import ForceField
gbsa_ff = ForceField(
get_data_file_path("test_forcefields/GBSA_HCT-1.0.offxml"))
with pytest.raises(SMIRNOFFHandlersNotImplementedError,
match=r"SMIRNOFF parameters not.*GBSA"):
gbsa_ff.create_openff_system(topology=None)
def test_library_charge_assignment(self):
from openff.toolkit.tests.test_forcefield import xml_ethanol_library_charges_ff
from openff.system.stubs import ForceField
forcefield = ForceField("openff-1.3.0.offxml")
top = Topology.from_molecules(
[Molecule.from_smiles(smi) for smi in ["[Na+]", "[Cl-]"]])
forcefield.create_openff_system(top)
def test_sanity_grompp():
"""Basic test to ensure that a topology can be processed without errors"""
mol = Molecule.from_smiles("CC")
mol.generate_conformers(n_conformers=1)
top = mol.to_topology()
parsley = ForceField("openff-1.0.0.offxml")
off_sys = parsley.create_openff_system(top)
off_sys.box = [4, 4, 4] * np.eye(3)
off_sys.positions = mol.conformers[0] / omm_unit.angstrom
off_sys.to_gro("out.gro", writer="internal")
off_sys.to_top("out.top", writer="internal")
# TODO: Replace with intermol.gromacs.gmx_energy call after resolving
# atomtype name differences that currently force -maxwarn 7
import os
from pkg_resources import resource_filename
mdp_file = resource_filename("intermol", "tests/gromacs/grompp.mdp")
exit_code = os.system(
f"gmx grompp -f {mdp_file} -c out.gro -p out.top -maxwarn 1")
assert exit_code == 0
def test_from_toolkit_packmol_boxes(self, pdb_path, unique_molecules):
"""
Test loading some pre-prepared PACKMOL-generated systems.
These use PDB files already prepared in the toolkit because PDB files are a pain.
"""
ff = ForceField("openff-1.0.0.offxml")
pdb_file_path = get_data_file_path("systems/packmol_boxes/" + pdb_path)
pdbfile = openmm.app.PDBFile(pdb_file_path)
top = Topology.from_openmm(
pdbfile.topology,
unique_molecules=unique_molecules,
)
box = pdbfile.topology.getPeriodicBoxVectors()
box = box.value_in_unit(nm) * unit.nanometer
out = ff.create_openff_system(top)
out.box = box
out.positions = pdbfile.getPositions()
assert np.allclose(
out.positions.to(unit.nanometer).magnitude,
pdbfile.getPositions().value_in_unit(nm),
)
get_openmm_energies(out, hard_cutoff=True).compare(
_get_openmm_energies(
omm_sys=ff.create_openmm_system(top),
box_vectors=pdbfile.topology.getPeriodicBoxVectors(),
positions=pdbfile.getPositions(),
hard_cutoff=True,
))
def test_from_openmm_single_mols(mol, n_mols):
"""
Test that ForceField.create_openmm_system and System.to_openmm produce
objects with similar energies
TODO: Tighten tolerances
TODO: Test periodic and non-periodic
"""
parsley = ForceField(get_test_file_path("parsley.offxml"))
mol = Molecule.from_smiles(mol)
mol.generate_conformers(n_conformers=1)
top = Topology.from_molecules(n_mols * [mol])
mol.conformers[0] -= np.min(mol.conformers) * unit.angstrom
top.box_vectors = np.eye(3) * np.asarray([10, 10, 10]) * unit.nanometer
if n_mols == 1:
positions = mol.conformers[0]
elif n_mols == 2:
positions = np.vstack(
[mol.conformers[0], mol.conformers[0] + 3 * unit.nanometer])
positions = positions * unit.angstrom
toolkit_system = parsley.create_openmm_system(top)
native_system = parsley.create_openff_system(topology=top).to_openmm()
compare_system_energies(
system1=toolkit_system,
system2=native_system,
positions=positions,
box_vectors=top.box_vectors,
)
def test_basic_conversion_params(self, box):
top = top_from_smiles("C")
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
off_sys = parsley.create_openff_system(topology=top, box=box)
# UnitArray(...)
off_sys.positions = np.zeros(shape=(top.n_topology_atoms, 3))
struct = off_sys.to_parmed()
sigma0 = struct.atoms[0].atom_type.sigma
epsilon0 = struct.atoms[0].atom_type.epsilon
sigma1 = struct.atoms[1].atom_type.sigma
epsilon1 = struct.atoms[1].atom_type.epsilon
bond_k = struct.bonds[0].type.k
req = struct.bonds[0].type.req
angle_k = struct.angles[0].type.k
theteq = struct.angles[0].type.theteq
assert sigma0 == pytest.approx(3.3996695084235347)
assert epsilon0 == pytest.approx(0.1094)
assert sigma1 == pytest.approx(2.649532787749369)
assert epsilon1 == pytest.approx(0.0157)
assert bond_k == pytest.approx(379.04658864565)
assert req == pytest.approx(1.092888378383)
assert angle_k == pytest.approx(37.143507635885)
assert theteq == pytest.approx(107.5991506326)
assert np.allclose(struct.box, np.array([40, 40, 40, 90, 90, 90]))
def test_library_charge_assignment(self):
from openff.system.stubs import ForceField
forcefield = ForceField("openff-1.3.0.offxml")
forcefield.deregister_parameter_handler("ToolkitAM1BCC")
top = Topology.from_molecules(
[Molecule.from_smiles(smi) for smi in ["[Na+]", "[Cl-]"]])
reference = forcefield.create_openmm_system(top)
new = forcefield.create_openff_system(top)
compare_charges_omm_off(reference, new)
def test_to_lammps_single_mols(mol, n_mols):
"""
Test that ForceField.create_openmm_system and System.to_openmm produce
objects with similar energies
TODO: Tighten tolerances
TODO: Test periodic and non-periodic
"""
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
mol = Molecule.from_smiles(mol)
mol.generate_conformers(n_conformers=1)
top = Topology.from_molecules(n_mols * [mol])
mol.conformers[0] -= np.min(mol.conformers) * omm_unit.angstrom
top.box_vectors = np.eye(3) * np.asarray([10, 10, 10]) * omm_unit.nanometer
if n_mols == 1:
positions = mol.conformers[0]
elif n_mols == 2:
positions = np.vstack(
[mol.conformers[0], mol.conformers[0] + 3 * omm_unit.nanometer]
)
positions = positions * omm_unit.angstrom
openff_sys = parsley.create_openff_system(topology=top)
openff_sys.positions = positions.value_in_unit(omm_unit.nanometer)
openff_sys.box = top.box_vectors
reference = get_openmm_energies(
off_sys=openff_sys, round_positions=3, electrostatics=False
)
lmp_energies = get_lammps_energies(
off_sys=openff_sys, round_positions=3, electrostatics=False
)
_write_lammps_input(
off_sys=openff_sys,
file_name="tmp.in",
electrostatics=False,
)
lmp_energies.compare(
reference,
custom_tolerances={
"Nonbonded": 999 * omm_unit.kilojoule_per_mole,
"Torsion": 0.005 * omm_unit.kilojoule_per_mole,
},
)
def test_internal_gromacs_writers(mol):
mol = Molecule.from_smiles(mol)
mol.name = "FOO"
mol.generate_conformers(n_conformers=1)
top = mol.to_topology()
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
out = parsley.create_openff_system(top)
out.box = [4, 4, 4] * np.eye(3)
out.positions = mol.conformers[0]
out.positions = np.round(out.positions, 2)
openmm_sys = parsley.create_openmm_system(top)
struct = pmd.openmm.load_topology(
topology=top.to_openmm(),
system=openmm_sys,
xyz=out.positions.to(unit.angstrom),
)
struct.box = [40, 40, 40, 90, 90, 90]
with tempfile.TemporaryDirectory() as off_tempdir:
with temporary_cd(off_tempdir):
struct.save("reference.top")
struct.save("reference.gro")
out.to_top("internal.top", writer="internal")
out.to_gro("internal.gro", writer="internal", decimal=3)
compare_gro_files("internal.gro", "reference.gro")
# TODO: Also compare to out.to_gro("parmed.gro", writer="parmed")
reference_energy = run_gmx_energy(
top_file="reference.top",
gro_file="reference.gro",
mdp_file=get_mdp_file("default"),
)
internal_energy = run_gmx_energy(
top_file="internal.top",
gro_file="internal.gro",
mdp_file=get_mdp_file("default"),
)
reference_energy.compare(
internal_energy,
custom_tolerances={"Bond": 2e-2 * omm_unit.kilojoule_per_mole},
)
def openff_pmd_gmx_direct(
topology: Topology,
forcefield: ForceField,
box: ArrayQuantity,
prefix: str,
) -> None:
off_sys = forcefield.create_openff_system(topology=topology)
off_sys.box = box
ref_mol = topology.topology_molecules[0].reference_molecule
off_top_positions = ref_mol.conformers[0] / omm_unit.nanometer * unit.nanometer
# TODO: Update this when better processing of OFFTop positions is supported
off_sys.positions = off_top_positions
off_sys.to_gro(prefix + ".gro")
off_sys.to_top(prefix + ".top")
def test_nonbonded_compatibility():
mol = Molecule.from_smiles("CCO")
mol.name = "FOO"
mol.generate_conformers(n_conformers=1)
top = mol.to_topology()
positions = mol.conformers[0].in_units_of(
omm_unit.nanometer) / omm_unit.nanometer
box = [4, 4, 4] * np.eye(3)
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
off_sys = parsley.create_openff_system(top)
off_sys.box = box
off_sys.handlers["Electrostatics"].method = "reaction-field"
with pytest.raises(NonbondedCompatibilityError,
match="reaction-field is not "):
off_sys.to_openmm()
off_sys.handlers["Electrostatics"].method = "Coulomb"
with pytest.raises(
MissingNonbondedCompatibilityError,
match="Coulomb",
):
off_sys.to_openmm()
off_sys.box = None
with pytest.raises(
NonbondedCompatibilityError,
match="Coulomb",
):
off_sys.to_openmm()
off_sys.box = box
off_sys.handlers["Electrostatics"].method = "PME"
with pytest.raises(MissingPositionsError):
off_sys.to_gro("out.gro", writer="internal")
off_sys.positions = positions
# Ensure nothing obvious was mangled
off_sys.to_top("out.top", writer="internal")
off_sys.to_gro("out.gro", writer="internal")
def test_internal_gro_writer():
mol = Molecule.from_smiles("C")
mol.generate_conformers(n_conformers=1)
top = mol.to_topology()
parsley = ForceField("openff-1.0.0.offxml")
out = parsley.create_openff_system(top)
out.box = [4, 4, 4] * np.eye(3)
out.positions = mol.conformers[0] / omm_unit.nanometer
out.to_gro("internal.gro", writer="internal")
out.to_gro("parmed.gro", writer="parmed")
with open("internal.gro", "r") as file1:
with open("parmed.gro", "r") as file2:
# Ignore first two lines and last line
assert file1.readlines()[2:-1] == file2.readlines()[2:-1]
def test_argon(n_mol):
from openff.system.utils import get_test_file_path
ar_ff = ForceField(get_test_file_path("argon.offxml"))
mol = Molecule.from_smiles("[#18]")
mol.add_conformer(np.array([[0, 0, 0]]) * omm_unit.angstrom)
mol.name = "FOO"
top = Topology.from_molecules(n_mol * [mol])
off_sys = ar_ff.create_openff_system(top)
mol.to_file("out.xyz", file_format="xyz")
compound: mb.Compound = mb.load("out.xyz")
packed_box: mb.Compound = mb.fill_box(
compound=compound,
n_compounds=[n_mol],
box=mb.Box([4, 4, 4]),
)
positions = packed_box.xyz * unit.nanometer
positions = np.round(positions, 3)
off_sys.positions = positions
box = np.asarray(packed_box.box.lengths) * unit.nanometer
off_sys.box = box
omm_energies = get_openmm_energies(
off_sys, round_positions=8, hard_cutoff=True, electrostatics=False
)
gmx_energies = get_gromacs_energies(
off_sys, writer="internal", electrostatics=False
)
lmp_energies = get_lammps_energies(off_sys)
omm_energies.compare(lmp_energies)
omm_energies.compare(
gmx_energies,
custom_tolerances={
"Nonbonded": 2e-5 * omm_unit.kilojoule_per_mole,
},
)
def test_getitem():
"""Test behavior of System.__getitem__"""
mol = Molecule.from_smiles("CCO")
parsley = ForceField("openff-1.0.0.offxml")
out = parsley.create_openff_system(mol.to_topology())
out.box = [4, 4, 4]
assert not out.positions
np.testing.assert_equal(out["box"].m, (4 * np.eye(3) * unit.nanometer).m)
np.testing.assert_equal(out["box"].m, out["box_vectors"].m)
assert out["Bonds"] == out.handlers["Bonds"]
with pytest.raises(LookupError, match="Only str"):
out[1]
with pytest.raises(LookupError, match="Could not find"):
out["CMAPs"]
def test_water_dimer():
from openff.system.utils import get_test_file_path
tip3p = ForceField(get_test_file_path("tip3p.offxml"))
water = Molecule.from_smiles("O")
top = Topology.from_molecules(2 * [water])
pdbfile = openmm.app.PDBFile(get_test_file_path("water-dimer.pdb"))
positions = np.array(pdbfile.positions / omm_unit.nanometer) * unit.nanometer
openff_sys = tip3p.create_openff_system(top)
openff_sys.positions = positions
openff_sys.box = [10, 10, 10] * unit.nanometer
omm_energies = get_openmm_energies(
openff_sys,
hard_cutoff=True,
electrostatics=False,
)
toolkit_energies = _get_openmm_energies(
tip3p.create_openmm_system(top),
openff_sys.box,
openff_sys.positions,
hard_cutoff=True,
electrostatics=False,
)
omm_energies.compare(toolkit_energies)
# TODO: Fix GROMACS energies by handling SETTLE constraints
# gmx_energies, _ = get_gromacs_energies(openff_sys)
# compare_gromacs_openmm(omm_energies=omm_energies, gmx_energies=gmx_energies)
lmp_energies = get_lammps_energies(openff_sys, electrostatics=False)
lmp_energies.compare(omm_energies)
def test_water_dimer():
"""Test that a water dimer can be written and the files can be grommp'd"""
from openff.system.utils import get_test_file_path
tip3p = ForceField(get_test_file_path("tip3p.offxml"))
water = Molecule.from_smiles("O")
top = Topology.from_molecules(2 * [water])
from simtk import openmm
from simtk import unit as omm_unit
pdbfile = openmm.app.PDBFile(get_test_file_path("water-dimer.pdb"))
positions = np.array(
pdbfile.positions / omm_unit.nanometer) * unit.nanometer
openff_sys = tip3p.create_openff_system(top)
openff_sys.positions = positions
openff_sys.box = [10, 10, 10] * unit.nanometer
gmx_energies = get_gromacs_energies(openff_sys, writer="internal")
assert gmx_energies is not None
def test_energies_single_mol(constrained, n_mol, mol_smi):
mol = Molecule.from_smiles(mol_smi)
mol.generate_conformers(n_conformers=1)
mol.name = "FOO"
top = Topology.from_molecules(n_mol * [mol])
if constrained:
parsley = ForceField("openff-1.0.0.offxml")
else:
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
off_sys = parsley.create_openff_system(top)
mol.to_file("out.xyz", file_format="xyz")
compound: mb.Compound = mb.load("out.xyz")
packed_box: mb.Compound = mb.fill_box(
compound=compound,
n_compounds=[n_mol],
density=500, # kg/m^3
)
positions = packed_box.xyz * unit.nanometer
off_sys.positions = positions
box = np.asarray(packed_box.box.lengths) * unit.nanometer
if np.any(box < 4 * unit.nanometer):
off_sys.box = np.array([4, 4, 4]) * unit.nanometer
else:
off_sys.box = box
# Compare directly to toolkit's reference implementation
omm_energies = get_openmm_energies(
off_sys, round_positions=8, hard_cutoff=True, electrostatics=False
)
omm_reference = parsley.create_openmm_system(top)
reference_energies = _get_openmm_energies(
omm_sys=omm_reference,
box_vectors=off_sys.box,
positions=off_sys.positions,
round_positions=8,
hard_cutoff=True,
electrostatics=False,
)
try:
omm_energies.compare(reference_energies)
except EnergyError as e:
if "Nonbonded" in str(e):
# If nonbonded energies differ, at least ensure that the nonbonded
# parameters on each particle match
from openff.system.tests.utils import (
_get_charges_from_openmm_system,
_get_lj_params_from_openmm_system,
)
else:
raise e
omm_sys = off_sys.to_openmm()
np.testing.assert_equal(
np.asarray([*_get_charges_from_openmm_system(omm_sys)]),
np.asarray([*_get_charges_from_openmm_system(omm_reference)]),
)
np.testing.assert_equal(
np.asarray([*_get_lj_params_from_openmm_system(omm_sys)]),
np.asarray([*_get_lj_params_from_openmm_system(omm_reference)]),
)
mdp = "cutoff_hbonds" if constrained else "cutoff"
# Compare GROMACS writer and OpenMM export
gmx_energies = get_gromacs_energies(off_sys, mdp=mdp, electrostatics=False)
custom_tolerances = {
"Bond": 2e-5 * n_mol * omm_unit.kilojoule_per_mole,
"Nonbonded": 1e-3 * n_mol * omm_unit.kilojoule_per_mole,
}
if constrained:
# GROMACS might use the initial bond lengths, not the equilibrium bond lengths,
# in the initial configuration, making angles differ slightly
custom_tolerances.update(
{
"Angle": 5e-2 * n_mol * omm_unit.kilojoule_per_mole,
"Nonbonded": 2.0 * n_mol * omm_unit.kilojoule_per_mole,
}
)
gmx_energies.compare(
omm_energies,
custom_tolerances=custom_tolerances,
)
if not constrained:
other_energies = get_openmm_energies(
off_sys,
round_positions=8,
hard_cutoff=True,
electrostatics=True,
)
lmp_energies = get_lammps_energies(off_sys)
custom_tolerances = {
"Nonbonded": 0.5 * n_mol * omm_unit.kilojoule_per_mole,
}
lmp_energies.compare(other_energies, custom_tolerances=custom_tolerances)
def test_packmol_boxes(toolkit_file_path):
# TODO: Isolate a set of systems here instead of using toolkit data
# TODO: Fix nonbonded energy differences
from openff.toolkit.utils import get_data_file_path
pdb_file_path = get_data_file_path(toolkit_file_path)
pdbfile = openmm.app.PDBFile(pdb_file_path)
ethanol = Molecule.from_smiles("CCO")
cyclohexane = Molecule.from_smiles("C1CCCCC1")
omm_topology = pdbfile.topology
off_topology = Topology.from_openmm(
omm_topology, unique_molecules=[ethanol, cyclohexane]
)
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
off_sys = parsley.create_openff_system(off_topology)
off_sys.box = np.asarray(
pdbfile.topology.getPeriodicBoxVectors() / omm_unit.nanometer,
)
off_sys.positions = np.asarray(
pdbfile.positions / omm_unit.nanometer,
)
sys_from_toolkit = parsley.create_openmm_system(off_topology)
omm_energies = get_openmm_energies(off_sys, hard_cutoff=True, electrostatics=False)
reference = _get_openmm_energies(
sys_from_toolkit,
off_sys.box,
off_sys.positions,
hard_cutoff=True,
electrostatics=False,
)
omm_energies.compare(
reference,
custom_tolerances={
"Nonbonded": 2e-2 * omm_unit.kilojoule_per_mole,
},
)
# custom_tolerances={"HarmonicBondForce": 1.0}
# Compare GROMACS writer and OpenMM export
gmx_energies = get_gromacs_energies(off_sys, electrostatics=False)
omm_energies_rounded = get_openmm_energies(
off_sys,
round_positions=8,
hard_cutoff=True,
electrostatics=False,
)
omm_energies_rounded.compare(
other=gmx_energies,
custom_tolerances={
"Angle": 1e-2 * omm_unit.kilojoule_per_mole,
"Torsion": 1e-2 * omm_unit.kilojoule_per_mole,
"Nonbonded": 3200 * omm_unit.kilojoule_per_mole,
},
)
def test_ethanol_opls():
mol = Molecule.from_smiles("CC")
mol.generate_conformers(n_conformers=1)
top = mol.to_topology()
parsley = ForceField("openff-1.0.0.offxml")
out = parsley.create_openff_system(top)
out.box = [4, 4, 4]
out.positions = mol.conformers[0]
out.positions = np.round(out.positions, 2)
rb_torsions = RBTorsionHandler()
smirks = "[#1:1]-[#6X4:2]-[#6X4:3]-[#1:4]"
pot_key = PotentialKey(id=smirks)
for proper in top.propers:
top_key = TopologyKey(atom_indices=tuple(a.topology_atom_index
for a in proper))
rb_torsions.slot_map.update({top_key: pot_key})
# Values from HC-CT-CT-HC RB torsion
# https://github.com/mosdef-hub/foyer/blob/7816bf53a127502520a18d76c81510f96adfdbed/foyer/forcefields/xml/oplsaa.xml#L2585
pot = Potential(
parameters={
"c0": 0.6276 * kj_mol,
"c1": 1.8828 * kj_mol,
"c2": 0.0 * kj_mol,
"c3": -2.5104 * kj_mol,
"c4": 0.0 * kj_mol,
"c5": 0.0 * kj_mol,
})
rb_torsions.potentials.update({pot_key: pot})
out.handlers.update({"RBTorsions": rb_torsions})
out.handlers.pop("ProperTorsions")
gmx = get_openmm_energies(out, round_positions=3).energies["Torsion"]
omm = get_gromacs_energies(out).energies["Torsion"]
assert (gmx - omm).value_in_unit(omm_unit.kilojoule_per_mole) < 1e-3
# Given that these force constants are copied from Foyer's OPLS-AA file,
# compare to processing through the current MoSDeF pipeline
try:
import foyer
import mbuild
except ModuleNotFoundError:
return
comp = mbuild.load("CC", smiles=True)
comp.xyz = mol.conformers[0].value_in_unit(omm_unit.nanometer)
ff = foyer.Forcefield(name="oplsaa")
from_foyer = ff.apply(comp)
from_foyer.box = [40, 40, 40, 90, 90, 90]
from_foyer.save("from_foyer.top")
from_foyer.save("from_foyer.gro")
rb_torsion_energy_from_foyer = run_gmx_energy(
top_file="from_foyer.top",
gro_file="from_foyer.gro",
mdp_file=get_mdp_file("default"),
).energies["Torsion"]
assert (omm - rb_torsion_energy_from_foyer).value_in_unit(
omm_unit.kilojoule_per_mole) < 1e-3