def test_packmol_failed():
from openff.toolkit.topology import Molecule
molecules = [Molecule.from_smiles("O")]
with pytest.raises(PackmolRuntimeException):
packmol.pack_box(molecules, [10], box_size=([0.1] * 3) * unit.angstrom)
def test_packmol_bad_input():
from openff.toolkit.topology import Molecule
molecules = [Molecule.from_smiles("O")]
with pytest.raises(ValueError):
packmol.pack_box(molecules, [10, 20],
box_size=([20] * 3) * unit.angstrom)
def test_packmol_ions():
from openff.toolkit.topology import Molecule
molecules = [
Molecule.from_smiles("[Na+]"),
Molecule.from_smiles("[Cl-]"),
Molecule.from_smiles("[K+]"),
]
trajectory, _ = packmol.pack_box(molecules, [1, 1, 1],
box_size=([20] * 3) * unit.angstrom)
assert trajectory is not None
assert trajectory.n_chains == 3
assert trajectory.n_residues == 3
assert trajectory.n_atoms == 3
assert trajectory.topology.n_bonds == 0
assert trajectory.top.residue(0).name == "Na+"
assert trajectory.top.residue(1).name == "Cl-"
assert trajectory.top.residue(2).name == "K+"
assert trajectory.top.atom(0).name == "Na+"
assert trajectory.top.atom(1).name == "Cl-"
assert trajectory.top.atom(2).name == "K+"
def _execute(self, directory, available_resources):
molecules, number_of_molecules, exception = self._build_molecule_arrays()
packmol_directory = path.join(directory, "packmol_files")
# Create packed box
trajectory, residue_names = packmol.pack_box(
molecules=molecules,
number_of_copies=number_of_molecules,
structure_to_solvate=self.solute_coordinate_file,
center_solute=self.center_solute_in_box,
mass_density=self.mass_density,
box_aspect_ratio=self.box_aspect_ratio,
tolerance=self.tolerance,
verbose=self.verbose_packmol,
working_directory=packmol_directory,
retain_working_files=self.retain_packmol_files,
)
if trajectory is None:
raise RuntimeError("Packmol failed to complete.")
self.assigned_residue_names = dict()
for component, residue_name in zip(self.substance, residue_names):
self.assigned_residue_names[component.identifier] = residue_name
self._save_results(directory, trajectory)
def test_packmol_paracetamol():
from openff.toolkit.topology import Molecule
# Test something a bit more tricky than water
molecules = [Molecule.from_smiles("CC(=O)NC1=CC=C(C=C1)O")]
trajectory, _ = packmol.pack_box(molecules, [1],
box_size=([20] * 3) * unit.angstrom)
assert trajectory is not None
assert trajectory.n_chains == 1
assert trajectory.n_residues == 1
assert trajectory.n_atoms == 20
assert trajectory.topology.n_bonds == 20
def test_amino_acids():
amino_residues = {
"C[C@H](N)C(=O)O": "ALA",
# Undefined stereochemistry error.
# "N=C(N)NCCC[C@H](N)C(=O)O": "ARG",
"NC(=O)C[C@H](N)C(=O)O": "ASN",
"N[C@@H](CC(=O)O)C(=O)O": "ASP",
"N[C@@H](CS)C(=O)O": "CYS",
"N[C@@H](CCC(=O)O)C(=O)O": "GLU",
"NC(=O)CC[C@H](N)C(=O)O": "GLN",
"NCC(=O)O": "GLY",
"N[C@@H](Cc1c[nH]cn1)C(=O)O": "HIS",
"CC[C@H](C)[C@H](N)C(=O)O": "ILE",
"CC(C)C[C@H](N)C(=O)O": "LEU",
"NCCCC[C@H](N)C(=O)O": "LYS",
"CSCC[C@H](N)C(=O)O": "MET",
"N[C@@H](Cc1ccccc1)C(=O)O": "PHE",
"O=C(O)[C@@H]1CCCN1": "PRO",
"N[C@@H](CO)C(=O)O": "SER",
"C[C@@H](O)[C@H](N)C(=O)O": "THR",
"N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O": "TRP",
"N[C@@H](Cc1ccc(O)cc1)C(=O)O": "TYR",
"CC(C)[C@H](N)C(=O)O": "VAL",
}
smiles = [*amino_residues]
from openff.toolkit.topology import Molecule
molecules = [Molecule.from_smiles(x) for x in smiles]
counts = [1] * len(smiles)
trajectory, _ = packmol.pack_box(molecules,
counts,
box_size=([1000] * 3) * unit.angstrom)
assert trajectory is not None
assert trajectory.n_chains == len(smiles)
assert trajectory.n_residues == len(smiles)
for index, smiles in enumerate(smiles):
assert trajectory.top.residue(index).name == amino_residues[smiles]
def test_packmol_box_size():
from openff.toolkit.topology import Molecule
molecules = [Molecule.from_smiles("O")]
trajectory, _ = packmol.pack_box(molecules, [10],
box_size=([20] * 3) * unit.angstrom)
assert trajectory is not None
assert trajectory.n_chains == 1
assert trajectory.n_residues == 10
assert trajectory.n_atoms == 30
assert trajectory.topology.n_bonds == 20
assert all(x.name == "HOH" for x in trajectory.top.residues)
assert np.allclose(trajectory.unitcell_lengths, 2.2)
def test_packmol_water():
from openff.toolkit.topology import Molecule
molecules = [Molecule.from_smiles("O")]
trajectory, _ = packmol.pack_box(
molecules,
[10],
mass_density=1.0 * unit.grams / unit.milliliters,
)
assert trajectory is not None
assert trajectory.n_chains == 1
assert trajectory.n_residues == 10
assert trajectory.n_atoms == 30
assert trajectory.topology.n_bonds == 20
assert all(x.name == "HOH" for x in trajectory.top.residues)
def compare_condensed_systems(mol, force_field):
from openff.evaluator import unit as evaluator_unit
from openff.evaluator.utils.packmol import pack_box
mass_density = 500 * evaluator_unit.kilogram / evaluator_unit.meter ** 3
trj, assigned_residue_names = pack_box(
molecules=[mol], number_of_copies=[100], mass_density=mass_density
)
try:
openff_top = Topology.from_openmm(trj.top.to_openmm(), unique_molecules=[mol])
except ValueError:
print(f"Molecule failed! (conversion from OpenMM)\t{mol.to_inchi()}")
return
box_vectors = trj.unitcell_vectors[0] * simtk_unit.nanometer
openff_top.box_vectors = box_vectors
try:
toolkit_sys = force_field.create_openmm_system(
openff_top,
charge_from_molecules=[mol],
)
except (
UnassignedBondParameterException,
UnassignedAngleParameterException,
UnassignedProperTorsionParameterException,
):
print(f"Molecule failed! (missing valence parameters)\t{mol.to_inchi()}")
return
positions = trj.xyz[0] * simtk_unit.nanometer
toolkit_energy = _get_openmm_energies(
toolkit_sys,
box_vectors=box_vectors,
positions=positions,
)
openff_sys = Interchange.from_smirnoff(force_field=force_field, topology=openff_top)
openff_sys.box = box_vectors
openff_sys.positions = trj.xyz[0] * unit.nanometer
new_sys = openff_sys.to_openmm(combine_nonbonded_forces=True)
system_energy = _get_openmm_energies(
new_sys,
box_vectors=box_vectors,
positions=positions,
)
# Where energies to not precisely match, inspect all parameters in each force
try:
toolkit_energy.compare(
system_energy,
custom_tolerances={
"Bond": 1e-6 * kj_mol,
"Angle": 1e-6 * kj_mol,
"Torsion": 4e-5 * kj_mol,
"Nonbonded": 1e-5 * kj_mol,
},
)
except EnergyError as e:
if "Torsion" in str(e):
_compare_torsion_forces(
_get_force(toolkit_sys, openmm.PeriodicTorsionForce),
_get_force(new_sys, openmm.PeriodicTorsionForce),
)
if "Nonbonded" in str(e):
_compare_nonbonded_settings(
_get_force(toolkit_sys, openmm.NonbondedForce),
_get_force(new_sys, openmm.NonbondedForce),
)
_compare_nonbonded_parameters(
_get_force(toolkit_sys, openmm.NonbondedForce),
_get_force(new_sys, openmm.NonbondedForce),
)
if "Bond" in str(e):
raise e
if "Angle" in str(e):
raise e