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_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_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.
"""
pdb_file_path = get_data_file_path("systems/packmol_boxes/" + pdb_path)
pdbfile = openmm.app.PDBFile(pdb_file_path)
Topology.from_openmm(
pdbfile.topology,
unique_molecules=unique_molecules,
)
def setup_class(cls):
cls.thing = Thing("blorb", [1, 2, 3])
# Create an example object holding the SMIRNOFF xmltodict dictionary representation
import xmltodict
from openff.toolkit.utils import get_data_file_path
filename = get_data_file_path("test_forcefields/test_forcefield.offxml")
with open(filename, "r") as f:
xml = f.read()
dictionary = xmltodict.parse(xml)
cls.thing = DictionaryContainer(dictionary)
def run_script_file(file_path):
"""Run through the shell a python script."""
with tempfile.TemporaryDirectory() as tmp_dir:
with temporary_cd(tmp_dir):
cmd = ["python", file_path]
if "conformer_energies.py" in file_path:
cmd.append("--filename")
mol_file = get_data_file_path(
"molecules/ruxolitinib_conformers.sdf")
cmd.append(mol_file)
try:
subprocess.check_call(cmd)
except subprocess.CalledProcessError:
raise Exception(f"Example {file_path} failed")
def untar_full_alkethoh_and_freesolv_set():
"""When running slow tests, we unpack the full AlkEthOH and FreeSolv test
sets in advance to speed things up.
See
test_forcefield.py::test_alkethoh_parameters_assignment
test_forcefield.py::test_freesolv_parameters_assignment
"""
import os
import tarfile
from openff.toolkit.utils import get_data_file_path
molecule_dir_path = get_data_file_path("molecules")
for tarfile_name in ["AlkEthOH_tripos.tar.gz", "FreeSolv.tar.gz"]:
tarfile_path = os.path.join(molecule_dir_path, tarfile_name)
with tarfile.open(tarfile_path, "r:gz") as tar:
tar.extractall(path=molecule_dir_path)
mol_filename = 'ETH.mol2'
# Define a few simulation parameters
time_step = 2 * unit.femtoseconds # simulation timestep
temperature = 300 * unit.kelvin # simulation temperature
friction = 1 / unit.picosecond # collision rate
num_steps = 1000000 # number of steps to run
trj_freq = 1000 # number of steps per written trajectory frame
data_freq = 1000 # number of steps per written simulation statistics
# Load molecule and create pdb object
pdb = PDBFile(pdb_filename)
# Load a SMIRNOFF force field
forcefield = ForceField(
get_data_file_path('test_forcefields/Frosst_AlkEthOH_parmAtFrosst.offxml'))
# Load molecule using OpenEye tools
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(mol_filename)
# LPW: I don't understand the meaning of these lines.
# 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)
# Create the OpenMM system
system = forcefield.createSystem(pdb.topology, [mol],
nonbondedMethod=PME,
nonbondedCutoff=1.0 * unit.nanometers,
rigidWater=True)
def test_get_data_file_path():
"""Test get_data_file_path()"""
from openff.toolkit.utils import get_data_file_path
filename = get_data_file_path("test_forcefields/tip3p.offxml")
assert os.path.exists(filename)
"DrugBank_4662",
"DrugBank_7108",
"DrugBank_7124",
"DrugBank_2140",
"DrugBank_2148",
"DrugBank_2186",
"DrugBank_2237",
"DrugBank_4959",
"DrugBank_2429",
"DrugBank_5154",
"DrugBank_2563",
"DrugBank_2570",
"DrugBank_2584",
"DrugBank_2585",
"DrugBank_2684",
]
mini_drug_bank = Molecule.from_file(
get_data_file_path("molecules/MiniDrugBank.sdf"),
allow_undefined_stereo=True)
mols = [mol for mol in mini_drug_bank if mol.name in trimmed_mol_names]
with Chem.SDWriter("MiniDrugBankTrimmed.sdf") as f:
for openff_mol in mols:
try:
openff_mol.assign_partial_charges(partial_charge_method="am1bcc")
rdmol = openff_mol.to_rdkit()
except: # noqa
continue
f.write(rdmol)
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,
},
)
#!/bin/env python
"""
Illustrate how to combine a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd.
"""
#
# Load and parameterize the small molecule
#
# Load the small molecule
from openff.toolkit.utils import get_data_file_path
ligand_filename = get_data_file_path('molecules/toluene.mol2')
molecule = Molecule.from_file(ligand_filename)
# Load the smirnoff99Frosst force field
from openff.toolkit.typing.engines import smirnoff
forcefield = smirnoff.ForceField('test_forcefields/test_forcefield.offxml')
# Create a ParmEd structure for the molecule
molecule_structure = forcefield.create_parmed_structure(
topology=molecule.to_topology(), positions=molecule.positions)
print('Molecule:', molecule_structure)
#
# Load and parameterize the protein
#
# Load the protein topology
protein_pdb_filename = get_data_file_path('proteins/T4-protein.pdb')
protein_pdbfile = app.PDBFile(protein_pdb_filename)