def test_generate_optimise_in(tmpdir, biphenyl):
"""
Test generating an optimize in file which captures the correct forcebalance run time settings.
"""
with tmpdir.as_cwd():
# parametrise the molecule
OpenFF().run(biphenyl)
# set some non-default values
fb = ForceBalanceFitting(penalty_type="L2",
max_iterations=100,
minimum_trust_radius=10)
tp = TorsionProfile(restrain_k=100)
fb.add_target(target=tp)
# now run the setup
target_folders = tp.prep_for_fitting(molecule=biphenyl)
fb.generate_optimise_in(target_data={tp.target_name: target_folders})
# read the file back in
with open("optimize.in") as opt_in:
opt_data = opt_in.read()
assert "penalty_type L2" in opt_data
assert "maxstep 100" in opt_data
assert "mintrust 10" in opt_data
assert "restrain_k 100" in opt_data
assert "type TorsionProfile_OpenMM" in opt_data
def test_target_prep_no_data(tmpdir, biphenyl):
"""
Make sure an error is raised if we try and prep the target with misssing data.
"""
with tmpdir.as_cwd():
torsion_target = TorsionProfile()
biphenyl.qm_scans = []
with pytest.raises(MissingReferenceData):
torsion_target.prep_for_fitting(molecule=biphenyl)
def test_forcebalance_add_target():
"""
Make sure the forcebalance optimiser can add targets when needed.
"""
fb = ForceBalanceFitting()
fb.targets = {}
torsion_target = TorsionProfile()
fb.add_target(target=torsion_target)
assert torsion_target.target_name in fb.targets
def test_torsion_metadata(tmpdir, biphenyl):
"""
Make sure that the metadata.json has the correct torsion index and torsion grid values.
"""
with tmpdir.as_cwd():
torsion_target = TorsionProfile()
torsion_target.make_metadata(torsiondrive_data=biphenyl.qm_scans[0])
with open("metadata.json") as data:
metadata = json.load(data)
assert metadata["dihedrals"] == [
[6, 10, 11, 8],
]
assert metadata["grid_spacing"] == [
15,
]
assert metadata["dihedral_ranges"] == [
[-165, 180],
]
def test_torsion_target_generation(tmpdir, biphenyl):
"""
Make sure that we can make a target from a molecule with its torsion scan data.
"""
with tmpdir.as_cwd():
torsion_target = TorsionProfile()
target_folders = torsion_target.prep_for_fitting(molecule=biphenyl)
# the name we expect for the target folder
target_name = "TorsionProfile_OpenMM_10_11"
# now make sure the folders have been made
assert len(target_folders) == 1
assert target_folders[0] == target_name
assert target_name in os.listdir()
# now we need to check the forcebalance target files have been made
required_files = [
"molecule.pdb", "metadata.json", "qdata.txt", "scan.xyz"
]
for f in required_files:
assert f in os.listdir(target_name)
def test_target_generation_ub_terms(tmpdir, biphenyl):
"""
Make sure we can make a valid target folder when we have ub terms.
"""
with tmpdir.as_cwd():
mol = biphenyl.copy(deep=True)
# add a ub term for each angle
for angle in mol.angles:
mol.BondForce.create_parameter(atoms=(angle[0], angle[2]),
length=1,
k=1)
torsion_target = TorsionProfile()
target_folders = torsion_target.prep_for_fitting(molecule=mol)
with pytest.raises(
AtomValenceException,
match=
"Explicit valence for atom # 6 C, 5, is greater than permitted",
):
_ = Ligand.from_file(
os.path.join(target_folders[0], "molecule.pdb"))