def test_check_torsion_drive_scan_range():
"""
Make sure the scan range is always order lowest to largest.
"""
td = TorsionDriveData(dihedral=(6, 10, 11, 8),
torsion_drive_range=(10, -90))
assert td.torsion_drive_range == (-90, 10)
def test_from_qdata():
"""
Make sure we can create a valid TorsionDriveData from qdata.
"""
td = TorsionDriveData.from_qdata(dihedral=(6, 10, 11, 8),
qdata_file=get_data("biphenyl_qdata.txt"))
# validate all angles
td.validate_angles()
def test_max_min_angle():
"""
Make sure the max and min angle are updated.
"""
td = TorsionDriveData(dihedral=(6, 10, 11, 8),
torsion_drive_range=(-40, 40))
assert td.max_angle == 40
assert td.min_angle == -40
def test_missing_reference_data():
"""
Make sure that missing reference data is identified in a TorsionDriveData object.
"""
td = TorsionDriveData.from_qdata(dihedral=(6, 10, 11, 8),
qdata_file=get_data("biphenyl_qdata.txt"))
del td.reference_data[0]
with pytest.raises(MissingReferenceData):
td.validate_angles()
def test_inconsistent_scan_range():
"""
Make sure an error is raised if we try and make a torsiondrivedata object which is inconsistent.
"""
with pytest.raises(TorsionDriveDataError):
_ = TorsionDriveData.from_qdata(
dihedral=(6, 10, 11, 8),
qdata_file=get_data("biphenyl_qdata.txt"),
grid_spacing=10,
)
def test_qdata_round_trip(tmpdir):
"""
Try and round trip a qdata txt file to a TorsionDriveData object and back.
"""
with tmpdir.as_cwd():
mol = Ligand.from_file(file_name=get_data("biphenyl.sdf"))
td_ref = TorsionDriveData.from_qdata(
dihedral=(6, 10, 11, 8), qdata_file=get_data("biphenyl_qdata.txt"))
# now write to file
export_torsiondrive_data(molecule=mol, tdrive_data=td_ref)
# now make a second object
td_new = TorsionDriveData.from_qdata(dihedral=(6, 10, 11, 8),
qdata_file="qdata.txt")
assert td_ref.dihedral == td_new.dihedral
for angle, ref_result in td_ref.reference_data.items():
new_result = td_new.reference_data[angle]
assert ref_result.angle == new_result.angle
assert ref_result.energy == pytest.approx(new_result.energy)
assert np.allclose(ref_result.geometry.tolist(),
new_result.geometry.tolist())
def biphenyl():
"""
Load up a biphenyl molecule with some torsiondrive data.
"""
# load biphenyl
mol = Ligand.from_file(file_name=get_data("biphenyl.sdf"))
# load the torsiondrive data
td_data = TorsionDriveData.from_qdata(
qdata_file=get_data("biphenyl_qdata.txt"), dihedral=(6, 10, 11, 8))
mol.add_qm_scan(scan_data=td_data)
return mol
def _collect_results(self, td_state: Dict[str, Any],
molecule: "Ligand") -> "Ligand":
"""
After the torsiondrive has been completed collect the results and pack them into the ligand.
"""
# torsiondrive will only give us the lowest energy for each grid point
# we have to then work out what the final geometry is from this
optimised_energies = td_api.collect_lowest_energies(td_state=td_state)
final_grid = td_state["grid_status"]
# make a torsiondrive data store assuming 1D only
torsion_data = TorsionDriveData(
grid_spacing=self.grid_spacing,
dihedral=td_state["dihedrals"][0],
torsion_drive_range=td_state["dihedral_ranges"][0],
)
# now grab each grid point in sorted order
for (
angle,
energy,
) in sorted(optimised_energies.items()):
# grab all optimisation done at this angle
optimisations = final_grid[str(angle[0])]
# loop over each result and check if the energy matches the lowest
# results -> (initial geometry, final geometry, final energy)
for result in optimisations:
if result[-1] == energy:
grid_data = TorsionData(
angle=angle[0],
geometry=np.array(result[1]) * constants.BOHR_TO_ANGS,
energy=energy,
)
torsion_data.add_grid_point(grid_data=grid_data)
break
# validate the data
torsion_data.validate_angles()
# dump to file (qdata.txt and scan.xyz)
export_torsiondrive_data(molecule=molecule, tdrive_data=torsion_data)
# dump the qubekit torsion data to file
torsion_data.to_file("scan_data.json")
# save to mol
molecule.add_qm_scan(scan_data=torsion_data)
# dump the torsiondrive state to file
self._dump_state(td_state=td_state)
# now remove all temp folders
for f in os.listdir("."):
if os.path.isdir(f):
shutil.rmtree(f, ignore_errors=True)
return molecule
def test_central_bond():
"""
Check the central bond property.
"""
td = TorsionDriveData(dihedral=(6, 10, 11, 8))
assert td.central_bond == (10, 11)