def test_full_tdrive(tmpdir, workers, capsys):
"""
Try and run a full torsiondrive for ethane with a cheap rdkit method.
"""
with tmpdir.as_cwd():
ethane = Ligand.from_file(get_data("ethane.sdf"))
# make the scan data
bond = ethane.find_rotatable_bonds()[0]
dihedral = ethane.dihedrals[bond.indices][0]
dihedral_data = TorsionScan(torsion=dihedral, scan_range=(-165, 180))
qc_spec = QCOptions(program="rdkit", basis=None, method="uff")
local_ops = LocalResource(cores=workers, memory=2)
tdriver = TorsionDriver(
n_workers=workers,
grid_spacing=60,
)
_ = tdriver.run_torsiondrive(
molecule=ethane,
dihedral_data=dihedral_data,
qc_spec=qc_spec,
local_options=local_ops,
)
captured = capsys.readouterr()
# make sure a fresh torsiondrive is run
assert "Starting new torsiondrive" in captured.out
def test_tdrive_restarts(capsys, ethane_state, tmpdir):
"""
Make sure that an old torsiondrive is continued when possible from the current state file.
"""
with tmpdir.as_cwd():
ethane_state["grid_spacing"] = [
60,
]
mol = Ligand.from_file(get_data("ethane.sdf"))
tdriver = TorsionDriver(n_workers=1, grid_spacing=60)
qc_spec = QCOptions(program="rdkit", basis=None, method="uff")
local_ops = LocalResource(cores=1, memory=1)
geo_opt = tdriver._build_geometry_optimiser()
# get the job inputs
new_jobs = tdriver._get_new_jobs(td_state=ethane_state)
coords = new_jobs["-60"][0]
result = optimise_grid_point(
geometry_optimiser=geo_opt,
qc_spec=qc_spec,
local_options=local_ops,
molecule=mol,
coordinates=coords,
dihedral=ethane_state["dihedrals"][0],
dihedral_angle=-60,
job_id=0,
)
_ = tdriver._update_state(
td_state=ethane_state,
result_data=[
result,
],
)
# now start a run and make sure it continues
_ = tdriver.run_torsiondrive(
molecule=mol,
dihedral_data=TorsionScan(torsion=ethane_state["dihedrals"][0],
scan_range=(-165, 180)),
qc_spec=qc_spec,
local_options=local_ops,
)
capture = capsys.readouterr()
assert ("Compatible TorsionDrive state found restarting torsiondrive!"
in capture.out)
def test_full_tdrive(tmpdir):
"""
Try and run a full torsiondrive for ethane with a cheap rdkit method.
"""
with tmpdir.as_cwd():
ethane = Ligand.from_file(get_data("ethane.sdf"))
# make the scan data
bond = ethane.find_rotatable_bonds()[0]
dihedral = ethane.dihedrals[bond.indices][0]
dihedral_data = TorsionScan(torsion=dihedral, scan_range=(-165, 180))
tdriver = TorsionDriver(
program="rdkit",
method="uff",
basis=None,
memory=2,
cores=1,
n_workers=1,
grid_spacing=60,
)
_ = tdriver.run_torsiondrive(molecule=ethane,
dihedral_data=dihedral_data)