def test_reduced_box_vectors():
pytest.importorskip("mdtraj")
box = np.array([[6.70596027, 0., 0.], [0., 6.70596027, 0.],
[3.35299015, 3.35299015, 4.74183893]])
# TODO: replace this with a proper raises test in pytest
try:
check_reduced_box_vectors(box)
except BoxVectorWarning:
pass
else:
raise AssertionError("Box already reduced")
if not HAS_OPENMM:
pytest.skip()
snap = mock_snapshot_with_box_vector(box * nm)
reduced_box = reduced_box_vectors(snap).value_in_unit(nm)
check_reduced_box_vectors(reduced_box)
assert not all(box.flatten() == reduced_box.flatten())
orig_lengths_angles = box_vectors_to_lengths_and_angles(*box)
red_lengths_angles = box_vectors_to_lengths_and_angles(*reduced_box)
orig_lengths = orig_lengths_angles[:3]
red_lengths = red_lengths_angles[:3]
npt.assert_allclose(orig_lengths, red_lengths, atol=1e-4)
def test_reduce_trajectory_box_vectors():
box = np.array([[6.70596027, 0., 0.], [0., 6.70596027, 0.],
[3.35299015, 3.35299015, 4.74183893]])
snap_1 = mock_snapshot_with_box_vector(box)
reduced_box = reduced_box_vectors(snap_1).value_in_unit(nm)
snap_2 = mock_snapshot_with_box_vector(reduced_box)
traj = paths.Trajectory([snap_1, snap_2])
red_traj = reduce_trajectory_box_vectors(traj)
orig_box = traj.box_vectors
red_box = red_traj.box_vectors
assert not all(orig_box[0].flatten() == red_box[0].flatten())
npt.assert_allclose(red_box[0], red_box[1])
for reduced in red_box:
check_reduced_box_vectors(reduced.value_in_unit(nm))
def test_reduce_trajectory_box_vectors():
box = np.array([[ 6.70596027, 0., 0. ],
[ 0., 6.70596027, 0. ],
[ 3.35299015, 3.35299015, 4.74183893]])
snap_1 = mock_snapshot_with_box_vector(box)
reduced_box = reduced_box_vectors(snap_1).value_in_unit(nm)
snap_2 = mock_snapshot_with_box_vector(reduced_box)
traj = paths.Trajectory([snap_1, snap_2])
red_traj = reduce_trajectory_box_vectors(traj)
orig_box = traj.box_vectors
red_box = red_traj.box_vectors
assert not all(orig_box[0].flatten() == red_box[0].flatten())
npt.assert_allclose(red_box[0], red_box[1])
for reduced in red_box:
check_reduced_box_vectors(reduced.value_in_unit(nm))
def test_reduced_box_vectors():
box = np.array([[ 6.70596027, 0., 0. ],
[ 0., 6.70596027, 0. ],
[ 3.35299015, 3.35299015, 4.74183893]])
# TODO: replace this with a proper raises test in pytest
try:
check_reduced_box_vectors(box)
except BoxVectorWarning:
pass
else:
raise AssertionError("Box already reduced")
snap = mock_snapshot_with_box_vector(box * nm)
reduced_box = reduced_box_vectors(snap).value_in_unit(nm)
check_reduced_box_vectors(reduced_box)
assert not all(box.flatten() == reduced_box.flatten())
orig_lengths_angles = box_vectors_to_lengths_and_angles(*box)
red_lengths_angles = box_vectors_to_lengths_and_angles(*reduced_box)
orig_lengths = orig_lengths_angles[:3]
red_lengths = red_lengths_angles[:3]
npt.assert_allclose(orig_lengths, red_lengths, atol=1e-4)