def test_fit_rot_trans_no_options(fit_universe):
test_u = fit_universe[0]
ref_u = fit_universe[1]
ref_com = ref_u.atoms.center(None)
ref_u.trajectory.ts.positions -= ref_com
R = rotation_matrix(np.pi / 3, [1, 0, 0])[:3, :3]
ref_u.trajectory.ts.positions = np.dot(ref_u.trajectory.ts.positions, R)
ref_u.trajectory.ts.positions += ref_com
fit_rot_trans(test_u, ref_u)(test_u.trajectory.ts)
assert_array_almost_equal(test_u.trajectory.ts.positions,
ref_u.trajectory.ts.positions,
decimal=3)
def test_fit_rot_trans_plane(fit_universe, plane):
# the reference is rotated in the x axis so removing the translations and rotations
# in the yz plane should return the same as the fitting without specifying a plane
test_u = fit_universe[0]
ref_u = fit_universe[1]
ref_com = ref_u.atoms.center(None)
mobile_com = test_u.atoms.center(None)
axes = {'yz': 0, 'xz': 1, 'xy': 2}
idx = axes[plane]
rotaxis = np.asarray([0, 0, 0])
rotaxis[idx] = 1
ref_u.trajectory.ts.positions -= ref_com
R = rotation_matrix(np.pi / 3, rotaxis)[:3, :3]
ref_u.trajectory.ts.positions = np.dot(ref_u.trajectory.ts.positions, R)
ref_com[idx] = mobile_com[idx]
ref_u.trajectory.ts.positions += ref_com
fit_rot_trans(test_u, ref_u, plane=plane)(test_u.trajectory.ts)
assert_array_almost_equal(test_u.trajectory.ts.positions[:, idx],
ref_u.trajectory.ts.positions[:, idx],
decimal=3)
def test_fit_rot_trans_bad_plane(fit_universe, plane):
test_u = fit_universe[0]
ref_u = fit_universe[1]
with pytest.raises(ValueError):
fit_rot_trans(test_u, ref_u, plane=plane)(test_u.trajectory.ts)
def test_fit_rot_trans_bad_weights(fit_universe, weights):
test_u = fit_universe[0]
ref_u = fit_universe[1]
bad_weights = weights
with pytest.raises(ValueError):
fit_rot_trans(test_u, ref_u, weights=bad_weights)(test_u.trajectory.ts)
def test_fit_rot_trans_shorter_universe(fit_universe):
ref_u = fit_universe[1]
bad_u = fit_universe[0].atoms[0:5]
test_u = bad_u
with pytest.raises(ValueError):
fit_rot_trans(test_u, ref_u)(test_u.trajectory.ts)
def test_fit_rot_trans_bad_universe(fit_universe, universe):
test_u = fit_universe[0]
ref_u = universe
with pytest.raises(AttributeError):
fit_rot_trans(test_u, ref_u)(test_u.trajectory.ts)