def test_fit_translation_bad_plane(fit_universe, plane):
ts = fit_universe[0].trajectory.ts
test_u = fit_universe[0]
ref_u = fit_universe[1]
# what happens if a bad string for center is given?
with pytest.raises(ValueError):
fit_translation(test_u, ref_u, plane=plane)(ts)
def test_fit_translation_bad_ag(fit_universe, universe):
ts = fit_universe[0].trajectory.ts
test_u = fit_universe[0]
ref_u = fit_universe[1]
# what happens if something other than an AtomGroup or Universe is given?
with pytest.raises(AttributeError):
fit_translation(universe, ref_u)(ts)
def test_fit_translation_no_options(fit_universe):
test_u = fit_universe[0]
ref_u = fit_universe[1]
fit_translation(test_u, ref_u)(test_u.trajectory.ts)
# what happens when no options are passed?
assert_array_almost_equal(test_u.trajectory.ts.positions,
ref_u.trajectory.ts.positions,
decimal=6)
def test_fit_translation_com(fit_universe):
test_u = fit_universe[0]
ref_u = fit_universe[1]
fit_translation(test_u, ref_u, weights="mass")(test_u.trajectory.ts)
# what happens when the center o mass is used?
assert_array_almost_equal(test_u.trajectory.ts.positions,
ref_u.trajectory.ts.positions,
decimal=6)
def test_fit_translation_no_masses(fit_universe):
ts = fit_universe[0].trajectory.ts
test_u = fit_universe[0]
# create a universe without masses
ref_u = make_Universe()
# what happens Universe without masses is given?
with pytest.raises(AttributeError):
fit_translation(test_u, ref_u, weights="mass")(ts)
def test_fit_translation_no_masses(fit_universe):
ts = fit_universe[0].trajectory.ts
test_u = fit_universe[0]
# create a universe without masses
ref_u = make_Universe()
# what happens Universe without masses is given?
with pytest.raises(TypeError) as exc:
fit_translation(test_u, ref_u, weights="mass")(ts)
assert 'atoms.masses is missing' in str(exc.value)
def test_fit_translation_all_options(fit_universe):
test_u = fit_universe[0]
ref_u = fit_universe[1]
# translate the test universe on the x and y coordinates only
fit_translation(test_u, ref_u, plane="xy",
weights="mass")(test_u.trajectory.ts)
# the reference is 10 angstrom in the z coordinate above the test universe
shiftz = np.asanyarray([0, 0, -10], np.float32)
ref_coordinates = ref_u.trajectory.ts.positions + shiftz
assert_array_almost_equal(test_u.trajectory.ts.positions,
ref_coordinates,
decimal=6)
def test_fit_translation_plane(fit_universe, plane):
test_u = fit_universe[0]
ref_u = fit_universe[1]
axes = {'yz': 0, 'xz': 1, 'xy': 2}
idx = axes[plane]
# translate the test universe on the plane coordinates only
fit_translation(test_u, ref_u, plane=plane)(test_u.trajectory.ts)
# the reference is 10 angstrom in all coordinates above the test universe
shiftz = np.asanyarray([0, 0, 0], np.float32)
shiftz[idx] = -10
ref_coordinates = ref_u.trajectory.ts.positions + shiftz
assert_array_almost_equal(test_u.trajectory.ts.positions,
ref_coordinates,
decimal=6)
def test_fit_translation_transformations_api(fit_universe):
test_u = fit_universe[0]
ref_u = fit_universe[1]
transform = fit_translation(test_u, ref_u)
test_u.trajectory.add_transformations(transform)
assert_array_almost_equal(test_u.trajectory.ts.positions,
ref_u.trajectory.ts.positions,
decimal=6)
def test_fit_translation_residue_mismatch(fit_universe):
test_u = fit_universe[0]
ref_u = fit_universe[1].residues[:-1].atoms
with pytest.raises(ValueError, match='number of residues'):
fit_translation(test_u, ref_u)(test_u.trajectory.ts)
