def test_select_average(self, universe: md.Trajectory) -> None:
"""Test get_average_structure function using atom selection.
GIVEN topology and trajectory filenames and an atom selection
WHEN the get_average_structure function is called
THEN the average coordinates are computed
Parameters
----------
universe : Trajectory
Molecular dynamics trajectory
"""
mask = "protein and name CA"
atoms = universe.topology.select(mask)
n_atoms = atoms.size
average = utils.get_average_structure(
TOPWW,
[
TRJWW,
],
mask=mask,
)
assert average.xyz.shape == (1, n_atoms, 3)
universe_average = universe.atom_slice(atoms).xyz.mean(axis=0)
testing.assert_allclose(average.xyz[0], universe_average)
def test_select_positions(self, universe: md.Trajectory,
n_frames: int) -> None:
"""Test get_positions function using atom selection.
GIVEN topology and trajectory filenames and an atom selection
WHEN the get_positions function is called
THEN return a array of positions with shape (n_frames, n_atoms, 3)
Parameters
----------
universe : Trajectory
Molecular dynamics trajectory
n_frames : int
Number of frames
"""
mask = "protein and name CA"
atoms = universe.topology.select(mask)
n_atoms = atoms.size
array = utils.get_positions(
TOPWW,
[
TRJWW,
],
mask=mask,
)
assert array.shape == (n_frames, n_atoms, 3)
testing.assert_allclose(array[0],
universe.atom_slice(atoms).xyz[0] * 10)
assert isinstance(array, np.ndarray)
