def test_join_failures(self):
dt = load(xtc, top=pdb)
dt2 = "not a trajectory"
# Not a trajectory
with pytest.raises(TypeError) as err:
_ = dt.join(dt2)
assert "must be a list of Trajectory" in str(err.value)
with pytest.raises(TypeError) as err:
_ = dt.join([dt2])
assert "only join Trajectory instances" in str(err.value)
dt2 = load(xtc, top=pdb)
dt2.top = None # Remove topology
with pytest.raises(ValueError) as err:
_ = dt.join([dt2])
assert "The topologies of the Trajectories are not" in str(err.value)
dt2 = load(xtc, top=pdb)
_ = dt2.unitcell_lengths
dt2.atom_slice([1, 2, 3], inplace=True)
with pytest.raises(ValueError) as err:
_ = dt.join([dt2])
assert "Number of atoms" in str(err.value)
dt2 = load(xtc, top=pdb)
dt2.unitcell_vectors = None # Remove unitcell
with pytest.raises(ValueError) as err:
_ = dt.join([dt2])
assert "unitcell" in str(err.value)
def test_trajectory_to_mdtraj_with_unitcell_lengths(self):
dask_traj = load(xtc, top=pdb)
# Trigger the calculation of unitcell lengths
_ = dask_traj.unitcell_lengths
md_traj = md.load(xtc, top=pdb)
dask_traj.to_mdtraj()
assert dask_traj == md_traj
def test_wrong_uv_length(self):
dask_traj = load(xtc, top=pdb)
with pytest.raises(TypeError) as err:
dask_traj._calc_length_and_angles([1, 2, 3])
def test_calc_uv_without_ul_or_ua(self):
dask_traj = load(xtc, top=pdb)
dask_traj.unitcell_vectors = None
assert dask_traj._calc_unitcell_vectors() is None
def test_set_xyz_without_top(self):
dask_traj = load(xtc, top=pdb)
dask_traj.top = None
assert dask_traj.top is None
dask_traj.xyz = np.array([[[1.0, 2.0, 3.0]]], dtype=np.float32)
assert (dask_traj._xyz == np.array([[[1.0, 2.0, 3.0]]])).all()
def test_trajectory_to_mdtraj(self):
dask_traj = load(xtc, top=pdb)
md_traj = md.load(xtc, top=pdb)
dask_traj.to_mdtraj()
assert dask_traj == md_traj
def test_hash(self):
dt = load(xtc, top=pdb)
dt2 = load(xtc, top=pdb)
assert dt == dt2 # This will compare hashes
def test_join_discard_overlap(self):
dt = load(xtc, top=pdb)
dt2 = load(xtc, top=pdb)
dt3 = dt.join(dt2[::-1], discard_overlapping_frames=True)
assert len(dt3) == len(dt) + len(dt2) - 1
def test_join(self):
dt = load(xtc, top=pdb)
dt2 = load(xtc, top=pdb)
dt3 = dt.join(dt2)
assert len(dt3) == len(dt) + len(dt2)