def test_fail_without_top(self):
# This should fail
try:
visualize.traj(self.MD_trajectory_files, "unexisting_file", self.Y)
except (OSError, IOError):
pass
# This should pass
visualize.traj(self.MD_geoms, "unexisting_file", self.Y)
def test_fail_on_FES(self):
try:
fake_4D_Ys = [np.hstack((iY, iY)) for iY in self.Ys]
visualize.traj(self.MD_trajectories,
self.MD_topology,
fake_4D_Ys,
sharey_traj=True,
plot_FES=True,
proj_idxs=[0, 1, 2])
except Exception as e:
assert isinstance(e, NotImplementedError)
def test_listify_inputs(self):
visualize.traj(self.MD_trajectories[0], self.MD_topology, self.Ys[0])
def test_simplest_inputs_memory_FES(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
plot_FES=True)
def test_simplest_inputs_memory_just_one_row(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
traj_selection=0,
proj_idxs=0)
def test_simplest_inputs_memory_and_proj_just_matrix(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
projection=self.tica.feature_TIC_correlation)
def test_simplest_inputs_memory_and_proj(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
projection=self.tica)
def test_simplest_inputs_disk(self):
visualize.traj(self.MD_trajectory_files, self.MD_topology_file,
self.projected_files)
visualize.traj(
self.MD_trajectory_files, self.MD_topology_file,
[ifile.replace('.npy', '.dat') for ifile in self.projected_files])
def test_simplest_inputs_memory_stride(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
stride=2)
def test_fail_on_FES(self):
try:
visualize.traj(self.MD_geoms, self.MD_top, self.Y, sharey_traj=True, plot_FES=True, proj_idxs=[0,1,2])
except NotImplementedError:
pass
def test_plotting_params(self):
visualize.traj(self.MD_geoms, self.MD_top, self.Y, sharey_traj=True)
def test_listify_params(self):
visualize.traj(self.MD_geoms, self.MD_top, self.Y, proj_idxs=1)
visualize.traj(self.MD_geoms, self.MD_top, self.Y, active_traj=1)
def test_listify_inputs(self):
visualize.traj(self.MD_geoms[0], self.MD_top, self.Y[0])
def test_listify_params(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
proj_idxs=1)
def test_simplest_inputs_memory_small_max_frames(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
max_frames=3)
def test_plotting_params(self):
visualize.traj(self.MD_trajectories,
self.MD_topology,
self.Ys,
sharey_traj=True)
def test_simplest_inputs_memory(self):
visualize.traj(self.MD_geoms, self.MD_top, self.Y)