dynsight.trajectory.OnionSmoothInsight¶

class dynsight.trajectory.OnionSmoothInsight(labels, state_list, meta=<factory>)[source]¶

Contains a smooth onion-clustering analysis.

Parameters:

labels (NDArray[np.int64])
state_list (list[StateUni] | list[StateMulti])
meta (dict[str, Any])

labels¶: The labels assigned by the clustering algorithm.

state_list¶

List of the onion-clustering Gaussian states.

Type:: list[StateUni] | list[StateMulti]

meta¶

A dictionary containing the relevant parameters.

Type:: dict[str, Any]

Methods

`dump_colored_trj`	Save an .xyz file with the clustering labels for each atom.
`dump_to_json`	Save the OnionSmoothInsight object to JSON and .npy for labels.
`load_from_json`	Load the OnionSmoothInsight from JSON and associated .npy file.
`plot_one_trj`	Plot one particle's trajectory colored according to clustering.
`plot_output`	Plot the overall onion clustering result.
`plot_sankey`	Plot the Sankey diagram of the onion clustering.
`plot_state_populations`	Plot each state's population along the trajectory.

Attributes

`state_list`
`meta`
`labels`

dump_colored_trj(trj, file_path)[source]¶

Save an .xyz file with the clustering labels for each atom.

Parameters:

trj (Trj)
file_path (Path)

Return type:

None

dump_to_json(file_path)[source]¶

Save the OnionSmoothInsight object to JSON and .npy for labels.

Parameters:: file_path (Path)
Return type:: None

classmethod load_from_json(file_path, mmap_mode=None)[source]¶

Load the OnionSmoothInsight from JSON and associated .npy file.

Parameters:

file_path (Path) – Path to the .json file.
mmap_mode (Literal['r', 'r+', 'w+', 'c'] | None) – If given, used as np.load(…, mmap_mode=mmap_mode) for memory mapping.

Raises:

ValueError – if required keys are missing.

Return type:

OnionSmoothInsight

plot_one_trj(file_path, data_insight, particle_id)[source]¶

Plot one particle’s trajectory colored according to clustering.

Parameters:

file_path (Path)
data_insight (Insight)
particle_id (int)

Return type:

None

plot_output(file_path, data_insight)[source]¶

Plot the overall onion clustering result.

Parameters:

file_path (Path)
data_insight (Insight)

Return type:

None

plot_sankey(file_path, frame_list)[source]¶

Plot the Sankey diagram of the onion clustering.

Parameters:

file_path (Path)
frame_list (list[int])

Return type:

None

plot_state_populations(file_path)[source]¶

Plot each state’s population along the trajectory.

Parameters:: file_path (Path)
Return type:: None