nanover.jupyter.ghosts module

class nanover.jupyter.ghosts.GhostMoleculeData(*, system_atom_indices: collections.abc.Sequence[int], ghost_atom_positions: NDArray, ghost_bond_pairs: collections.abc.Sequence[collections.abc.Sequence[int]])

Bases: object

draw(key, *, visuals: SceneObjectsUtility, parent='simulation')

classmethod from_atom_group(atom_group: AtomGroup)

classmethod from_frame_data(frame_data: FrameData, *, atom_indices: Iterable[int] | None = None)

ghost_atom_positions: NDArray

ghost_bond_pairs: Sequence[Sequence[int]]

system_atom_indices: Sequence[int]

class nanover.jupyter.ghosts.GhostMoleculeObject(key: str, ghost_data: nanover.jupyter.ghosts.GhostMoleculeData, utilities: nanover.jupyter.utilities.NanoverServerUtilities, visuals: nanover.jupyter.utilities.SceneObjectsUtility)

Bases: object

clear()

classmethod from_ghost_data(key: str, *, utilities, ghost_data: GhostMoleculeData, parent='simulation')

ghost_data: GhostMoleculeData

key: str

redraw()

utilities: NanoverServerUtilities

visuals: SceneObjectsUtility

nanover.jupyter.ghosts.draw_ghost(key: str, *, visuals: SceneObjectsUtility, positions: NDArray, bond_pairs: Sequence[Sequence[int]], parent='simulation')