molsysviewer.MolSysView

class molsysviewer.MolSysView(*, debug_js=None)

Mol* viewer widget with a Python-facing API.

Provides structure loading, visibility control, shape management, and utilities to export static HTML views for documentation or sharing.

Parameters:

debug_js (bool | None)

__init__(*, debug_js=None)

Parameters:

debug_js (bool | None)

Return type:

None

Methods

__init__(*[, debug_js])
add(from_molecular_system, *[, selection, ...])	Add atoms/structures from another system into this view and refresh the viewer (live).
append_structures(from_molecular_system, *)	Append structures (frames) to the loaded system and refresh the viewer (live).
clear_decorations(*[, shapes, styles, labels])	Clear decorative elements (shapes/styles/labels) without touching the loaded structure or camera.
get([element, selection, structure_indices, ...])	Retrieve attribute values from the current molecular system (MolSysMT get).
get_camera_snapshot(*[, pretty])	Return the last camera snapshot received from the frontend.
hide([selection, structure_indices, syntax])	Hide atoms matching the given selection (MolSysMT syntax by default).
info([element, selection, syntax, mask, ...])
isolate([selection, structure_indices, syntax])	Show only the atoms in selection; hide everything else (reset if selection == 'all').
load(molecular_system[, selection, ...])	Load a molecular system (MolSysMT-compatible) into the viewer.
new_layer(*[, tag, kind])	Create a new layer (non-structural visual group).
new_region([selection, atom_indices, tag, ...])	Create a new region (structural subset) with an optional representation.
remove(*[, selection, structure_indices, syntax])	Remove atoms and/or structures from this view and refresh the viewer (live).
reset_camera()	Reset the camera / view in the frontend.
reset_viewer()	Fully clear the viewer and reset internal state (requires a new load(...)).
select([selection, structure_indices, ...])	Select indices from the current molecular system (MolSysMT selection language).
set(*[, element, selection, ...])	Set attribute values on the loaded system and refresh the viewer (live).
set_camera_snapshot(snapshot, *[, duration_ms])	Apply a previously saved camera snapshot.
set_controls_visible(visible, *[, autohide, ...])	Show or hide the on-canvas controls (reset/full/bg/spin/swing + trajectory bar).
show([selection, structure_indices, syntax, ...])	Show the widget (first call or if force=True) and optionally adjust visibility.
write_html(output_filename, *[, title, ...])	Export this viewer widget to an HTML file.
zoom([selection, structure_indices, syntax, ...])	Focus the camera on the geometric center of a selection of atoms.

Attributes

js_logs	Logs received from the frontend when debug_js is enabled.
layers	Public registry of layers (non-structural visuals).
molsys	Read-only handle to the loaded MolSysMT molecular system.
regions	Public registry of regions (structural selections).
visible_atom_indices	Return the indices of currently visible atoms.
visible_structure_indices	Return the indices of currently visible structures.