nanome.api.plugin_instance module

class AsyncPluginInstance

Bases: nanome.api.plugin_instance.PluginInstance

Base class of any asynchronous plugin.

Constructor should never be called by the user as it is network-instantiated when a session connects.

All methods available to PluginInstance are available to AsyncPluginInstance.

Decorating these methods with @async_callback will allow them to use the async keyword in their definition

is_async = True

class PluginInstance

Bases: object

Base class of any plugin.

Constructor should never be called by the user as it is network-instantiated when a session connects.

Start, update, and all methods starting by “on” can be overridden by user, in order to get requests results

add_bonds(complex_list, callback=None, fast_mode=None)

Calculate bonds

Requires openbabel to be installed

Parameters:

• complex_list (list of Complex) – List of complexes to add bonds to
• callback (Callable[[List[Complex]], None]) – Callback when bonds are calculated.

add_dssp(complex_list, callback=None)

Use DSSP to calculate secondary structures

Parameters:

• complex_list (list of Complex) – List of complexes to add ribbons to
• callback (Callable[[List[Complex]], None]) – Callback when DSSP is calculated.

add_to_workspace(complex_list, callback=None)

Add a list of complexes to the current workspace

Parameters:

• complex_list (list of Complex) – List of Complexes to add
• callback (Callable[[], None]) – Callback when request is done.

add_volume(complex, volume, properties, complex_to_align_index=-1, callback=None)

apply_color_scheme(color_scheme, target, only_carbons)

Applies a color scheme to selected atoms.

Parameters:

• color_scheme (ColorScheme) – the color scheme to use on atoms
• target (ColorSchemeTarget) – whether you want to color the atom, the surface, or the ribbon
• only_carbons (bool) – whether you want to only color carbons, or all atoms.

center_on_structures(structures, callback=None)

Repositions the workspace such that the provided structure(s) will be in the

center of the world.

Parameters:

• structures (list of Base) – Molecular structure(s) to update.
• callback (Callable[[], None]) – Callback when center is done.

create_atom_stream(atom_indices_list, stream_type, callback)

create_reading_stream(indices_list, stream_type, callback=None)

Create a stream allowing the plugin to continuously receive properties of many objects

Parameters:

• indices_list (list of int) – List of indices of all objects that should be in the stream
• stream_type (list of Type) – Type of stream to create
• callback (Callable[[Stream, StreamCreationError], None]) – Callback to receive the created stream.

create_shape(shape_type)

create_stream(atom_indices_list, callback)

create_writing_stream(indices_list, stream_type, callback=None)

Create a stream allowing the plugin to continuously update properties of many objects

Parameters:

• indices_list (list of int) – List of indices of all objects that should be in the stream
• stream_type (list of Type) – Type of stream to create
• callback (Callable[[Stream, StreamCreationError], None]) – Callback to receive the created stream.

custom_data

Get custom data set with Plugin.set_custom_data

Type:tuple of objects or None if no data has been set

is_async = False

menu

on_advanced_settings()

Called when user presses “Advanced Settings”

on_complex_added()

Called whenever a complex is added to the workspace.

on_complex_list_changed()

Called whenever a complex is added or removed from the workspace.

on_complex_removed()

Called whenever a complex is removed from the workspace.

on_presenter_change()

Called when room’s presenter changes.

on_run()

Called when user presses “Run”

on_stop()

Called when user disconnects or plugin crashes

open_url(url, desktop_browser=False)

Opens a URL alongside the Nanome session in the default web browser.

Parameters:

• url (str) – url to open
• desktop_browser (bool) – Whether to open the URL in the default web browser or in the Nanome session

plugin_files_path

remove_from_workspace(complex_list, callback=None)

Remove a list of complexes from the current workspace

Parameters:

• complex_list (list of Complex) – List of Complexes to remove
• callback (Callable[[], None]) – Callback when request is done.

request_complex_list(callback=None)

Request the list of all complexes in the workspace, in shallow mode.

Parameters:callback (Callable[[List[Complex]], None]) – Callback to receive list of complexes.

request_complexes(id_list, callback=None)

Requests a list of complexes by their indices

Complexes returned contains the full structure (atom/bond/residue/chain/molecule)

Parameters:

• id_list (list of int) – List of indices
• callback (Callable[[List[Complex]], None]) – Callback to receive list of complexes.

request_controller_transforms(callback=None)

Requests presenter controller info (head position, head rotation, left controller position, left controller rotation, right controller position, right controller rotation)

Parameters:callback (Callable[[Vector3, Quaternion, Vector3, Quaternion, Vector3, Quaternion], None]) – Callback to receive the presenter controller info.

request_directory(path, callback=None, pattern='*')

Requests the content of a directory on the machine running Nanome

Parameters:

• path (str) – Path to request. E.g. “.” means Nanome’s running directory
• pattern (str) – Pattern to match. E.g. “.txt” will match all .txt files. Default value is “” (match everything)

request_export(format, callback=None, entities=None)

Request a file export using Nanome exporters Can request either molecule or workspace export, for entities in Nanome workspace or directly sent by the plugin (without begin uploaded to workspace)

Parameters:

• format (ExportFormats) – File format to export
• entities (list of or unique object of type Workspace or Complex, or None, or list of or unique int) – Entities to export (complexes to send, or indices if referencing complexes in workspace, or a workspace, or nothing if exporting Nanome workspace)
• callback (Callable[[Union[str, bytes]], None]) – Callback when file is exported.

request_files(file_list, callback=None)

Reads files on the machine running Nanome, and returns them

Parameters:file_list (list of str) – List of file name (with path) to read. E.g. [“a.sdf”, “../b.sdf”] will read a.sdf in running directory, b.sdf in parent directory, and return them

request_menu_transform(index, callback=None)

Requests spatial information of the plugin menu (position, rotation, scale)

Parameters:

• index (int) – Index of the menu you wish to read
• callback (Callable[[Vector3, Quaternion, Vector3], None]) – Callback to receive the menu’s position, rotation, and scale.

request_presenter_info(callback=None)

Requests presenter account info (unique ID, name, email)

Parameters:callback (Callable[[PresenterInfo], None]) – Callback to receive the presenter account info.

request_workspace(callback=None)

Request the entire workspace, in deep mode

Parameters:callback (Callable[[Workspace], None]) – Callback to receive workspace.

save_files(file_list, callback=None)

Save files on the machine running Nanome, and returns result

Parameters:

• file_list (list of FileSaveData) – List of files to save with their content
• callback – Callback to receive save file results.

send_files_to_load(files_list, callback=None)

Send file(s) to Nanome to load directly using Nanome’s importers.

Can send just a list of paths, or a list of tuples containing (path, name)

Parameters:

• files_list (list of or unique object of type str or (str, str)) – List of files to load
• callback (Callable[[], None]) – Callback when files are loaded.

send_notification(type, message)

Send a notification to the user

Parameters:

• type (NotificationTypes) – Type of notification to send.
• message (str) – Text to display to the user.

set_menu_transform(index, position, rotation, scale)

Update the position, scale, and rotation of the menu

Parameters:

• index (int) – Index of the menu you wish to update
• position (vector3) – New position of the menu
• rotation (quaternion) – New rotation of the menu
• scale (vector3) – New scale of the menu

set_plugin_list_button(button, text=None, usable=None)

Set text and/or usable state of the buttons on the plugin connection menu in Nanome

Parameters:

• button (ButtonType) – Button to set
• text (str) – Text displayed on the button. If None, doesn’t set text
• usable (bool) – Set button to be usable or not. If None, doesn’t set usable text

start()

Called when user “Activates” the plugin

update()

Called when instance updates (multiple times per second)

update_content(*content)

Update specific UI elements (button, slider, list…)

Parameters:content (UIBase or multiple UIBase or a list of UIBase) – UI elements to update

update_menu(menu, shallow=False)

Update the menu in Nanome

Parameters:

• menu (Menu) – Menu to update
• shallow (bool) – Whether you want to update only the menu’s top level, or the whole tree.

update_node(*nodes)

Updates layout nodes and their children

Parameters:nodes (LayoutNode or multiple LayoutNode or a list of LayoutNode) – Layout nodes to update

update_structures_deep(structures, callback=None)

Update the specific molecular structures in the scene to match the structures in parameter.

Will also update descendent structures and can be used to remove descendent structures.

Parameters:

• structures (list of Base) – List of molecular structures to update.
• callback (Callable[[], None]) – Callback when update is done.

update_structures_shallow(structures)

Update the specific molecular structures in the scene to match the structures in parameter

Only updates the structure’s data, will not update children or other descendents.

Parameters:structures (list of Base) – List of molecular structures to update.

update_workspace(workspace)

Replace the current workspace in the scene by the workspace in parameter

Parameters:workspace (Workspace) – New workspace

zoom_on_structures(structures, callback=None)

Repositions and resizes the workspace such that the provided structure(s) will be in the

center of the users view.

Parameters:

• structures (list of Base) – Molecular structure(s) to update.
• callback (Callable[[], None]) – Callback when zoom is done.