jhsmit / ipymolstar Goto Github PK

The aim of this issue is to track which of the traitlets on PDBeMolstar are implemented and which are tested and confirmed to work.
For each traitlet we keep track of correct behaviour on initial load and triggering upon changing the value.

Untested (might work):

• assembly_id (initial/trigger)
• default_preset (initial/trigger)
• ligand_view (initial/trigger)
• alphafold_view (initial/trigger)
• superposition (initial/trigger)
• superposition_params (initial/trigger)
• visual_style (initial/trigger)
• hide_non_standard (initial/trigger)
• hide_coarse (initial/trigger)
• load_maps (initial/trigger)
• map_settings (initial/trigger)
• highlight_color (initial/trigger)
• select_color (initial/trigger)
• validation_annotation (initial/trigger)
• domain_annotation (initial/trigger)
• symmetry_annotation (initial/trigger)
• pdbe_url (initial/trigger)
• encoding (initial/trigger)
• low_precision_coords (initial/trigger)
• select_interaction (initial/trigger)
• granularity (initial/trigger)
• subscribe_events (initial/trigger)
• hide_controls (initial/trigger)
• hide_controls_icon (initial/trigger)
• hide_expand_icon (initial/trigger)
• hide_settings_icon (initial/trigger)
• hide_selection_icon (initial/trigger)
• hide_animation_icon (initial/trigger)
• sequence_panel (initial/trigger)
• pdbe_link (initial/trigger)
• loading_overlay (initial/trigger)
• expanded (initial/trigger)
• landscape (initial/trigger)
• _focus (initial/trigger)
• _highlight (initial/trigger)
• _clear_highlight (initial/trigger)
• color_data (initial/trigger)
• _clear_selection (initial/trigger)
• _set_color (initial/trigger)
• _reset (initial/trigger)
• _update (initial/trigger)

Works and tested:

• height (initial)
• molecule_id (initial/trigger) (must be lower case str, cannot be empty unless custom_data is given)
• custom_data (initial/trigger)
• bg_color (initial/trigger)
• spin (initial/trigger)
• hide_polymer (initial/trigger)
• hide_water (initial/trigger)
• hide_heteroatoms (initial/trigger)
• hide_carbs (initial/trigger)

Does not work

• height (trigger); a new height can be set but a new render is needed
• lighting (initial/trigger); not working in JS plugin plunkr example

(this post is edited when traitlets are tested and confirmed to work / not work)

Full list can be found here:

https://github.com/molstar/pdbe-molstar/blob/ab7efdb4bc55536afc95a0282e4fd17b609d3035/src/app/spec.ts#L67

• moleculeId
• customData
• assemblyId
• defaultPreset
• ligandView
• alphafoldView
• superposition
• superpositionParams
• selection
• visualStyle
• hideStructure
• loadMaps
• mapSettings
• bgColor
• highlightColor
• selectColor
• lighting
• validationAnnotation
• domainAnnotation
• symmetryAnnotation
• pdbeUrl
• encoding
• lowPrecisionCoords
• selectInteraction
• selectBindings
• focusBindings
• granularity
• subscribeEvents
• hideControls
• hideCanvasControls
• sequencePanel
• pdbeLink
• loadingOverlay
• expanded
• landscape
• reactive

Hello,

It looks like the Jupyterlite demo is not working.

When running the demo at https://jhsmit.github.io/ipymolstar-demo/lab/index.html with the notebook ipymolstar_example.ipynb, I got this Javascript error:

Do you have any idea what it should be done with AnyModel ?

There seems to be an issue importing PDBeMolstarPlugin from npm

molstar/pdbe-molstar#99

Hello,

It looks like the Ploomber demo site (https://purple-glade-1760.ploomberapp.io/) is not working. The link leads to an authentication page at Ploomber, that eventually shows an empty dashboard-like page:

Do you have any idea how I could run the demo at Ploomber?

hi @Jhsmit, can it support reading local files to display this feature? I think this feature is handy 😀

When there are numpy uints in the color data, coloring won't (always) work correctly, but no error is raised

Trying out the demo, I notice that spin is only triggered on change. So if you were to:

view = PDBeMolstar(
    molecule_id="1qyn",
    theme="light",
    hide_water=True,
    visual_style="cartoon",
)
view.spin = True
view

the viewer wouldn't be spinning. I'm not sure if this is something that can be set in initial options:

or must be set initially. Great work!

Hi !
Was wondering if we can save the view as an HTML for later use?