As chemo-informaticians nowadays who use Python, are mainly relied on RDKit to compute about molecule information, it is preferable that that RDKit could be easily bundled in panel-chemistry. But, since RDKit installation with pip is really tedious, registering panel-chemistry in Anaconda repository could help users to use it easily.

Continuation of #19

A Panel Pane to wrap the PDBe implementation of the Mol* ('MolStar') viewer.

Check out

• PDBe Mol*
• Mol*
• Mol* GitHub

Cite Mol*: David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; https://doi.org/10.1093/nar/gkab314.

Todo:

• [] Test that dynamic updates work
• [] Decide if light theme should be could default as is custom in Panel.
• [] Decide if default theme should be dark or default/ light.
• [] Add/ use utility functions
• [] Add events.
• [] Fix that the component get slower and slower on each rerender.
• [] Reference Notebook
• [] Add automated tests
• [] Test, Test, Test
• [] pypi package
• [] conda package
• [] Communication

Nice to have

• Some Gallery notebook showing an example application.
• Some way to update the css file across all PdbeMolstar instances when the theme changes.
• Set default theme based on theme=default or them=dark url query args.

Current status of the PR adds the PBDe webcomponent implementation of the molstar viewer

The webcomponent works well although there are some bugs/confusion around setting of some boolean parameters: https://github.com/PDBeurope/pdbe-molstar/issues/44

I'm planning to further add the PDBe JS plugin as ReactiveHTML and perhaps also the Mol* viewer

A Panel Pane to wrap the PDBe implementation of the Mol* ('MolStar') viewer.

Check out

• PDBe Mol*
• Mol*
• Mol* GitHub

Cite Mol*: David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; https://doi.org/10.1093/nar/gkab314.

Continuation of #20

Changes:

• Adding a default visual style hides waters by default, set default to None
• Theme default to default (= light)
• Hide structure split per boolean, update via visual.visibility
• Hide canvas button split per boolean, update via rerender (only works for some buttons)
• Added function for coloring a selection (one color)
• Add function for coloring a selection (many colors)

I've changed the theme to 'default' (which is light). Since this is the default in panel I think it makes the most sense. It looks like the CSS theme already updates across PDBeMolStar instances (at least in jupyer notebooks) Ideally we would also couple the background color to the theme. Previously I used bg_color with default=None and set the bg color depending on the theme but that is currently bugged (https://github.com/holoviz/panel/issues/3058). Ideally as you state under 'nice to have' would be nice to have it like that :)

The selection and coloring API has a few more options (color by auth_residue_number,) which I'm not familiar with but I suspect its related to the mmCIF protein structure data format

Current (known) bugs:

• [ ] If you set hide_water is True via __init__ they cannot be switched back to show

Previous:

Todo:

• [x] Test that dynamic updates work
• [x] Decide if light theme should be could default as is custom in Panel.
• [x] Decide if default theme should be dark or default/ light.
• [x] Add/ use utility functions
  • [x] ~~.select()~~ color() function can be used for coloring
  • [x] `.clear_selection()
  • [x] highlight()
  • [x] clear_highlight()
  • [x] reset()
• [x] Add events.
  • [x] hide/show water, het, polymer, etc
  • [x] hide/show some (but not all) canvas buttons
• [ ] Fix that the component get slower and slower on each rerender. (I have not experienced this)
• [x] Reference Notebook
• [x] Add automated tests
• [ ] Test, Test, Test
  • [ ] Test on non-protein molecules
  • [ ] Test other formats than pdb (mmcif, mdtraj?)
• [ ] pypi package
• [ ] conda package
• [ ] Communication

Nice to have

• Some Gallery notebook showing an example application.
• Some way to update the css file across all PdbeMolstar instances when the theme changes (this seems to happen already, at least in the notebook example).
• Set default theme based on theme=default or them=dark url query args.

I was following the instructions from video 0.1:

git clone https://github.com/MarcSkovMadsen/panel-chemistry.git
 cd panel-chemistry
 conda create --name panel-chemistry
 conda activate panel-chemistry
 pip install -e .[all]

this resulted in an error for pywinpty

 Cargo, the Rust package manager, is not installed or is not on PATH.
    This package requires Rust and Cargo to compile extensions.

Hi, I've been working with the pdbe molstar code and I think it's fantastic. I'm a little confused about how static files would work for panel in a jupyter notebook though. Is there a way to specify an assets directory in a notebook without running panel serve --static-dirs from the command line?

Fixing issue in #23 : cannot import name 'string_types' from 'panel.util' They removes from six import string_types in panel 0.13, so I juste replaced

from panel.util import lazy_load, string_types

by

from panel.util import lazy_load
from six import string_types

We also need to setup the project to support pre-built Bokeh Extensions.

This is described in https://awesome-panel.readthedocs.io/en/latest/guides/awesome-panel-extensions-guide/bokeh-extensions.html#prebuilt-bokeh-extensions. If possible we should record and distribute this as a video to make it easier for the Panel Community to build new packages/ extensions in the future.

Request

Make it dead easy to try panel-chemistry. I would like a CLI tool panel-chemistry with the commands

• hello which panel serves the example notebooks
• examples which copies the example notebooks to /examples/panel-chemistry.

Motivation

Currently there is some friction to try out panel-chemistry. You have to open Binder (slow) or download the notebooks from github. It takes some time and some users might now how to do or understand its possible. You can also git clone the repo. There are 4 commands you have to execute and it might fail.

Drawbacks

It would add dependencies like Typer and Rich to the package if we implement it like the awesome-panel-cli.

Alternatives

• Not do it.
• I've also considered whether the awesome-panel-cli should enable plugins. So having one cli to collect everything. But I think

Additional Context

We should do this in a general way that is consistent with awesome-panel-cli, panel-highcharts etc.

Updates the package to v 0.0.2 and

• adds Panel 0.14.0 support and Python 3.10 support
• removes Python 3.6 support
• refactors to an awesome-panel-cli powered project.

When testing on panel 0.13.0rc5 I get

2022-04-07 21:06:14,769 Error running application handler <bokeh.application.handlers.script.ScriptHandler object at 0x0000029BC5655100>: cannot import name 'string_types' from 'panel.util' (c:\repos\private\awesome-panel\.venv\lib\site-packages\panel\util.py)
File 'ngl_viewer.py', line 15, in <module>:
from panel.util import lazy_load, string_types Traceback (most recent call last):
  File "c:\repos\private\awesome-panel\.venv\lib\site-packages\bokeh\application\handlers\code_runner.py", line 231, in run
    exec(self._code, module.__dict__)
  File "C:\repos\private\awesome-panel\awesome_panel\apps\py3dmol.py", line 4, in <module>
    from panel_chemistry.pane import Py3DMol
  File "c:\repos\private\awesome-panel\.venv\lib\site-packages\panel_chemistry\pane\__init__.py", line 6, in <module>
    from .ngl_viewer import NGLViewer
  File "c:\repos\private\awesome-panel\.venv\lib\site-packages\panel_chemistry\pane\ngl_viewer.py", line 15, in <module>
    from panel.util import lazy_load, string_types
ImportError: cannot import name 'string_types' from 'panel.util' (c:\repos\private\awesome-panel\.venv\lib\site-packages\panel\util.py)

Request

Align the panel-chemistry intro video

with the awesome-panel-cli video

Motivation

• I think the awesome-panel-cli video communicates better.
• I would like the same look and feel across awesome-panel projects.

Drawbacks

Takes time.

Alternatives

Keep it as it is.

Additional Context

The panel-chemistry video is

https://github.com/awesome-panel/panel-chemistry/blob/main/assets/panel-chemistry-teaser.gif

The awesome-panel-cli video is

https://github.com/awesome-panel/awesome-panel-cli/blob/main/assets/videos/awesome-panel-cli-intro.gif

PyHDX has an existing NGL Molecule Viewer which is ok to copy or get inspiration from.

https://github.com/Jhsmit/PyHDX/blob/master/dev/bokeh_extension.py

https://twitter.com/Jhsmit_/status/1398233190519693317