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awesome-panel / panel-chemistry

πŸ§ͺπŸ“ˆ 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.
MIT License
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added sequence panel capabilities #38

Closed CrisSherban closed 1 year ago

CrisSherban commented 1 year ago

I thought that adding the ability to show the sequence panel would be nice.
For now this works out of the box. However, it's still bound to the controls in the sense that the sequence panel, when set to True, is shown only when the controls are toggled.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.08 :tada:

Comparison is base (11be20f) 83.78% compared to head (8c46000) 83.87%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #38 +/- ## ========================================== + Coverage 83.78% 83.87% +0.08% ========================================== Files 9 9 Lines 185 186 +1 ========================================== + Hits 155 156 +1 Misses 30 30 ``` | [Impacted Files](https://codecov.io/gh/awesome-panel/panel-chemistry/pull/38?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=awesome-panel) | Coverage Ξ” | | |---|---|---| | [src/panel\_chemistry/pane/pdbe\_molstar.py](https://codecov.io/gh/awesome-panel/panel-chemistry/pull/38?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=awesome-panel#diff-c3JjL3BhbmVsX2NoZW1pc3RyeS9wYW5lL3BkYmVfbW9sc3Rhci5weQ==) | `100.00% <100.00%> (ΓΈ)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=awesome-panel). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=awesome-panel)

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Jhsmit commented 1 year ago

Thanks for your contribution. The default behavior of the previous implementation was to not show the sequence when opening the controls? Either way I think it makes sense to show it by default

CrisSherban commented 1 year ago

Thanks for your contribution. The default behavior of the previous implementation was to not show the sequence when opening the controls? Either way I think it makes sense to show it by default

Yeah, unfortunately the sequence panel was not available by default, you can check it also here in the JS plugin demo for example: https://github.com/molstar/pdbe-molstar/wiki.

But I ended up using the sequence panel quite often, so I thought that it might be nice to add the capability to panel-chemistry to show it.

Another very cool feature would be the ability to color amino acids in the sequence panel. I'll try to dig into it but it looks a bit more difficult.

Jhsmit commented 1 year ago

There is also the rcsb molstar

This example here looks interesting: https://www.rcsb.org/3d-sequence/4hhb This has a more extensive sequence viewer

not sure how easy it would be to add to panel-chemistry or if they allow custom colors