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Nucleic Acid builder and general improvements #354

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merged 7 commits into from
Apr 8, 2024
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@JarrettSJohnson JarrettSJohnson commented Apr 1, 2024

Addresses #102 #351

Migrating support from Incentive for the following:

  • Nucleic Acid builder in the Builder panel (Jarrett Johnson @JarrettSJohnson)
  • fnab command to build nucleic acid chains by sequence (Jarrett Johnson @JarrettSJohnson)
  • Improvements to nucleic acid building from native structures (Thomas Stewart @TstewDev)
  • highlight attachment points for improved usability (Thomas Holder @speleo3)

Co-authored-by: Jarrett Johnson jarrett.johnson@schrodinger.com
Co-authored-by: Thomas Stewart thomas.stewart@schrodinger.com
Co-authored-by: Thomas Holder thomas@thomas-holder.de

@JarrettSJohnson JarrettSJohnson self-assigned this Apr 1, 2024
@JarrettSJohnson JarrettSJohnson requested a review from TstewDev April 5, 2024 19:44
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JarrettSJohnson commented Apr 5, 2024

Requesting reviews from co-authors: @TstewDev @speleo3

(There's ofc a lot to be done with general good practices, cleanup--but for now just pulled straight from incentive to make the code difference minimal)

@JarrettSJohnson JarrettSJohnson changed the title Nucleic Acid builder and general improvements (WIP) Nucleic Acid builder and general improvements Apr 5, 2024
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@TstewDev TstewDev left a comment

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I agree with the point that there is a lot to be done here with regard to refactoring and improving readability (looking at you editor.py). However, for now I think this is everything we need to add this feature to open-source. We should file a ticket on the incentive side of things to get this cleaned up and then merge those changes in later on.

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speleo3 commented Apr 5, 2024

I also agree, first sync with open-source, then refactor.

But before jumping to refactoring: Are there any tests? There are none in this pull request.

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I also agree, first sync with open-source, then refactor.

But before jumping to refactoring: Are there any tests? There are none in this pull request.

Removed the incentive requirement. All previous tests (which included 'fnab') for this module were brought over during the pymol-testing migration.

@JarrettSJohnson JarrettSJohnson marked this pull request as ready for review April 5, 2024 21:01
@JarrettSJohnson JarrettSJohnson merged commit 246e0a4 into master Apr 8, 2024
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@JarrettSJohnson JarrettSJohnson deleted the fnab branch April 10, 2024 16:31
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3 participants