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Extend NGL dynophore visualization #28

Merged
merged 9 commits into from
May 26, 2021
Merged

Extend NGL dynophore visualization #28

merged 9 commits into from
May 26, 2021

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dominiquesydow
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@dominiquesydow dominiquesydow commented May 9, 2021 •
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Description

Extend dynophore NGL visualization style.

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Add opacity to SphereBuffer representation
  • Show ligand as hyperball
  • Add PointBuffer representation (WIP - still a few artifacts, see issue Dynophore 3D viz: NGL PointBuffer artifacts #27) > let's keep the code for now but set SphereBuffer as default
    image
  • Add Dynophore.unique_envpartners_chain_residue_number to fetch all interacting pocket residues and visualize them in the 3D view
  • Add unit tests
  • Rerun 3D docs tutorial

Questions

  • Color interacting pocket residues in same color as protein? Doesn't look so good: some bonds are not properly colored. See issue How to change atom color ? nglviewer/nglview#913 > Let's not recolor side chains but show them as licorice for some visual contrast
    image

Status

  • Ready to go

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@dominiquesydow dominiquesydow self-assigned this May 9, 2021
@dominiquesydow dominiquesydow linked an issue May 9, 2021 that may be closed by this pull request
Move to JupyterLab 3 #26
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@dominiquesydow dominiquesydow changed the title Extend ngl Extend NGL dynophore visualization May 9, 2021
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codecov-commenter commented May 9, 2021 •
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Codecov Report

Merging #28 (09ae52d) into master (ddc06ab) will increase coverage by 0.31%.
The diff coverage is 100.00%.

@dominiquesydow dominiquesydow mentioned this pull request May 9, 2021
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@dominiquesydow dominiquesydow mentioned this pull request May 26, 2021
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@dominiquesydow dominiquesydow merged commit 4dcb7ef into master May 26, 2021
@dominiquesydow dominiquesydow deleted the extend-ngl branch May 26, 2021 08:13
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Move to JupyterLab 3
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