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feat: find pi cation interactions#810

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padix-key merged 9 commits into
biotite-dev:mainfrom
Jaakik:feat/pi-cation-interactions
Jun 10, 2025
Merged

feat: find pi cation interactions#810
padix-key merged 9 commits into
biotite-dev:mainfrom
Jaakik:feat/pi-cation-interactions

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@Jaakik Jaakik commented Jun 5, 2025

Add π-cation interaction detection

Adds find_pi_cation_interactions() function to biotite.structure.rings module for detecting interactions between aromatic rings and positively charged atoms.

  • Follows same optimization patterns as find_stacking_interactions (vectorized operations, squared distances)
  • Requires charge annotation to identify cations
  • test with (3wip.cif) structure that includes cation-π interactions between the positively charged quaternary ammonium group of acetylcholine and aromatic residues in the binding pocket from Tryptophan and Tyrosine.

@Jaakik Jaakik marked this pull request as ready for review June 5, 2025 15:50
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Hi, thanks for the feature! I left a few comments below. In addition, could you add this function to doc/apidoc.json so it is findable in the API reference?

Comment thread src/biotite/structure/rings.py Outdated
Comment thread src/biotite/structure/rings.py Outdated
Comment thread src/biotite/structure/rings.py
Comment thread src/biotite/structure/rings.py Outdated
Comment thread src/biotite/structure/rings.py Outdated
Comment thread tests/structure/test_rings.py
@padix-key padix-key force-pushed the feat/pi-cation-interactions branch from 9abcd6c to 9e6ab90 Compare June 6, 2025 12:15
@padix-key padix-key force-pushed the feat/pi-cation-interactions branch from 9e6ab90 to 323fbe5 Compare June 6, 2025 12:17
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codspeed-hq Bot commented Jun 6, 2025

CodSpeed Performance Report

Merging #810 will not alter performance

Comparing Jaakik:feat/pi-cation-interactions (427ee57) with main (f796577)

Summary

✅ 59 untouched benchmarks

@Jaakik Jaakik requested a review from padix-key June 10, 2025 08:50
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Thanks for the changes! I just fixed a typo in the doctest and wait until the CI passes.

@padix-key padix-key merged commit ba3e1c1 into biotite-dev:main Jun 10, 2025
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2 participants