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Support for MSA contexts and .aligned.pqt format #109

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merged 36 commits into from
Oct 21, 2024
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wukevin
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@wukevin wukevin commented Oct 14, 2024

Description

Add code for:

  • Going from a3m files > aligned.pqt files
  • Loading aligned.pqt files to MSAContext
  • Handling correct merging and pairing of MSAContext across multiple chains.

Also added README and example files.

Motivation

Enable loading MSA for inference; closes #73 and closes #42

Test plan

Tested that the example folds correctly and msa plot looks as expected when MSAs are enabled.

examples/msas/README.md Outdated Show resolved Hide resolved
@arogozhnikov
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(rebased on main)

@arogozhnikov arogozhnikov changed the title Support for MSA contexts Support for MSA contexts and .aligned.pqt format Oct 20, 2024
chai_lab/data/dataset/msas/load.py Outdated Show resolved Hide resolved
chai_lab/data/dataset/msas/preprocess.py Outdated Show resolved Hide resolved
chai_lab/data/parsing/msas/aligned_pqt.py Outdated Show resolved Hide resolved
@wukevin wukevin enabled auto-merge (squash) October 21, 2024 04:53
@wukevin wukevin disabled auto-merge October 21, 2024 04:53
@wukevin wukevin enabled auto-merge (squash) October 21, 2024 04:53
@wukevin wukevin merged commit 756437e into main Oct 21, 2024
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@wukevin wukevin deleted the kevin/msa-context branch October 21, 2024 04:53
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