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Commits on Aug 29, 2025

• Update get_columns_to_randomize to use local variable

  iamysk

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• Updated logging and keys_to_keep logic

  iamysk

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• Updated get_columns_to_randomize function to remove redundancy, removed --msa_perturbation_mode flag

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  iamysk

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• Removed the touching of model files, if this function is needed it should be handled by the user outside, to avoid creating zero-sized files that needs to be cleaned up.

  bjornwallner

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• Added flag '--keys_to_key' for which keys in the results pickle to keep

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Commits on Jul 25, 2025

• Updated instructions in favour of using container images, also listed all valid combinations of methods nad model presets

  iamysk

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Commits on Jul 24, 2025

• Merge pull request #14 from iamysk/multimer

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  iamysk

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• Updated paths

  iamysk

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• Update path for local use

  iamysk

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• Fixed pipeline error while using multimer preset

  iamysk

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Commits on Jun 26, 2025

• Merge pull request #13 from akors/flagfile-dbpaths

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  iamysk

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• README.md: Update flagfile path in container examples

  akors

  committed
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• Update default flag file to work out of the box for a standard AlphaFold database dir

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  akors

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Commits on May 30, 2025

• Merge branch 'main' of https://github.com/iamysk/AFsample2

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  iamysk

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• Addeed functionaly to randomzie MSA for msasubsampling as well.

  iamysk

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Commits on May 14, 2025

• Updated .gitignore

  iamysk

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Commits on May 12, 2025

• Updated running instructions to v1.1

  iamysk

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Commits on May 9, 2025

• Dockerignore file

  iamysk

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• Added Dockerfile and updated requirements file

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  iamysk

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• Update user-specific flagfile

  iamysk

  committed
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• Update openmm imports for openmm v8.0.0

  iamysk

  committed
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• Removed redundant example

  iamysk

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Commits on Apr 14, 2025

• Merge pull request #12 from iamysk/anymsa

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  iamysk

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• Added functionality to provide single MSA file as input (.a3m format). Will ignore/won"t-check any database paths provided in flagfile.

  iamysk

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Commits on Mar 11, 2025

• Merge pull request #11 from iamysk/profile

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  iamysk

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• Renamed af2 with canilla

  iamysk

  committed
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Commits on Mar 7, 2025

• Updated msa folder handing id use_msa_features=True

  iamysk

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Commits on Mar 6, 2025

• Added link to publication

  iamysk

  committed
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• fixed msasubsamolling

  iamysk

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Commits on Mar 4, 2025

• SPEACHAF now works with the updated modular code

  iamysk

  committed
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• Set ensemble_representations=False

  iamysk

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• Update Zenodo link iN README

  iamysk

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Commits on Mar 3, 2025

• updated notebook to show all figures

  iamysk

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• Merge pull request #10 from iamysk/cfold

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  iamysk

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• Setup for cfold_og implementation: ensemble_rep, data.resample_msa, config-resample_msa = False

  iamysk

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