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Feature/performance improvements#10

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DimaMolod merged 2 commits into
KosinskiLab:mainfrom
HenriettaHolze:feature/performance-improvements
May 4, 2026
Merged

Feature/performance improvements#10
DimaMolod merged 2 commits into
KosinskiLab:mainfrom
HenriettaHolze:feature/performance-improvements

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@HenriettaHolze
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Hi,

Thanks for developing this very useful tool.
AlphaJudge crashed my laptop when using 8 cores with big AF3 models, so I tried to optimize.

  1. Keeping PAE matrices as numpy arrays gives ~3x memory improvement and is ~2x faster.
  2. I added an option to only return the QC metrics and not calculate the biophysical metrics which is ~20x faster.

Hope this is useful :)

Best,
Henrietta

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Thank you @HenriettaHolze for these very helpful suggestions!

@DimaMolod DimaMolod merged commit b075cc7 into KosinskiLab:main May 4, 2026
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2 participants