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Accept --fast_kernels for AlphaFold2 - #58
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AlphaPulldown's new AF2-only flag (ColabFold's fused Pallas kernels for AF2-Multimer, off|on|auto). The copied flag table gains it for alphafold2 only, so the parse-time check does not warn about it; the README flag list shows it. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
Accept AlphaPulldown's new AF2-only flag
--fast_kernels(KosinskiLab/AlphaPulldown#645): ColabFold's fused Pallas kernels, about 2× faster AF2-Multimer on NVIDIA GPUs of compute capability 8.0+.workflow/rules/common.smkgains_AF2_EXTRA_FLAGS = {"fast_kernels"}, foralphafold2only, so the parse-time check doesn't warn about it. AF3 and AlphaLink still reject it.on/offas a boolean; AlphaPulldown acceptstrue/falsetoo, but quoting avoids the surprise.Set it in
structure_inference_arguments, e.g.--fast_kernels: "auto".Also relevant to this workflow: AlphaPulldown#645 fixes padded AF2 predictions reporting scores over the padding. Every AF2-multimer batch with
batch_size > 1is padded to its largest fold, so it is affected.Validation
alphafold2.🤖 Generated with Claude Code