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Improve Morgan FP invariant extraction performance - #293

Merged
scal444 merged 5 commits into
NVIDIA-BioNeMo:mainfrom
scal444:perf/morgan-invariant-preprocessing
Sep 11, 2026
Merged

Improve Morgan FP invariant extraction performance#293
scal444 merged 5 commits into
NVIDIA-BioNeMo:mainfrom
scal444:perf/morgan-invariant-preprocessing

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@scal444

@scal444 scal444 commented Sep 10, 2026

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PR 1/5 for #267

@greptile-apps

greptile-apps Bot commented Sep 10, 2026

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RetriggerConfidence Score: 5/5

The changes since the previous review appear safe to merge, with no new actionable correctness or rule-compliance issues identified.

Summary

  • Replaces repeated atom-centric bond traversal with single-pass adjacency construction.
  • Parallelizes molecule-size classification for large inputs.
  • Routes molecules exceeding the GPU adjacency-degree limit through the CPU fallback.
  • Adds RDKit-reference, classification-boundary, and high-degree fallback coverage.

Reviews (4) · Last reviewed commit: "Merge branch 'main' into perf/morgan-inv..."

@scal444
scal444 requested a review from evasnow1992 September 10, 2026 14:55
@scal444
scal444 force-pushed the perf/morgan-invariant-preprocessing branch from b224a3f to 502323c Compare September 10, 2026 20:04

@evasnow1992 evasnow1992 left a comment

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Changes look good to me.

@scal444
scal444 merged commit 317f273 into NVIDIA-BioNeMo:main Sep 11, 2026
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2 participants