Skip to content

Deduplicate Recursive SMARTS Solves - #313

Open
scal444 wants to merge 1 commit into
NVIDIA-BioNeMo:mainfrom
scal444:codex/dedup-recursive-smarts
Open

scal444 wants to merge 1 commit into
NVIDIA-BioNeMo:mainfrom
scal444:codex/dedup-recursive-smarts

Conversation

@scal444

@scal444 scal444 commented Sep 18, 2026

Copy link
Copy Markdown
Collaborator

When the same recursive SMARTS occurs multiple times at the same level, we should solve it once and broadcast rather than solving multiple times. We do that simply by mapping the pattern to multiple output bits. If that ever becomes a problem we could alias bits.

@greptile-apps

greptile-apps Bot commented Sep 18, 2026

Copy link
Copy Markdown
Contributor

RetriggerConfidence Score: 5/5

The PR appears safe to merge, with no outstanding correctness, security, or repository-rule violations identified.

Summary

This PR deduplicates equivalent recursive SMARTS patterns at each nesting depth and broadcasts one computed result to every corresponding recursive-pattern bit.

  • Uses depth-qualified SMARTS serialization to share device-side pattern molecules.
  • Replaces single pattern IDs with masks representing equivalent occurrences.
  • Precomputes per-query, per-depth entries for recursive preprocessing.
  • Adds direct and end-to-end coverage for repeated flat and nested recursive patterns.

Reviews (2) · Last reviewed commit: "Deduplicate repeated recursive SMARTS wo..."

@scal444
scal444 force-pushed the codex/dedup-recursive-smarts branch from 07315b6 to c7a9ff4 Compare September 18, 2026 22:18
@scal444
scal444 requested a review from evasnow1992 September 19, 2026 09:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant