Butina clustering bench improvements#188
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- Flip `--no-rdkit-lowmem` to opt-in `--rdkit-lowmem`. The lowmem backend builds its distance matrix in a pure-Python O(n^2) loop that doesn't finish in reasonable time at sizes >= 40k, so default off. - Drop `--include-tanimoto-matrix` and always report both rdkit variants (`rdkit_cluster_only_*` and `rdkit_with_tanimoto_*`) so a single run characterises both the inner-loop and the with-distance-build timings. - Allow rdkit_cluster_only / fused / nvmolkit to run on synthetic-fill fingerprints when the input has fewer mols than `size`; with_tanimoto and lowmem rows are skipped in that case (they need real fingerprints). - Edge-case cutoff changes from 1.1 to 1.0.
evasnow1992
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Jun 1, 2026
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Changes look good to me. Thanks!
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Fixed an error when tanimoto similarity of 1.1 was an option, it causes an error in some paths. 1.0 still does the same thing without the error.
Standardizes measurements for different modes. When we run the fused or low mem rdkit/nvmolkit versions, the proper comparison is against the tanimoto matrix THEN Butina for the non-fused versions. However, when directly comparing non-fused, it makes more sense to leave out the tanimoto aspect.