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bio-similarity-searching

Maintainer FreedomIntelligence · Last updated April 1, 2026

Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules by structural similarity using Butina clustering. Use when finding analogs of a query compound or clustering chemical libraries.

OpenClawNanoClawAnalysisReproductionbio-similarity-searching🧬 bioinformatics (gptomics bio-* suite)bioinformatics — structural biology & cheminformaticsperforms

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-similarity-searching

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Python: DataStructs.TanimotoSimilarity(), Butina.ClusterData() (RDKit).
  • Find compounds similar to my query molecule" → Compute pairwise Tanimoto similarity on molecular fingerprints to rank a library by structural resemblance to a query, or cluster compounds by chemical similarity using Butina clustering. Python: DataStructs.TanimotoSimilarity(), Butina.ClusterData() (RDKit).
  • Find structurally similar molecules and cluster compound libraries.
  • mol1 = Chem.MolFromSmiles('CCO') mol2 = Chem.MolFromSmiles('CCCO').
  • fp1 = AllChem.GetMorganFingerprintAsBitVect(mol1, radius=2, nBits=2048) fp2 = AllChem.GetMorganFingerprintAsBitVect(mol2, radius=2, nBits=2048).

Source Doc

Excerpt From SKILL.md

Tanimoto Similarity

from rdkit import Chem, DataStructs
from rdkit.Chem import AllChem

## Tanimoto similarity (0-1)

similarity = DataStructs.TanimotoSimilarity(fp1, fp2)
print(f'Tanimoto similarity: {similarity:.3f}')

Similarity Thresholds

ThresholdInterpretation
> 0.85Very similar (likely same scaffold)
> 0.70Similar (likely related series)
> 0.50Moderate similarity
< 0.50Dissimilar

Use cases

  • Use when finding analogs of a query compound or clustering chemical libraries.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • molecular-descriptors - Generate fingerprints for similarity
  • substructure-search - Pattern-based searching
  • molecular-io - Load molecules for searching

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