bio-similarity-searching
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-similarity-searching --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: RDKit 2024.03+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Similarity Searching **"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. ## Tanimoto Similarity ```python from rdkit import Chem, DataStructs from rdkit.Chem import AllChem # Generate fingerprints mol1 = Chem.MolFromSmiles('CCO') mol2 = Chem.MolFromSmiles('CCCO') fp1 = AllChem.GetMorganFingerprintAsBitVect(mol1, radius=2, nBits=2048) fp2 = AllChem.GetMorganFingerprintAsBitVect(mol2, radius=2, nBits=2048) # Tanimoto similarity (0-1) similarity = DataStructs.TanimotoSimi
- Version Compatibility
- Tanimoto Similarity
- Similarity Thresholds
- Search Library Against Query
- Bulk Similarity Search
- Butina Clustering
- Maximum Common Substructure
- Related Skills
What does the bio-similarity-searching skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-similarity-searching --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.