bio-substructure-search
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.
npx skills add BioTender-max/awesome-bio-agent-skills --skill substructure-search --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 2024.09+. SMARTS dialect follows Daylight specification with RDKit extensions. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show rdkit` then `help(rdkit.Chem.MolFromSmarts)` 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. # Substructure Search Search molecular collections for structural patterns using SMARTS. The choice of SMARTS dialect, atom/bond matching mode, and structural-alert catalog determines whether the search is correctly capturing the intended chemistry. PAINS (Baell & Holloway 2010) is the most-cited but most-misunderstood filter -- it identifies patterns of assay interference, not "bad molecules". Knowing when to apply each catalog and how to interpret hits is essential. For SMARTS-based reactions (transforming matched substructures), see `chemoinformatics/reaction-enumeration`. For 3D pharmacophore matching, see `chemoinformatics/pharmacophore-modeling`. ## SMARTS Grammar Essentials | Token | Meaning | Example | |-------|----
- Version Compatibility
- SMARTS Grammar Essentials
- Common SMARTS Patterns
- Basic Substructure Match
- Recursive SMARTS (key for postdoc-grade patterns)
- Structural-Alert Filter Catalogs
- When to Apply Each Filter
- PAINS Filter
- Reaction-Reactive Group Filter (custom)
- Library Filtering with Multiple Patterns
- Atom Map Indices in SMARTS
- Per-Tool Failure Modes
- PAINS -- false positive on natural product
- Aromaticity dialect mismatch
What does the bio-substructure-search skill do?
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill substructure-search --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.