bio-substructure-search
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-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 2024.03+ 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. # Substructure Search **"Filter my library for compounds containing a specific functional group"** → Search molecular collections for substructure matches using SMARTS patterns, identifying compounds that contain specified chemical moieties, scaffolds, or pharmacophore features. - Python: `mol.HasSubstructMatch()`, `Chem.MolFromSmarts()` (RDKit) Find molecules containing specific structural patterns using SMARTS. ## Basic Substructure Search ```python from rdkit import Chem mol = Chem.MolFromSmiles('c1ccc(O)cc1CCO') # Check if pattern exists pattern = Chem.MolFromSmarts('[OH]') # Hydroxyl group has_hydroxyl = mol.HasSubstructMatch(pattern) print(f'Contains hydroxyl: {has_hydroxyl}') # Get all matches (atom indices) matches = mol.GetSubstructMatches(pattern) print(f'Hydroxyl positions: {matches}')
- Version Compatibility
- Basic Substructure Search
- Common SMARTS Patterns
- Library Filtering
- Multiple Pattern Filtering
- Atom Mapping
- Recursive SMARTS
- Visualization with Highlighting
- Related Skills
What does the bio-substructure-search skill do?
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-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 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.