bio-reaction-enumeration
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration --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. # Reaction Enumeration **"Generate a combinatorial library from my building blocks"** → Enumerate virtual compound libraries by applying reaction SMARTS transformations to sets of building-block molecules, producing and validating all product combinations for a defined synthetic route. - Python: `AllChem.ReactionFromSmarts()`, `rxn.RunReactants()` (RDKit) Generate virtual compound libraries using reaction SMARTS. ## Reaction SMARTS Basics ```python from rdkit import Chem from rdkit.Chem import AllChem # Define reaction (reactants >> products with atom mapping) # Amide coupling: carboxylic acid + amine -> amide amide_rxn = AllChem.ReactionFromSmarts( '[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]' ) # Validate reaction definition n_errors = amide_rxn.Validate() if n_errors[0] == 0: print('Reaction is va
- Version Compatibility
- Reaction SMARTS Basics
- Common Reaction SMARTS
- Combinatorial Library Enumeration
- Multi-Step Synthesis
- Product Validation
- Reaction Templates
- Related Skills
What does the bio-reaction-enumeration skill do?
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-reaction-enumeration --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.