bio-reaction-enumeration
Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill 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 2024.09+, mmpdb 3.1+, scikit-learn 1.4+, numpy 1.26+. 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 virtual libraries by applying reaction SMARTS to building blocks, enumerate analog series via matched molecular pairs, decompose into R-groups for SAR modeling, or extract transformations from reaction data. Reaction enumeration sits at the intersection of medicinal chemistry, lead optimization, and de novo design. The two key operations: **transform** (apply known rxn to make new compounds) and **mine** (extract rules from observed analog series). RDKit's reaction SMARTS handles the former; mmpdb / Free-Wilson handle the latter. For retrosynthetic planning (target-to-starting-material decomposition), see `chemoinformatics/retrosynthesis`. For ML-driven design, see `chemoinformatics/generative-design`. For scaffold-based
- Version Compatibility
- Operation Taxonomy
- Reaction SMARTS Basics
- Common Reaction Templates
- Combinatorial Library Enumeration
- RECAP Fragmentation
- BRICS Fragmentation
- R-Group Decomposition
- Matched Molecular Pairs Analysis (MMPA)
- Free-Wilson Analysis
- Template Extraction from Reaction Data
- Per-Tool Failure Modes
- Reaction SMARTS -- atom mapping mismatch
- RECAP/BRICS -- over-fragmentation
mmpdb fragment data.smi -o data.fragments mmpdb index data.fragments -o data.mmpdb mmpdb transform --smiles 'COc1ccccc1' data.mmpdb
What does the bio-reaction-enumeration skill do?
Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill 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 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.