bio-reaction-enumeration skillA
bio-reaction-enumeration is agent-read markdown (skill) from pku-yuangroup/openai4s: Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: RDKit 2024.09+, RDChiral 1.1+, 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; DOGS is one published example of reaction-driven de novo design (Hartenfeller et al. 2012). The two key operations are **transform** (apply known reactions to make new compounds) and **mine** (extract rules from observed analog series). RDKit's reaction SMARTS handles the former; mmpdb / Free-Wilson handle analog-series analysis, while mapped-reaction template extraction requires separate… …
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How to install
mdr add pku-yuangroup/openai4s/bio-reaction-enumeration@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-reaction-enumeration@sha256:d9d065b1cd8170fbPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_eqpbhjubigljhezr)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_eqpbhjubigljhezr GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-reaction-enumeration GET https://markdownregistry.com/api/v1/blob/d9d065b1cd8170fb8ffb3b37987ddbae163648d5a3e0636910125b1d218f3929
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