bio-reaction-enumeration SKILL.md skillA
bio-reaction-enumeration from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-reaction-enumeration@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-chemoinformatics-reaction-enumeration/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 19,864 bytes
- Repository stars
- 662
- License
- MIT
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file 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… …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-reaction-enumeration@sha256:d9d065b1cd8170fbThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_eqpbhjubigljhezr)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · 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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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.