bio-substructure-search SKILL.md skillA
bio-substructure-search 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-substructure-search@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-substructure-search/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,532 bytes
- Repository stars
- 662
- License
- MIT
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.
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+. SMARTS dialect follows Daylight specification with RDKit extensions. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show rdkit` then `help(rdkit.Chem.MolFromSmarts)` 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 Search molecular collections for structural patterns using SMARTS. The choice of SMARTS dialect, atom/bond matching mode, and structural-alert catalog determines whether the search is correctly capturing the intended chemistry. PAINS (Baell & Holloway 2010) is the most-cited but most-misunderstood filter -- it identifies patterns of assay interference, not "bad molecules". Knowing when to apply each catalog and how to interpret hits is essential. For SMARTS-based reactions (transforming matched substructures), see `chemoinformatics/reaction-enumeration`. For 3D pharmacophore matching, see `chemoinformatics/pharmacophore-modeling`. ## SMARTS Grammar Essentials | Token | Meaning | Example | …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-substructure-search@sha256:f9117e3223249274The 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_tlhpeihmv3yv5gc6)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_tlhpeihmv3yv5gc6 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-substructure-search GET https://markdownregistry.com/api/v1/blob/f9117e32232492749df99dd0e7c40e8798b700ec66e25c5d6ca1c74079fe6c4b
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
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.