bio-substructure-search skillA
bio-substructure-search is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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+. 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 | …
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How to install
mdr add pku-yuangroup/openai4s/bio-substructure-search@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-substructure-search@sha256:f9117e3223249274Pin 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_tlhpeihmv3yv5gc6)
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Versions
Audit of the latest version
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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_tlhpeihmv3yv5gc6 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-substructure-search GET https://markdownregistry.com/api/v1/blob/f9117e32232492749df99dd0e7c40e8798b700ec66e25c5d6ca1c74079fe6c4b
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