bio-molecular-standardization skillA
bio-molecular-standardization is agent-read markdown (skill) from pku-yuangroup/openai4s: Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization, salt/solvent stripping, charge handling, stereochemistry handling, mixture selection, and isotope normalization. Explicitly compares ChEMBL, canSARchem, RDKit, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound c.
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+ and chembl_structure_pipeline 1.2+. MolVS 0.1.1 is a legacy package; use RDKit's maintained `rdMolStandardize` module for custom pipelines. 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. # Molecular Standardization Convert raw molecular structures into a consistent form for ML training data, deduplication, registry, and cross-database joining. Skipping standardization can create data leakage when alternate representations of one compound enter different splits, distort QSAR inputs, and cause database join misses. The ChEMBL structure pipeline (Bento et al. 2020) is built on RDKit and applies ChEMBL-specific normalization and parent-selection rules. canSARchem (Dolciami et al. 2022) adds canonical-tautomer selection before parent extraction. RDKit's maintained `rdMolStandardize` module provides primitives for building an explicit custom… …
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How to install
mdr add pku-yuangroup/openai4s/bio-molecular-standardization@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-molecular-standardization@sha256:74781a7841eb6034Pin 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_ivyezdhtdirjspyw)
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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_ivyezdhtdirjspyw GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-molecular-standardization GET https://markdownregistry.com/api/v1/blob/74781a7841eb60342ca83299f613231db387e76151b5a874fef54451adcfdf7f
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