bio-molecular-standardization SKILL.md skillA
bio-molecular-standardization 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-molecular-standardization@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-molecular-standardization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 18,384 bytes
- Repository stars
- 662
- License
- MIT
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…
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+ 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… …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-molecular-standardization@sha256:74781a7841eb6034The 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_ivyezdhtdirjspyw)
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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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- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
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- pass: No curl or wget piped into a shell
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- pass: No instruction to read or print local credentials
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- 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_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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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.