datamol-cheminformatics SKILL.md skillA
datamol-cheminformatics from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/datamol-cheminformatics@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/datamol-cheminformatics/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 17,739 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.
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
# Datamol Cheminformatics Toolkit ## Overview Datamol provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. It simplifies common drug discovery operations — SMILES parsing, standardization, descriptors, fingerprints, clustering, scaffolds, conformers, and visualization — with sensible defaults, built-in parallelization, and cloud storage support via fsspec. All molecular objects are native `rdkit.Chem.Mol` instances, ensuring full RDKit compatibility. ## When to Use - Parsing, validating, and standardizing molecular structures from SMILES, SDF, or other formats - Computing molecular descriptors and fingerprints for ML featurization - Similarity searching and diversity selection from compound libraries - Clustering compounds by structural similarity (Butina clustering) - Scaffold analysis and scaffold-based train/test splitting for ML - BRICS/RECAP molecular fragmentation for fragment-based design - 3D conformer generation and analysis - Visualizing molecules as grids with alignment and highlighting - Batch processing molecular datasets with parallelization …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/datamol-cheminformatics@sha256:715f3c2dfa04e266The line at the top of this page pins the label git:20260428.81ea2d2, 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_dtledp7ip7okwydr)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 17,739 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 17,891 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (17739 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_dtledp7ip7okwydr GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/datamol-cheminformatics GET https://markdownregistry.com/api/v1/blob/715f3c2dfa04e266ecdd60fe6b283238e299ee7b656ac039e4241af017143756
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.