rdkit-repr SKILL.md skillA
rdkit-repr from jinzhezenggroup/computational-chemistry-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jinzhezenggroup/computational-chemistry-agent-skills/rdkit-repr@v1.0Pins v1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jinzhezenggroup/computational-chemistry-agent-skills
- Path
molecular-representation/rdkit-repr/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Mar 24, 2026
- Size
- 9,193 bytes
- Repository stars
- 156
- License
- LGPL-3.0
A standardized CLI wrapper for RDKit molecular featurization workflows that handles physicochemical descriptor computation (outputs .csv) and molecular fingerprint extraction (outputs .npy or .csv), with built-in SMILES validation. USE WHEN you need to compute RDKit molecular descriptors or fingerprints from SMILES datasets (.csv/.smi), or when you want to list all available descriptor names and presets.
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
# RDKit Molecular Featurization This skill provides practical command patterns for **RDKit descriptor and fingerprint extraction** using the standardized CLI wrapper: `<skill_path>/scripts/rdkit_helper.py`. Key behaviors (important for Agents): - The script prints **environment detection** (Python/RDKit/NumPy/Pandas) by default. - Bad/illegal SMILES are **skipped and logged** to `*.skipped.csv` (no crash). - Each run ends by printing **absolute output paths** like: - `[RESULT] desc_csv=/abs/path.csv` - `[RESULT] fp_npy=/abs/path.npy` - `[RESULT] fp_csv=/abs/path.csv` ## Quick Start Check CLI help: ```bash uv run <skill_path>/scripts/rdkit_helper.py --help ``` Check subcommand help: ```bash uv run <skill_path>/scripts/rdkit_helper.py desc --help uv run <skill_path>/scripts/rdkit_helper.py fp --help uv run <skill_path>/scripts/rdkit_helper.py list-desc --help ``` Disable environment printing (optional): ```bash uv run <skill_path>/scripts/rdkit_helper.py --no-env desc --smiles "CCO" --output out.csv ``` ## Core Tasks ### 1) Compute physicochemical descriptors → .csv Single SMILES (default preset: `physchem`, 25 descriptors): ```bash …
Read the whole file at its exact version.
How to install
mdr add jinzhezenggroup/computational-chemistry-agent-skills/rdkit-repr@sha256:0f22d67ad7118079The line at the top of this page pins the label v1.0, 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_n3zinfz53thzhdf6)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Mar 24, 2026.
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 (9193 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
jinzhezenggroup/computational-chemistry-agent-skills · 156 stars · license LGPL-3.0 · pushed 2026-11-02 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_n3zinfz53thzhdf6 GET https://markdownregistry.com/api/v1/resolve?ref=jinzhezenggroup/computational-chemistry-agent-skills/rdkit-repr GET https://markdownregistry.com/api/v1/blob/0f22d67ad711807972605f7d83872f3c61451d2c34ab7104c5345108b2b3e20a
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.
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