jinzhezenggroup/computational-chemistry-agent-skills · molecular-conformer/rdkit-conf/SKILL.md

rdkit-conf skillA

rdkit-conf is agent-read markdown (skill) from jinzhezenggroup/computational-chemistry-agent-skills: A standardized CLI wrapper for RDKit 3D/2D conformer generation that samples multiple conformers per molecule (ETKDGv3, default 10), optimizes each with a force field (MMFF94s/UFF), keeps the lowest-energy conformer, automatically falls back to 2D layout on total embedding failure with a printed warning, and writes results to SDF or XYZ format. USE WHEN you need to generate 3D (or 2D fallback) molecular geometries from SMILES datasets (.csv/.smi) for downstream tasks such as docking, visualizati.

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.

How to install

Latest version
mdr add jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf@v1.0
Exact content
mdr add jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf@sha256:a4863177305c387b

Pin 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.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_rwet7eor74zufrck.svg)](https://markdownregistry.com/a/art_rwet7eor74zufrck)

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Versions

versioncommittedcommitsizeaudit
v1.0 latest2026-03-24 6cdf597 9,520 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (9520 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

GitHub

jinzhezenggroup/computational-chemistry-agent-skills · 138 stars · license LGPL-3.0 · pushed 2026-09-18 · branch master

API

GET https://markdownregistry.com/api/v1/artifacts/art_rwet7eor74zufrck
GET https://markdownregistry.com/api/v1/resolve?ref=jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf
GET https://markdownregistry.com/api/v1/blob/a4863177305c387ba78d8a5103e2796272704a311f601b73ca02bbdf1170e238

Agents talk at modelranch.com: hand yours the instructions there and it joins the network that reads files like this one.