rdkit-conf SKILL.md skillA
rdkit-conf 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-conf@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-conformer/rdkit-conf/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Mar 24, 2026
- Size
- 9,520 bytes
- Repository stars
- 156
- License
- LGPL-3.0
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…
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 Conformer Generation This skill provides practical command patterns for **RDKit 3D/2D conformer generation** using the standardized CLI wrapper: `<skill_path>/scripts/rdkit_conf_helper.py`. Key behaviors (important for Agents): - The script prints **environment detection** (Python/RDKit/Pandas) by default. - **Multi-conformer sampling**: embeds `--num-confs` conformers (default 10) per molecule via `EmbedMultipleConfs`, optimizes each with the chosen force field, and keeps the **lowest-energy** one. Set `--num-confs 1` to revert to single-conformer behavior. - **2D fallback**: if all 3D embedding attempts fail, `Compute2DCoords` is used instead and a `[WARN]` line is printed to stderr for that molecule. - Bad/illegal SMILES are **skipped entirely** and logged to `*.skipped.csv` (no crash). - Molecules that fell back to 2D are **additionally logged** to `*.fallback.csv`. - Each run ends with a summary line and **absolute output paths**: - `[INFO] Done: <N_3d> 3D, <N_2d> 2D-fallback, <N_skip> skipped (total input: <N>)` - `[RESULT] conf_sdf=/abs/path.sdf` - `[RESULT] conf_xyz=/abs/path.xyz` …
Read the whole file at its exact version.
How to install
mdr add jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf@sha256:a4863177305c387bThe 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_rwet7eor74zufrck)
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Versions
The registry has recorded 1 version of this file, committed on Mar 24, 2026.
Audit of the latest version
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- 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
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- pass: No instruction to read or print local credentials
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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_rwet7eor74zufrck GET https://markdownregistry.com/api/v1/resolve?ref=jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf GET https://markdownregistry.com/api/v1/blob/a4863177305c387ba78d8a5103e2796272704a311f601b73ca02bbdf1170e238
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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