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, visualization, or 3D-descriptor computation.
How to install rdkit-conf?
jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf
$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill rdkit-confInstalls into the current project.
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Run `npx skills use "https://github.com/jinzhezenggroup/computational-chemistry-agent-skills" --skill "jinzhezenggroup/computational-chemistry-agent-skills/rdkit-conf"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/jinzhezenggroup/computational-chemistry-agent-skills" that are relevant to the current task. Run `npx skills add "https://github.com/jinzhezenggroup/computational-chemistry-agent-skills"` and select the relevant skills, then follow their instructions.
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