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.
At a glance
git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills
cp -r computational-chemistry-agent-skills/molecular-conformer/rdkit-conf ~/.claude/skills/rdkit-conf
Setup, runtime and requirements describe jinzhezenggroup/computational-chemistry-agent-skills, the repo this skill ships in.
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