Rdkit Conformer Generation Starter

RDKit Conformer Generation Starter

Use this skill to generate a small deterministic conformer ensemble with RDKit ETKDG and summarize the lowest-energy structures.

What it does

• Reads a small TSV of molecules with name and smiles.
• Generates multiple 3D conformers per molecule with a fixed random seed.
• Optimizes them with UFF and reports the ranked conformer energies.
• Writes compact JSON suitable for smoke tests or later structure-aware workflows.

When to use it

• You need a verified local starter for small-molecule conformer generation.
• You want a deterministic 3D-geometry precursor before docking, force-field setup, or descriptor work.

Example

./slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter/scripts/run_rdkit_conformer_generation.py \
  --input skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter/examples/molecules.tsv \
  --num-confs 4 \
  --out scratch/rdkit-conformers/summary.json

Verification

• Skill-local tests: python3 -m unittest discover -s skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter/tests -p 'test_*.py'
• Repository smoke target: make smoke-rdkit-conformers

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: ma-compbio-lab
• Source: ma-compbio-lab/SkillFoundry
• License: Apache-2.0
• Homepage: https://ma-compbio-lab.github.io/SkillFoundry/

Install and usage instructions live in the source repository linked above.