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Rdkit conformer generation starter

Skill ma-compbio-lab/SkillFoundry/skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-conformer-generation-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.3 KB, as published. Nobody here has run it

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

Keep looking

Skills are one crate of 328,083. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.