rdkit-conformer-generation-starter

Name: rdkit-conformer-generation-starter
Author: ma-compbio-lab

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How to install rdkit-conformer-generation-starter?

ma-compbio-lab/skillfoundry/rdkit-conformer-generation-starter

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

Installs into the current project.

Summary

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

Files · 1

SKILL.md

1	# RDKit Conformer Generation Starter
2
3	Use this skill to generate a small deterministic conformer ensemble with RDKit ETKDG and summarize the lowest-energy structures.
4
5	## What it does
6
7	- Reads a small TSV of molecules with `name` and `smiles`.
8	- Generates multiple 3D conformers per molecule with a fixed random seed.
9	- Optimizes them with UFF and reports the ranked conformer energies.
10	- Writes compact JSON suitable for smoke tests or later structure-aware workflows.
11
12	## When to use it
13
14	- You need a verified local starter for `small-molecule conformer generation`.
15	- You want a deterministic 3D-geometry precursor before docking, force-field setup, or descriptor work.
16
17	## Example
18
19	```bash
20	./slurm/envs/chem-tools/bin/python skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter/scripts/run_rdkit_conformer_generation.py \
21	--input skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter/examples/molecules.tsv \
22	--num-confs 4 \
23	--out scratch/rdkit-conformers/summary.json
24	```
25
26	## Verification
27
28	- Skill-local tests: `python3 -m unittest discover -s skills/computational-chemistry-and-molecular-simulation/rdkit-conformer-generation-starter/tests -p 'test_*.py'`
29	- Repository smoke target: `make smoke-rdkit-conformers`

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