Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundrynpx agentmods add skills/ma-compbio-lab/skillfoundry/rdkit-conformer-generation-starterWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/rdkit-conformer-generation-starter)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/rdkit-conformer-generation-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/rdkit-conformer-generation-starter.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00000 | $0.00301 |
| Opus 5 | $0.00000 | $0.00151 |
| Sonnet 5 | $0.00000 | $0.00060 |
| Haiku 4.5 | $0.00000 | $0.00030 |
Grade A, and why
rdkit-conformer-generation-starter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
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
nameandsmiles. - 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
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 30 lines · 0 tokens per session scan A 1a6e5c7b9fd6
rdkit-conformer-generation-starter is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It costs nothing until one of its globs matches a file; then it loads 301 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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