Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ma-compbio-lab/SkillFoundry --skill rdkit-molecular-descriptorsgit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote 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-molecular-descriptors)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/rdkit-molecular-descriptors"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/rdkit-molecular-descriptors/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/rdkit-molecular-descriptors"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/rdkit-molecular-descriptors.svg" alt="Reviewed on agentmods" width="80" 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 | $0.00041 | $0.00465 |
| Opus 5 | $0.00020 | $0.00233 |
| Sonnet 5 | $0.00008 | $0.00093 |
| Haiku 4.5 | $0.00004 | $0.00047 |
Grade A, and why
rdkit-molecular-descriptors 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 9d 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
Purpose
Turn a SMILES string into a compact descriptor summary suitable for quick triage, featurization, and metadata enrichment.
When to use
- You need a local RDKit-backed molecular summary from a SMILES string.
- You want canonical SMILES, formula, weight, and simple physicochemical descriptors.
When not to use
- You need conformer generation, docking, or reaction modeling.
- You need batch-scale descriptor computation for millions of compounds.
Inputs
- One SMILES string
- Optional molecule name
- Optional JSON output path
Outputs
- JSON summary with canonical SMILES, formula, exact mass, logP, TPSA, HBA/HBD, rotatable bonds, ring count, and heavy-atom count
Requirements
slurm/envs/chem-toolswith RDKit available
Procedure
- Run
slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecular-descriptors/scripts/compute_rdkit_descriptors.py --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --name aspirin. - Inspect
canonical_smiles,formula,molecular_weight, andtpsa. - Reuse the JSON payload for downstream filtering or reporting.
Validation
- The command exits successfully.
canonical_smilesis non-empty for a known valid molecule.- Descriptor fields are numeric where expected.
Failure modes and fixes
- Invalid SMILES: verify the input string and quoting.
- Missing RDKit environment: run the script with
slurm/envs/chem-tools/bin/python.
Safety and limits
- Descriptor calculation only.
- No medicinal-chemistry or safety interpretation is implied.
Provenance
- RDKit docs: https://www.rdkit.org/docs/index.html
- RDKit repository: https://github.com/rdkit/rdkit
Related skills
chembl-molecule-search
What ships with it
10 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.
- assets/aspirin_descriptors.json 358 B
- assets/README.md 129 B
- examples/aspirin.smiles 25 B
- examples/molecules.tsv 90 B
- examples/README.md 396 B
- metadata.yaml 1018 B
- refs.md 127 B
- scripts/compute_rdkit_descriptors.py 2.0 KB runs code
- tests/README.md 98 B
- tests/test_compute_rdkit_descriptors.py 1.4 KB runs code
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.
- 9d ago First seen · 53 lines · 41 tokens per session scan A 3860eeace9ff
rdkit-molecular-descriptors is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 41 tokens to every session and 465 once invoked, about $0.0002 per session on Opus 5. 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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