synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and instructions.
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 synthetic-sciences/openscience --skill smiles-validationgit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote 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/synthetic-sciences/openscience/smiles-validation)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/smiles-validation"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/smiles-validation/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/synthetic-sciences/openscience/smiles-validation"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/smiles-validation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00024 | $0.00454 |
| Opus 5.5 | $0.00010 | $0.00182 |
| Sonnet 5.5 | $0.00005 | $0.00091 |
| Haiku 4.5 | $0.00002 | $0.00045 |
Grade A, and why
smiles-validation 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 1mo 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
SMILES Validation
Overview
LLMs frequently generate invalid SMILES or produce molecules that don't match their stated reasoning. This skill provides strict validation, structural comparison, and modification verification.
Key checks:
- Parse validation: RDKit sanitization, valence checking, parenthesis/bracket balance
- Structural comparison: Tanimoto similarity, scaffold preservation, MCS analysis
- Modification verification: Confirm claimed structural changes exist in the actual molecule
- Classification: Categorize changes as optimization (>0.6 similarity), significant modification (0.4-0.6), or de novo design (<0.4)
When to Use This Skill
- After molecule generation: Validate every SMILES before reporting results
- Optimization verification: Confirm proposed modifications match the actual structure
- Batch validation: Check a library of generated molecules for validity
- Quality control: Ensure reproducibility of molecular designs
Installation
pip install rdkit-pypi
Core Workflows
1. Validate a Single SMILES
python scripts/validate.py --smiles "c1ccccc1"
2. Compare Original vs Modified
python scripts/validate.py --original "c1ccccc1" --proposed "c1ccc(O)cc1" --check-modification "Added hydroxyl group"
3. Batch Validation
python scripts/validate.py --input generated_molecules.csv --output validation_report.json
Script Reference
| Script | Purpose | Key Outputs |
|---|---|---|
validate.py |
SMILES validation, comparison, and modification checking | JSON report with validity, similarity, scaffold match, modification verification |
What ships with it
1 file 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.
- 1mo ago First seen · 63 lines · 24 tokens per session scan A 351b7c62cfbf
smiles-validation is a skill published in the GitHub repository synthetic-sciences/openscience (4,082 stars, last pushed today), licensed Apache-2.0. It adds 24 tokens to every session and 454 once invoked, about $0.0001 per session on Opus 5.5. 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 2026-09-03.
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