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 GPTomics/bioSkills --skill retrosynthesisgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/retrosynthesis)<a href="https://agentmods.dev/skills/gptomics/bioskills/retrosynthesis"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/retrosynthesis/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/gptomics/bioskills/retrosynthesis"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/retrosynthesis.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 | $0.00093 | $0.03546 |
| Opus 5 | $0.00046 | $0.01773 |
| Sonnet 5 | $0.00019 | $0.00709 |
| Haiku 4.5 | $0.00009 | $0.00355 |
Grade A, and why
bio-retrosynthesis 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 6d 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-retrosynthesis — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 258 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: AiZynthFinder 4.4+, RDKit 2024.09+, RDChiral 1.1+, and ASKCOS Lite 0.5+. Chemformer is archived legacy research code; if reproducing it, pin an exact repository commit, checkpoint, and configuration rather than assuming a current pip package or stable Python API.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
aizynthcli --version
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Retrosynthesis
Plan synthetic routes from a target molecule back to commercially available building blocks. AiZynthFinder combines Monte Carlo Tree Search (MCTS), template-based expansion, configurable search rewards, and route scorers (Saigiridharan et al. 2024). Chemformer is a published template-free transformer baseline whose official repository is now archived; use its exact historical environment for reproduction or select a maintained model with a documented interface. ASKCOS is another open-source synthesis-planning platform. A useful workflow combines retrosynthesis with building-block availability and an independently configured forward-prediction check, while recognizing that a round-trip model match is not experimental validation.
For generative design pipelines that need synthetic feasibility, see chemoinformatics/generative-design. For reaction enumeration (forward direction), see chemoinformatics/reaction-enumeration.
Retrosynthesis Method Taxonomy
| Tool | Approach | Strength | Fails when |
|---|---|---|---|
| AiZynthFinder 4.4+ | Template-based MCTS | Maintained, configurable open-source planner | Beyond selected policy coverage |
| Chemformer (archived) | Template-free transformer | Reproducing the published baseline | Archived code and checkpoint/config coupling |
| ASKCOS | Template-based + neural | Open-source synthesis-planning platform | Setup complexity |
| Molecular Transformer | Forward + retro transformer | Single SMILES-to-SMILES | Less robust to non-training distribution |
| RetroSynFormer | Decision transformer | Modern method | Limited adoption |
What ships with it
2 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.
- 6d ago First seen · 258 lines · 93 tokens per session scan A a63a30a9a5e6
bio-retrosynthesis is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 25d ago), licensed MIT. It adds 93 tokens to every session and 3,546 once invoked, about $0.0005 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 2026-09-03.
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