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 scaffold-analysisgit 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/scaffold-analysis)<a href="https://agentmods.dev/skills/gptomics/bioskills/scaffold-analysis"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/scaffold-analysis/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/scaffold-analysis"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/scaffold-analysis.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 | $0.00097 | $0.03884 |
| Opus 5 | $0.00048 | $0.01942 |
| Sonnet 5 | $0.00019 | $0.00777 |
| Haiku 4.5 | $0.00010 | $0.00388 |
Grade A, and why
bio-scaffold-analysis 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-scaffold-analysis — 91% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 315 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: RDKit 2024.09+, mmpdb 3.1+, scikit-learn 1.4+, datamol 0.12+.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Scaffold Analysis
Analyze chemical libraries by their underlying scaffolds. Bemis-Murcko (1996) is the canonical scaffold decomposition: ring systems + linkers, with all R-groups stripped. Generic framework + cyclic skeleton are progressively-more-abstract views. Scaffold analysis underpins QSAR train/test splits (preventing data leakage), library diversity assessment, chemotype clustering, R-group decomposition for SAR modeling, and matched molecular pair analysis (MMPA). The choice of scaffold representation determines whether two compounds are "the same series" -- a critical decision for medicinal chemistry workflows.
For reaction-based enumeration and Free-Wilson, see chemoinformatics/reaction-enumeration. For scaffold-hopping via fingerprints, see chemoinformatics/similarity-searching. For 3D shape-based scaffold hopping, see chemoinformatics/shape-similarity.
Scaffold Representation Taxonomy
| Representation | Origin | Definition | Use case | Fails when |
|---|---|---|---|---|
| Bemis-Murcko scaffold | Bemis & Murcko 1996 | Ring systems + linkers, R-groups stripped | Default chemotype identifier | Linear molecules (no rings) -> empty scaffold |
| Generic framework | Bemis & Murcko 1996 | Bemis-Murcko with all atoms set to C, all bonds single | Topology comparison | Loses heteroatom info |
| Cyclic skeleton (CSK) | Custom RDKit transformation | Ring atoms only, all C, all single | Pure ring-topology view | Loses linker info; not a built-in Murcko option |
| Murcko atom indices | Derived by matching the scaffold to the parent | Parent-molecule atom indices | Programmatic operations | Symmetry can yield multiple equivalent matches |
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 · 315 lines · 97 tokens per session scan A 14cae7cd1b9a
bio-scaffold-analysis is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 25d ago), licensed MIT. It adds 97 tokens to every session and 3,884 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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