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 PKU-YuanGroup/OpenAI4S --skill bio-chemoinformatics-shape-similaritygit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-chemoinformatics-shape-similarity)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-chemoinformatics-shape-similarity"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-chemoinformatics-shape-similarity/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/pku-yuangroup/openai4s/bio-chemoinformatics-shape-similarity"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-chemoinformatics-shape-similarity.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 | $0.00121 | $0.03851 |
| Opus 5 | $0.00060 | $0.01925 |
| Sonnet 5 | $0.00024 | $0.00770 |
| Haiku 4.5 | $0.00012 | $0.00385 |
Grade A, and why
bio-shape-similarity 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.
This is a copy
94% identical to bio-shape-similarity — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 309 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+ (Open3DAlign and USRCAT); official ShaEP syntax checked against ShaEP 1.4.2; ROCS/FastROCS/ROCS X are commercial OpenEye products.
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.
Shape Similarity
Search for compounds with similar 3D shape (and optionally chemical features) to a query molecule. Shape-based screening complements 2D fingerprint search: it can find scaffold-hopped compounds that ECFP4 misses (different scaffolds with similar shape). ROCS (OpenEye) is the industry-standard commercial tool; Open3DAlign (RDKit), USRCAT (Schreyer & Blundell 2012), and ShaEP are open-source alternatives. Modern best practice combines shape with color (chemical-feature similarity) via Tanimoto-Combo: matches share both shape and pharmacophore feature distribution.
For 2D fingerprint similarity, see chemoinformatics/similarity-searching. For pharmacophore search (discrete feature constraints), see chemoinformatics/pharmacophore-modeling. For 3D conformer generation, see chemoinformatics/conformer-generation.
Shape Method Taxonomy
| Tool | Speed | Approach | Open-source | Fails when |
|---|---|---|---|---|
| ROCS / FastROCS (OpenEye) | Hardware/database/conformer-dependent; vendor reports millions of conformers/s for FastROCS | Gaussian shape + color | No | License and prepared database |
| ROCS X | Trillion-scale reaction/synthon space on Orion | FastROCS plus Bayesian-bandit sampling | No | Commercial cloud workflow |
| USRCAT | Very fast alignment-free descriptor comparison | Moment-based + atom types | Yes | Coarse approximation |
| Open3DAlign (RDKit) | Medium | MMFF atom-type/charge-weighted alignment | Yes | Requires compatible typed 3D structures |
| ShaEP | Benchmark on actual conformers/hardware | Field-based (shape + ESP) | Free binary; inspect license | Requires valid 3D structures and charges for ESP |
| ESPSim | Benchmark on actual workload | Electrostatic + shape | Yes | Limited public benchmarks |
| Phase-Shape (Schrödinger) | commercial | Shape + pharmacophore | No | Commercial |
| USR (original) | Very fast alignment-free comparison | Moment-based only | Yes | No atom-type information |
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.
- 9d ago First seen · 309 lines · 121 tokens per session scan A 23e8293d74a1
bio-shape-similarity is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 121 tokens to every session and 3,851 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. It is 94% identical to bio-shape-similarity, differing in 12 lines, and is treated as a copy.
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