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Bio Simplefold Inference

skill-onescience-ai-oneskills-simplefold-inference · by onescience-ai

SimpleFold 蛋白结构推理 skill。用于执行 OneScience SimpleFold flow-matching FoldingDiT 的 FASTA 到结构、sample、pLDDT 和 ESM 条件推理，收紧模型规模、ESM 特征、atom-token 特征、采样步数、checkpoint 和结构输出校验。

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Install

$ agentstack add skill-onescience-ai-oneskills-simplefold-inference

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

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About

SimpleFold 推理

使用边界

用于 OneScience SimpleFold 示例的蛋白折叠推理。它不是 AF2/OpenFold 或 AF3/Protenix feature pipeline，不要互换输入。

可复用资源

  • {onescience_path}/onescience/examples/biosciences/_manifests/model_requests/simplefold_request.yaml：FASTA、模型规模、采样、ESM、checkpoint 和输出模板。
  • references/simplefold_execution.md：SimpleFold 输入特征、采样参数和失败恢复。

推荐流程

  1. 读模型卡：onescience-coder/assets/models/simplefold.md。
  2. 确认入口：{onescience_path}/onescience/examples/biosciences/simplefold/inference.py，需要采样实验时看 sample.py。
  3. Preflight：FASTA、模型规模、checkpoint、ESM 表征路径或在线生成能力、GPU 显存。
  4. 参数收紧：num_steps、tau、nsample_per_protein、输出目录和 seed。
  5. Postflight：结构文件、残基数、pLDDT/置信度、空结构、采样多样性。

禁止事项

  • 不要把 OpenFold/Protenix batch 送入 SimpleFold。
  • 缺少 esm_s 或 atom-token 特征路径时，不要假装能直接最小 forward 完成结构推理。
  • 不要只看生成 PDB 是否存在，必须检查残基数和坐标是否非空。

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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