Bio Af3 Protenix Complex Inference
AlphaFold3 / Protenix 复合物结构推理 skill。用于执行 OneScience 中 AlphaFold3 JAX 或 Protenix PyTorch 的蛋白、核酸、配体、离子复合物推理，收紧 AF3 JSON、Protenix JSON、MSA/template/CCD/RDKit、checkpoint、diffusion samples、attention fallback 和 confidence 输出校验。
Install
$ agentstack add skill-onescience-ai-oneskills-af3-protenix-complex-inference ✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.
Security review
✓ PassedNo 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.
About
AF3 / Protenix 复合物结构推理
使用边界
用于 AF3 风格复合物结构预测。AlphaFold3 与 Protenix 概念相近但实现不兼容：AlphaFold3 是 JAX/Haiku，Protenix 是 PyTorch/OneScience 模块化。
可复用资源
{onescience_path}/onescience/examples/biosciences/_manifests/model_requests/af3_protenix_request.yaml：JSON、checkpoint、MSA、diffusion sample、attention 和输出模板。references/af3_protenix_execution.md：二者入口、输入协议、资源和失败恢复差异。
推荐流程
- 选择模型：需要 AF3 JAX data pipeline / model_dir 用
AlphaFold3；需要 Protenix unified PyTorch 入口用Protenix。 - 读模型卡：
alphafold3.md或protenix.md。 - 固定入口：
- AlphaFold3：
{onescience_path}/onescience/examples/biosciences/alphafold3/run_alphafold.py - Protenix：
{onescience_path}/onescience/examples/biosciences/protenix/runner/inference_unified.py
- Preflight：JSON schema、protein/RNA/DNA/ligand、MSA/template、CCD/RDKit、model checkpoint、attention 实现、输出目录。
- 运行策略：先小样本/少 diffusion sample 验证输入，再放大
num_diffusion_samples、N_sample、N_step。 - Postflight：结构文件、ranking/confidence、PAE/PDE/pLDDT/contact、链/配体/原子数、失败日志。
交接物
bio_task_family: bio-inference
selected_concrete_skill: af3-protenix-complex-inference
model_family: AlphaFold3_or_Protenix
inference_mode: biomolecular_complex_structure
input_protocol: AF3_JSON_or_Protenix_JSON
entrypoint:
checkpoint_or_model_dir:
msa_template_mode:
ligand_ccd_resources:
diffusion_sampling:
attention_fallback:
expected_outputs:
output_validation_plan:
execution_entry:禁止事项
- 不要把 AF3 JSON 直接当作 Protenix feature dict，或反过来复用。
- 不要忽略配体 CCD、SMILES/SDF、RDKit 和 bond 信息。
- Attention 报错时优先切换 fallback，不要改模型结构。
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: onescience-ai
- Source: onescience-ai/OneSkills
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.