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SKILL verified MIT Self-run

Bio Molsculptor Inference

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

MolSculptor 小分子生成与优化推理 skill。用于执行 OneScience MolSculptor 的 SMILES/分子图编码、latent diffusion、de novo generation、分子优化、reward 筛选和 case 脚本，收紧 RDKit sanitize、padding/vocab/checkpoint、采样策略、外部 docking 依赖和 SMILES/SDF 输出校验。

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Install

$ agentstack add skill-onescience-ai-oneskills-molsculptor-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.

Preview Execution monitoring

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About

MolSculptor 推理

使用边界

用于小分子/药物设计辅助推理。它不接受蛋白 FASTA、PDB folding batch 或 Evo2 DNA tokens。

可复用资源

  • {onescience_path}/onescience/examples/biosciences/_manifests/model_requests/molsculptor_request.yaml：SMILES/target case、checkpoint、采样、reward 和输出模板。
  • references/molsculptor_execution.md：SMILES/graph、RDKit、diffusion、case/docking 和输出检查。

推荐流程

  1. 读模型卡：onescience-coder/assets/models/molsculptor.md。
  2. 选择入口：通用推理看 src/onescience/flax_models/MolSculptor/train/inference.py；具体靶点优化看 examples/biosciences/molsculptor/inference/* 或 cases//。
  3. Preflight：RDKit、JAX/Flax、checkpoint、vocab、padding atom 上限、初始 SMILES/分子、case 配置。
  4. 若涉及 docking reward：确认 OpenBabel/PDBQT/DSDP 脚本和 receptor 文件，不默认运行。
  5. Postflight：SMILES validity、duplicate、property、reward、SDF/CSV/PKL、失败分子比例。

交接物

bio_task_family: bio-inference
selected_concrete_skill: molsculptor-inference
model_family: MolSculptor
inference_mode: de_novo_or_optimization
input_protocol: SMILES_or_molecule_graph
entrypoint:
checkpoint:
sampling_strategy:
reward_or_case:
expected_outputs:
output_validation_plan:
execution_entry:

禁止事项

  • 不要把 docking reward 当作已经运行，除非日志和产物证明完成。
  • 不要忽略 RDKit sanitize 失败和重复分子。
  • 不要把生成分子直接写成候选药物结论。

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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