菜单
Structure/sequence file preparation with VenusFactory file tools. Use for FASTA parsing, PDB chain extraction, PDB↔mmCIF conversion (MAXIT), apo checks, batch PDB→FASTA, and UniProt ID from RCSB metadata. Do NOT use for structure prediction (protein_structure_pipeline) or homology search.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/ai4protein/VenusFactory2 --skill structure-file-prep命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
Fine-tune and run custom protein models on VenusFactory (CSV/HF → config → train → predict). Use when the user brings labeled sequences, wants adapter training (ProtT5/ESM2/Ankh/QLoRA notes), or batch inference with a trained config. Do NOT use for zero-shot mutation without labels (zero_shot_mutation_workflow) or built-in function heads already covered by predict_protein_function.
AlphaFold DB structures and confidence analytics via VenusFactory tools. Use when the user needs predicted structures by UniProt ID, pLDDT/PAE analysis, or PDB/mmCIF download. Do NOT use for experimental PDB (rcsb_database), local ESMFold without UniProt (predict_structure_esmfold / protein_structure_pipeline), or sequence annotation (uniprot_database).
arXiv preprint server — keyword search the official API and download papers as PDF / HTML / source tarball. Use whenever the user mentions an arXiv ID (e.g. 2106.04559) or wants preprints on a topic in CS / physics / math / quantitative biology. For biomedical preprints specifically, prefer biorxiv skill.
基于 SOC 职业分类
正在显示 SKILL.md
| name | structure_file_prep |
| description | Structure/sequence file preparation with VenusFactory file tools. Use for FASTA parsing, PDB chain extraction, PDB↔mmCIF conversion (MAXIT), apo checks, batch PDB→FASTA, and UniProt ID from RCSB metadata. Do NOT use for structure prediction (protein_structure_pipeline) or homology search. |
| license | Apache-2.0 |
| metadata | {"version":"1.0","skill-author":"VenusFactory2"} |
| Tool | Purpose |
|---|---|
| read_fasta | Parse multi-FASTA → headers/sequences |
| extract_uids_from_fasta | Pull UIDs from headers |
| uid_file_to_chunks | Chunk UID lists for batch jobs |
| pdb_chain_sequences | Per-chain sequences from PDB |
| get_seq_from_pdb_chain_a | Chain A sequence shortcut |
| pdb_dir_to_fasta | Directory of PDBs → FASTA |
| check_pdb_apo | Ligand-free / apo heuristic |
| maxit_structure_convert | pdb2cif / cif2pdb / cif2mmcif (needs MAXIT) |
| extract_uniprot_id_from_rcsb_metadata | UniProt from RCSB metadata JSON |
| unzip_archive / ungzip_file | Unpack downloads |
check_pdb_apo (if apo backbone required)pdb_chain_sequences → choose designed chainsmaxit_structure_convert for format mismatchesdownload_rcsb_entry_metadata_by_pdb_idextract_uniprot_id_from_rcsb_metadataalphafold_database / protein_structure_pipelinepdb_chain_sequencespdb2cif/cif2pdb/cif2mmcif