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Perform normalized filesystem operations (list, read, write, append, mkdir, stat, copy, move, delete, search, replace) through a single skill script. Use when tasks require deterministic file manipulation through get_skill_script instead of built-in FileTools.
Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
SOC 직업 분류 기준
Execute Python snippets or Python files through a normalized skill entrypoint with explicit cwd, timeout, and argv. Use when tasks require ad-hoc Python execution and you want skill-based execution instead of built-in PythonTools.
Execute shell commands through a normalized skill entrypoint with explicit cwd and timeout. Use when tasks require command-line operations (tests, build, git, search, file inspection) and you want script-based execution via get_skill_script instead of built-in ShellTools.
Convert AlphaFold3 official inference JSON into Protenix, Boltz, or OpenFold3 inputs with schema validation. Use when an existing AF3 JSON must be reused by another folding stack, including batch conversion, target auto-detection from output filename, and best-effort mapping of AF3 `bondedAtomPairs`, MSA fields, templates, and ligand CCD/smiles data.
Convert CSV tables into valid AlphaFold3 input JSONs. Use this skill when you need to batch-generate AF3 JSONs from tabular inputs and run in MSA-free mode (protein uses empty unpairedMsa/pairedMsa, RNA uses empty unpairedMsa).
Extract deduplicated protein, DNA, and RNA sequences from AF3 or Protenix inference JSON files into per-entity-type FASTA files keyed by SHA-256 hash. Use as the first stage of the MSA pipeline before `af3-msa-search` and `af3-msa-injector`.
Inject cleaned ColabFold MSA artifacts from `af3-msa-search` into MSA-free AF3 or Protenix inference JSON files to produce complete inputs for downstream inference. Use when AF3 JSON contains empty `unpairedMsa`/`pairedMsa` fields or Protenix JSON lacks `unpairedMsaPath`/`pairedMsaPath`, including single-file and batch directory processing.
| name | file-operator |
| description | Perform normalized filesystem operations (list, read, write, append, mkdir, stat, copy, move, delete, search, replace) through a single skill script. Use when tasks require deterministic file manipulation through get_skill_script instead of built-in FileTools. |
Use one script for all common file operations:
scripts/file_ops.pyThis skill provides normalized commands for directory traversal and file edits.
.venv/bin/python skills/file-operator/scripts/file_ops.py list --path .
.venv/bin/python skills/file-operator/scripts/file_ops.py read --path src/agents/cli.py --start-line 1 --end-line 80
.venv/bin/python skills/file-operator/scripts/file_ops.py write --path tmp/demo.txt --text "hello"
.venv/bin/python skills/file-operator/scripts/file_ops.py search --path src --query "print_stream" --glob "*.py"
.venv/bin/python skills/file-operator/scripts/file_ops.py replace --path src --glob "*.py" --find "foo" --replace "bar" --dry-run
list: list directory entriesread: read text file (optionally line range)write: overwrite/create text fileappend: append text filemkdir: create directorystat: print JSON metadata for a pathcopy: copy file or directorymove: move/rename pathdelete: delete file or directory (--recursive required for non-empty dirs)search: search text in files (literal or regex)replace: batch replace text in files (literal or regex, supports --dry-run)read, prefer line ranges for large files.search and replace, narrow scope with --glob and --path.replace with --dry-run first, then execute without --dry-run.--backup-ext .bak when you want rollback copies during replace.delete, overwriting write), confirm intent in reasoning before execution.copy + move for reversible workflows when possible.--base-dir)Pass --base-dir <DIR> before the subcommand to restrict all path arguments to the given directory:
.venv/bin/python skills/file-operator/scripts/file_ops.py --base-dir /workspace \
read --path /workspace/src/main.py # OK
.venv/bin/python skills/file-operator/scripts/file_ops.py --base-dir /workspace \
read --path /etc/passwd # exit code 2
--path, --src, and --dst arguments are validated.--base-dir is omitted, behaviour is unchanged (no restriction).