The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill clones the official ProteinMPNN source code repository from GitHub (https://github.com/dauparas/ProteinMPNN.git). It also instructs the installation of standard data science libraries (torch, numpy) via pip. These are expected actions for the documented purpose of protein sequence design.
[COMMAND_EXECUTION]: The skill executes a locally cloned Python script (protein_mpnn_run.py) using system python. The commands are transparent and match the tool's intended scientific use case.
[INDIRECT_PROMPT_INJECTION]: The skill processes external data including PDB structure files and JSONL configuration files.
Ingestion points: Path to PDB files via --pdb_path and JSONL metadata via --fixed_positions_jsonl.
Boundary markers: None; uses standard bioinformatics file parsing.
Capability inventory: The skill has capabilities for file system access (via out_folder) and subprocess execution (python execution of the model script).
Sanitization: Standard parsing by the ProteinMPNN library; no specific sanitization is implemented in the skill instructions themselves.

proteinmpnn