The Agent Skills Directory

[COMMAND_EXECUTION]: The skill invokes external command-line tools like prepare_receptor and prepare_flexreceptor from the ADFR Suite using Python's subprocess.run to perform protein file conversion.
[INDIRECT_PROMPT_INJECTION]: The skill ingests untrusted external data such as PDB IDs and SMILES strings and possesses system-level capabilities including file writing and shell execution. This creates a vulnerability surface if the input values are sourced from an adversary without proper validation.
Ingestion points: prody.fetchPDB (PDB ID) and Chem.MolFromSmiles (SMILES strings) in SKILL.md.
Boundary markers: Not present in the provided scripts.
Capability inventory: subprocess.run for receptor preparation and open().write() for PDBQT files.
Sanitization: No explicit sanitization of PDB IDs or SMILES strings is shown before they are used in file paths or command arguments.
[EXTERNAL_DOWNLOADS]: The skill fetches protein structures from the Protein Data Bank using the ProDy library and directs users to download the ADFR Suite from the Scripps Research Institute. These are well-known scientific data sources and academic institutions.

autodock-vina-docking