The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill ingests external structural biology data through PDB and trajectory files. While these files represent an attack surface for data-driven instructions, the risk is localized to the parsing logic of the underlying scientific libraries (OpenMM/MDAnalysis), which treat inputs as structured coordinates rather than executable commands.
Ingestion points: prepare_system_from_pdb in SKILL.md and load_trajectory in references/mdanalysis_analysis.md.
Boundary markers: None explicitly defined; the skill relies on standard library file parsers.
Capability inventory: Local filesystem read/write for simulation states, trajectories, and plots.
Sanitization: Relies on structural validation performed by the OpenMM and MDAnalysis APIs.

molecular-dynamics