The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill processes external molecular structure and trajectory files, representing a potential surface for indirect prompt injection.
Ingestion points: The skill reads data from PDB, DCD, XTC, and other trajectory formats through functions like prepare_system_from_pdb and load_trajectory in SKILL.md and references/mdanalysis_analysis.md.
Boundary markers: There are no explicit delimiters or instructions provided to the agent to distinguish between data and control instructions within these files.
Capability inventory: The agent is granted Bash(python:*) and Bash(uv:*) tools, as well as Write and Edit permissions, allowing it to execute code and modify the file system based on its interpretation of the data.
Sanitization: The skill relies on the internal parsers of scientific libraries (OpenMM, MDAnalysis) for data handling; no additional sanitization or validation logic is specified in the prompt instructions.
[EXTERNAL_DOWNLOADS]: The skill documentation suggests installing the pdbfixer tool directly from a public Git repository (github.com/openmm/pdbfixer.git). While this targets an established scientific organization's repository, it involves fetching and installing code from a remote source at runtime.
[COMMAND_EXECUTION]: The skill makes extensive use of shell-based tools to run Python simulations and analysis scripts. The agent is instructed to perform complex operations, including system setup, energy minimization, and trajectory processing, via terminal commands.

alterlab-molecular-dynamics