The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill recommends installing the MDAnalysis package from PyPI. This is a well-known and reputable scientific library for molecular simulations.
[COMMAND_EXECUTION]: Includes instructions for standard package management using pip and environment verification using python -c commands.
[INDIRECT_PROMPT_INJECTION]: The skill identifies a surface for indirect prompt injection as it is designed to ingest and process external molecular topology and trajectory files.
Ingestion points: Data enters the environment via the mda.Universe function when loading files such as .gro, .xtc, and .pdb (referenced in SKILL.md).
Boundary markers: There are no specific instructions or delimiters provided to mitigate the processing of maliciously crafted data files.
Capability inventory: The skill possesses file-writing capabilities through MDAnalysis.Writer, pandas.DataFrame.to_csv, and matplotlib.pyplot.savefig.
Sanitization: No explicit sanitization or structural validation for input MD files is described.

mdanalysis-trajectory