The Agent Skills Directory

[SAFE]: The skill provides legitimate functionality for chemical library enumeration, fragmentation (RECAP/BRICS), and SAR analysis (Free-Wilson, MMPA) using industry-standard scientific tools.\n- [EXTERNAL_DOWNLOADS]: The skill references several well-known scientific Python packages including RDKit, scikit-learn, numpy, and pandas, as well as specialized chemoinformatics tools like mmpdb and RDChiral. These dependencies are standard and appropriate for the skill's stated purpose.\n- [COMMAND_EXECUTION]: SKILL.md includes documentation for the command-line usage of mmpdb for fragmentation and indexing of chemical data. This represents standard tool usage and does not involve risky parameters or obfuscated commands.\n- [INDIRECT_PROMPT_INJECTION]: The skill ingests chemical data in the form of SMILES and SMARTS strings. Ingestion points: enumerate_reaction and apply_rgroup_decoration in examples/enumerate_reactions.py. Boundary markers: Absent. Capability inventory: Functions are limited to in-memory chemical transformations with no network access or file system write operations. Sanitization: Chemical structure validation is performed via Chem.SanitizeMol. The risk is minimal as the data is processed by a specialized chemical engine rather than interpreted as natural language instructions.

bio-reaction-enumeration