Agent4Molecule

The system extensively uses `subprocess.Popen` and `os.system` with f-strings for building and executing shell commands, creating numerous potential command injection vulnerabilities. Parameters from user input are not consistently sanitized before being used in these commands. Critical paths to external tools and environments are hardcoded in multiple server scripts (`enzygen_server.py`, `heme_binder_server.py`, `ppdiff_server.py`), making the system less portable and potentially exposing sensitive file system structures. The use of `ast.literal_eval` on potentially unsanitized input is a minor but existing risk. The underlying scientific tools (e.g., Open Babel, Vina, ClustalW) and HPC environment (SLURM, Apptainer) add to the attack surface if not configured securely.