Agent4Molecule
by Frostday
Overview
The Agent4Molecule system provides an AI assistant for executing molecular discovery pipelines, including enzyme generation, heme binder design, protein-protein diffusion (PPDiff), molecular docking, and MD simulations.
Installation
streamlit run chat_interface.py --server.port=8050 --server.address=0.0.0.0Environment Variables
- GEMINI_API_KEY
- CONDA_EXE
- APPTAINER_CACHEDIR
- APPTAINER_TMPDIR
Security Notes
The codebase extensively uses `os.system()` and `subprocess.Popen(shell=True)` with dynamically constructed commands, which is a critical security vulnerability for command injection if user inputs are not rigorously sanitized across all functions. While `shlex.quote` is used in some parts, it's not universally applied, leaving many potential injection points. The Streamlit frontend binds to `0.0.0.0`, potentially exposing the UI to external networks without proper host-level firewalling. Interactions with SLURM (`sbatch`, `squeue`) assume a trusted HPC environment; a compromise could allow arbitrary job execution. Logs may contain sensitive file paths or intermediate data.
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