Known Limitations

These are current operational constraints to account for when planning runs.

Optional Tools

Full pipeline runs can require AiZynthFinder, GNINA/SMINA/Matcha, receptor structures, reference ligands, and CPU/GPU capacity. Use the descriptor + structural-filter smoke run for environment validation before enabling those stages.

Headerless SMI Inputs

Simple headerless .smi-style files are supported, but CSV/TSV with a smiles header is still the recommended production input format because it makes model_name and mol_idx explicit.

Matcha Reproducibility

Matcha setup may resolve a development checkout dynamically. For production runs, use a controlled local checkout or an explicitly pinned setup path.

TUI Cancellation

The TUI cancellation command requests cancellation. Long-running external tools may continue until the current subprocess or stage reaches a safe stopping point.

Config Ownership

Do not edit bundled configs inside an installed package in site-packages. Copy configs into your project or run directory and pass the copied master config with --config.

Package vs Source Checkout

The source checkout includes editable configs, examples, TUI sources, and the modules/ workspace used by setup commands. PyPI installs are best for users who already manage their own configs and input paths.