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name: planning-workflows description: "Run AiZynthFinder retrosynthesis planning and one-step expansion through CLI, Python APIs, and optional notebook interfaces." disable-model-invocation: true metadata: disco-role: operating license: MIT

Planning Workflows

Use this sub-skill when the task is to execute or script AiZynthFinder retrosynthesis planning, construct an aizynthcli command, call AiZynthFinder or AiZynthExpander from Python, debug target SMILES setup, checkpoint a batch run, or launch the optional notebook interface.

Before You Run

• Confirm aizynthfinder is importable and the aizynthcli entry point is on PATH.
• Confirm a configuration file or config dictionary is available and points to usable stock, expansion-policy, and optional filter assets.
• If config/assets are missing, first use ../configuration-and-data/SKILL.md.
• Decide whether --smiles is a literal single SMILES or a text file with one SMILES per row; multiprocessing requires a file.
• Decide which policy, filter, and stock keys to select at execution time; key names must match loaded config entries.
• Send output parsing, route images, scoring, clustering interpretation, and dataframe work to ../route-analysis/SKILL.md.
• Send custom pre/post-processing implementations, plugins, custom stocks, or custom search classes to ../extension-and-development/SKILL.md.

Workflow Map

• For safe CLI command construction, use scripts/build_aizynthcli_command.py and then run the printed command in the intended environment.
• For CLI behavior, flags, defaults, and command patterns, read references/cli-reference.md.
• For end-to-end single, batch, checkpointed, API, one-step expansion, and notebook recipes, read references/workflows.md.
• For public API signatures, lifecycle ordering, and return-object notes, read references/api-reference.md.
• For concrete failure symptoms and recoveries, read references/troubleshooting.md.

Quick Routes

• Single CLI target: build aizynthcli --config CONFIG --smiles SMILES, optionally with --output trees.json.
• Batch CLI targets: build aizynthcli --config CONFIG --smiles smiles.txt --output output.json.gz, optionally with --checkpoint checkpoint.json.gz.
• Parallel batch: use --nproc N only when --smiles names an existing file.
• Python planning: instantiate AiZynthFinder, select stock/policy/filter keys, set target_smiles, run prepare_tree(), tree_search(show_progress=False), build_routes(), then call extract_statistics() and stock_info().
• One-step expansion: instantiate AiZynthExpander, select policies and optional filters, then call do_expansion(smiles, return_n=5, filter_func=None).
• GUI/notebook: use aizynthapp --config CONFIG or create an AiZynthApp inside Jupyter only when an interactive notebook environment is available.