AiZynthFinder Repo Skill

Use this skill when a user is working with AiZynthFinder, a retrosynthetic route-finding package for planning molecule syntheses with policy-guided tree search.

First Steps

1. Confirm the user has AiZynthFinder installed in a Python >=3.10,<3.13 environment.
2. If the task mentions a config, stock, policy model, template library, public-data bundle, or optional service, start with configuration-and-data.
3. If the task is to run retrosynthesis or one-step expansion, use planning-workflows.
4. If the task starts from an existing output.json.gz, HDF5 output, trees.json, checkpoint, route collection, or reaction tree, use route-analysis.
5. If the task is about custom scorers, stocks, policies, search algorithms, plugin strategies, hooks, or source edits, use extension-and-development.

Install and Import Check

For end users, install the public package with base dependencies unless the task needs optional features:

python -m pip install aizynthfinder
python - <<'PY'
from aizynthfinder.aizynthfinder import AiZynthFinder, AiZynthExpander
print(AiZynthFinder, AiZynthExpander)
PY

Use python -m pip install "aizynthfinder[all]" only when the task needs optional MongoDB, molbloom, route-distance, timeout, or similar extras. Use TensorFlow/gRPC-related extras only for TensorFlow Serving or remote model workflows.

Run scripts/check_aizynthfinder_env.py when diagnosing import, version, CLI, or optional-dependency availability without launching a search.

Sub-Skill Routes

• planning-workflows: build and run aizynthcli commands, use AiZynthFinder or AiZynthExpander, handle single vs batch SMILES, checkpoints, multiprocessing, clustering flags, and GUI/notebook launch decisions.
• configuration-and-data: write and validate YAML configs, stock files, policy/filter model references, public data commands, smiles2stock, download_public_data, and optional dependency choices.
• route-analysis: inspect output.json.gz, HDF5 tables, trees.json, checkpoints, ReactionTree, RouteCollection, route scores, clustering, images, and result summaries.
• extension-and-development: implement or validate custom hooks, stocks, scorers, policies, plugin expansion strategies, search algorithms, and focused source-checkout tests.

Shared References

• Read references/troubleshooting.md for cross-cutting install, optional dependency, model/stock asset, CLI/API, and backend failures before drilling into sub-skill-specific troubleshooting.
• Read references/repo-provenance.md before deciding whether this skill is current for an AiZynthFinder checkout or should be refreshed.
• references/repo-routing-metadata.json is structured metadata used by the managed repo-skills-router during import.

Routing Guardrails

• Do not run download_public_data, MongoDB stock creation, long retrosynthesis batches, GUI launches, or plugin service calls unless the user explicitly asks for those side effects.
• Do not assume user assets exist. Configs normally require a stock file, an expansion policy model, and a reaction template library; filter policies are optional.
• Prefer static validation and CLI/API help checks before running searches with user data.
• Keep optional plugins and service-backed models separate from core install troubleshooting; missing Chemformer, ModelZoo, MongoDB, molbloom, route-distance, or TensorFlow Serving dependencies are feature-specific, not proof that core AiZynthFinder is broken.