---

name: configuration-and-data description: "Create, validate, and troubleshoot AiZynthFinder configuration files, stocks, model assets, public-data setup commands, and data-tool commands." disable-model-invocation: true metadata: disco-role: operating license: MIT

Configuration and Data

Use this sub-skill when the task is about AiZynthFinder YAML configuration, data assets, stock files, policy/filter model references, or the bundled data-preparation CLIs. Stay in this sub-skill for safe static validation and setup guidance; route out before running retrosynthesis or interpreting output.

Owns

• Creating and reviewing YAML sections: search, post_processing, expansion, filter, stock, and optional scorer.
• Explaining env-var interpolation with ${VAR} and the failure mode for missing variables.
• Choosing short-form versus full-form syntax for expansion policies, filter policies, and stocks.
• Documenting search defaults, algorithm_config, bond controls, post-processing keys, and stock stop criteria.
• Preparing asset guidance for model checkpoints, template tables, HDF5/CSV/text stocks, MongoDB stocks, and molbloom stocks.
• Giving safe recipes for smiles2stock and download_public_data without executing downloads, Mongo writes, or bloom creation unless explicitly requested.
• Running the bundled static validator script to catch schema-shape issues and missing local file references before a search run.

Routes

• Use planning-workflows to execute aizynthcli, aizynthapp, or an actual retrosynthesis run from a config.
• Use route-analysis to inspect outputs, route trees, statistics, clustering, or solved-route quality.
• Use extension-and-development to implement custom expansion strategies, stock query classes, scorers, filters, plugins, or custom search algorithms.

References

• Configuration reference covers YAML sections, defaults, env vars, policy/filter/stock syntax, and validation expectations.
• Stocks and assets covers model/template/stock file formats, optional dependencies, and service assumptions.
• CLI tools covers safe smiles2stock and download_public_data recipes and when commands mutate external state.
• Troubleshooting covers common configuration, data, optional dependency, and service failures.

Safe Validation

Before running a user-provided config, run the bundled validator from any working directory:

python skills/aizynthfinder/sub-skills/configuration-and-data/scripts/validate_aizynth_config.py path/to/config.yml --json

The validator intentionally does not import AiZynthFinder and does not load models, templates, stocks, MongoDB, TensorFlow servers, molbloom filters, or run tree search. Treat errors as blockers and warnings as setup issues to review with the user.

Operating Rules

• Keep public guidance asset-agnostic: use user-provided or project-relative paths, not local checkout paths or environment prefixes.
• Do not claim MongoDB, molbloom, TensorFlow serving, public downloads, or route-distance features work until the user confirms the needed optional dependencies and services.
• Do not execute download_public_data, Mongo writes, or molbloom creation without explicit user intent because they can use network, storage, or external services.
• If a config validates statically but no expansion policy will be selected during planning, route to planning-workflows for the runtime selection step.