User Guide

This guide is a practical, task-oriented path through SynPlanner.

What’s inside

• Concepts and algorithms → see Methods.

• Configuration of pipelines (YAML and Python) → see Configuration.

• CLI usage → see Command-line interface.

Run in Google Colab

Open selected tutorials directly in Google Colab (no local install):

• Retrosynthetic planning

• SynPlanner benchmarking

• Route clustering by strategic bonds

Tutorials

SynPlanner is supplemented by several tutorials explaining different aspects of tool usage. These tutorials included some advanced explanations and configurations, that can be used not only for demonstrative and educational purposes but also for creating flexible pipelines.

Introductory tutorials:

• Welcome to Chython - an introduction to the chython library and its core concepts.

• Coming from RDKit - a side-by-side comparison for users familiar with RDKit.

• 10 minutes to SynPlanner - a quickstart guide to run planning via Python or CLI.

Pipeline tutorials:

• Data Curation - demonstrates how to prepare data (reaction standardization and filtration) before reaction rules extraction and retrosynthetic model training.

• Rules Extraction - demonstrates how to extract reaction rules from reaction data.

• Policy Training - demonstrates how to train ranking and filtering policy networks.

• Retrosynthetic Planning - demonstrates how retrosynthetic planning can be performed for target molecules.

• Clustering - demonstrates how to cluster predicted retrosynthetic routes.

• Protection Scoring - demonstrates how to detect competing functional groups and score routes for selectivity issues, inspired by Westerlund et al. (2025).

Advanced tutorials:

• Combined Ranking and Filtering Policy - demonstrates how to combine ranking and filtering policy networks.

• NMCS Algorithms - demonstrates Nested Monte Carlo Search algorithms for retrosynthetic planning.

• Tree Analysis - demonstrates how to analyze tree search results: policy performance, winning rule ranks, branching profile, and route details.

• Planning with RDKit - demonstrates how to use SynPlanner with RDKit Mol objects for input and output.

• Rule Analysis - demonstrates how to analyze and visualize reaction rules.