path-finder-retrosynthesis 1.0.2

Retrosynthesis route finder — AiZynthFinder + Rxn-INSIGHT + Chemistry by Design

Path Finder

AiZynthFinder · Chemistry by Design · Rxn-INSIGHT

Yara Chahda · Corentin Postmann · Inès Ouchen — EPFL 2025

Retrosynthesis route finder: find, rank and compare synthesis routes for any target molecule.

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Installation

Step 1 — Install RDKit (conda only)

conda install -c conda-forge rdkit

RDKit cannot be installed via pip — this single conda step is required.

Step 2 — Install Path Finder

pip install path-finder-retrosynthesis

With predicted routes (Rxn-INSIGHT):

pip install path-finder-retrosynthesis[predicted]

Step 3 — First-time setup

path-finder-setup

The wizard copies the bundled datasets, creates data/config.yml, and tells you exactly which files to download.

Step 4 — Download AiZynthFinder model files

Go to https://github.com/MolecularAI/aizynthfinder/releases and download:

File	Purpose
uspto_model.onnx	Expansion policy network
uspto_templates.csv.gz	Reaction templates
uspto_filter_model.onnx	Filter policy (optional)
zinc_stock.hdf5	Purchasable building blocks

Place them in data/aizynthfinder/.

Step 5 — Edit config.yml

Open data/config.yml and replace /PATH/TO/AIZYNTHFINDER/ with the absolute path to your model files.

macOS / Linux:

expansion:
  uspto:
    - /Users/alice/data/aizynthfinder/uspto_model.onnx
    - /Users/alice/data/aizynthfinder/uspto_templates.csv.gz

Windows:

expansion:
  uspto:
    - C:/Users/alice/data/aizynthfinder/uspto_model.onnx
    - C:/Users/alice/data/aizynthfinder/uspto_templates.csv.gz

Step 6 — Launch

path-finder

Open http://localhost:8501 in your browser.

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Quick summary

conda install -c conda-forge rdkit
pip install path-finder-retrosynthesis
path-finder-setup
# edit data/config.yml
path-finder

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Data files

File	Bundled	Description
reaction_dataset.json	✅	Curated synthesis routes
toxicity_dataset.json	✅	Safety scores
generic_reactions.json	✅	10 000 USPTO reactions
config.yml	❌	Created by setup wizard
data/aizynthfinder/	❌	Model files — download separately
uspto_rxn_insight.gzip	❌	Rxn-INSIGHT database (optional)

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Troubleshooting

Problem	Solution
config.yml not found	Run path-finder-setup
AiZynthFinder crash	Check paths in config.yml are absolute
No routes found	Try Galanthamine or Morphine
Rxn-INSIGHT disabled	pip install path-finder-retrosynthesis[predicted]
Slow search (~2 min)	Normal — AiZynthFinder MCTS is intensive

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Developer setup

git clone https://github.com/YaraChahda/path_finder.git
cd path_finder
conda install -c conda-forge rdkit
pip install -e ".[predicted]"
path-finder-setup
path-finder

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Citation

• AiZynthFinder: Genheden et al., J. Cheminf. 2020
• Rxn-INSIGHT: Thakkar et al., J. Cheminf. 2023
• Open Reaction Database: Kearnes et al., JACS 2021