path_finder

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

Yara Chahda · Corentin Portmann · Inès Ouchen Laksiri — EPFL 2026

User installation

Platform: Tested on macOS only. Linux should work but has not been tested.

Requirements: Miniconda or Anaconda

1. Create a dedicated environment

Python 3.10 is required — newer versions are not compatible with AiZynthFinder.

conda create -n path-finder-env python=3.10 -y
conda activate path-finder-env

2. Install RDKit

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

conda install -c conda-forge rdkit -y

3. Install Path Finder

pip install path-finder-retrosynthesis

4. Run the setup wizard

path-finder-setup

This automatically:

• copies the bundled datasets into data/
• creates data/config.yml with the correct paths

If the wizard fails at step 3 (model download): download the files manually from https://github.com/MolecularAI/aizynthfinder/releases and place them in data/aizynthfinder/.

Files needed: uspto_model.onnx, uspto_templates.csv.gz, uspto_filter_model.onnx, zinc_stock.hdf5

5. Download the Rxn-INSIGHT USPTO database

Download uspto_rxn_insight.gzip from: https://zenodo.org/records/10171745

Place it in data/uspto_rxn_insight.gzip.

This file enables reaction condition prediction for novel routes. Without it, only dataset and validated routes are shown.

6. Launch

path-finder

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

Quick summary

conda create -n path-finder-env python=3.10 -y
conda activate path-finder-env
conda install -c conda-forge rdkit -y
pip install path-finder-retrosynthesis
path-finder-setup
# → place data/uspto_rxn_insight.gzip manually
path-finder

What the app does

Path Finder finds and ranks retrosynthesis routes for a target molecule using three sources:

Routes are scored using a weighted 1/i² scheme across three user-chosen criteria: steps, yield, atom economy, E-factor, or safety.

Data files

The construction, sources and reconstruction procedure of toxicity_dataset.json are documented in SOURCES_AND_RECONSTRUCTION.md.

Troubleshooting

Developer setup

git clone https://github.com/YaraChahda/path_finder.git
cd path_finder
conda create -n path-finder-dev python=3.10 -y
conda activate path-finder-dev
conda install -c conda-forge rdkit -y
pip install -e .
path-finder-setup
path-finder

In the app's left sidebar, set the AiZynthFinder config field to data/aizynthfinder/config.yml (the file written by path-finder-setup). Pointing to the wrong file makes the search fail with AttributeError: 'list' object has no attribute 'split'.

Running tests

pytest tests/

Repository structure

This section describes the purpose of every file and folder so that new contributors can orient themselves quickly.

Root-level files

.github/workflows/

assets/

data/

Working data directory — none of these files are committed to git.

docs/

notebooks/

scripts/

src/path_finder/

The installable Python package. All application logic lives here.

tests/