BR-SAScore

Implementation of BR-SAScore developed by Prof. Yousung Jung group at Seoul National University (contact: yousung@gmail.com).

Contents

• Developer
• OS Requirements
• Python Dependencies
• Installation Guide
• Usage
• Data
• Reproduce the results
• Publication
• License

Developer

Shuan Chen (shuan.micc@gmail.com)

OS Requirements

This repository has been tested on both Linux and Windows operating systems.

Python Dependencies

• Python (version >= 3.6)
• Numpy (version >= 1.16.4)
• rdkit (version >= 2019)

Installation Guide

From Github

pip install BRSAScore

From Github

git clone https://github.com/snu-micc/BR-SAScore.git
cd BR-SAScore
pip install -e .

Usage

from BRSAScore import SAScorer
scorer = SAScorer()
smi = 'CC(OC1=CC=CC=C1C(O)=O)=O' # Aspirin
score, contribution = scorer.calculateScore(smi)

The expected output of score should be

0.8789047205405656

See Demo.ipynb for the examples of estimating the synthetic accessibility of 18 structurally complex molecules shown in the paper.

Data

USPTO reaction dataset

The reactions of of the training reactions train_data.csv are downloaded from the Dropbox link available at the GitHub repo of GLN, originally from Figshare.

Building blocks

The zip file of eMolecules building blocks origin_dict.csv can be downloaded from the Dropbox link available the GitHub repo of Retro*.

Reproduce the results

[1] Download reaction and building-block data

Downlaod the data can put them in ./data/ and rename them to uspto.csv and emolecules.csv with column titled reactants>reagents>production and SMILES.

Feel free to change the (atom-mapped) reaction data and building blocks data as long as the data is correctly formatted. If the reaction data is not atom-mapped, we recommend to use LocalMapper to prepare high-quality the atom-mappings for your reactions.

[2] Prepare the BRScores from reaction and building-block data

Prepare the BRSAScores by

python scripts/prepare_Scores.py -r uspto -b emolecules

[3] Use BRSAScocre

from BRSAScore import SAScorer
reaction_from = 'uspto'
buildingblock_from = 'emolecules'
scorer = SAScorer(reaction_from=reaction_from, buildingblock_from=buildingblock_from)

To use the BRSAScore on you own data, replace the reaction_from and buildingblock_from

Publication

@article{chen2021deep, title={Estimating the synthetic accessibility of molecules with building block and reaction-aware SAScore}, author={Chen, Shuan and Jung, Yousung}, journal={Journal of Cheminformatics}, volume={}, number={}, pages={}, year={2024}, publisher={Springer} }

License

This project is covered under the MIT Liscence.