synspace 1.0.0

Generative model based on forward synthesis rules

synspace

This is early-stage code that is in progress. It is in flux

This package generates a local chemical space around a given molecule using retro and forward synthesis rules. The reactions used are the 50 robust medchem reactions proposed by Hartenfeller et al.. The retrosynthesis is done by reversing the 50 robust reactions. The purchasable building blocks come from the Purchasable Mcule supplier building block catalogs. All of these things can be customized though.

Installation

pip install synspace

Usage

Generate local chemical space given a SMILES string

mols, props = synspace.chemical_space('CCC=O')

props contains information like the synthesis route for the molecules. Note that all synthesis routes are relative to the given molecule (it is assumed to be synthetically feasible).

Citation

Cite the ChemCrow paper for now. Haven't really written up much on this package.

    @article{bran2023chemcrow,
  title={Chemcrow: Augmenting large-language models with chemistry tools},
  author={Bran, Andres M and Cox, Sam and Schilter, Oliver and Baldassari, Carlo and White, Andrew D and Schwaller, Philippe},
  journal={arXiv preprint arXiv:2304.05376},
  year={2023}
}

Also, this idea is similar to [Dolfus et al.](https://pubs.acs.org/doi/10.1021/acs.jcim.2c00246)

## NOTICE

This product includes software developed by Pat Walters (MIT Licensed)
https://github.com/PatWalters/useful_rdkit_utils
Copyright (c) 2022 Pat Walters