https://github.com/whitead/synspace

Synthesis generative model
https://github.com/whitead/synspace

Last synced: about 2 months ago
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Synthesis generative model

• Host: GitHub
• URL: https://github.com/whitead/synspace
• Owner: whitead
• License: mit
• Created: 2022-12-28T00:59:14.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2023-04-15T22:42:57.000Z (over 1 year ago)
• Last Synced: 2024-10-31T23:25:39.514Z (2 months ago)
• Language: Python
• Size: 19.1 MB
• Stars: 35
• Watchers: 3
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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.](https://pubs.acs.org/doi/10.1021/ci200379p). The retrosynthesis is done either via [PostEra Mannifold](https://postera.ai/) if you have an API key, or by reversing the 50 robust reactions. The purchasable building blocks come from the [Purchasable Mcule supplier building block catalogs](https://mcule.com/database/). All of these things can be customized though. 



## Installation

```sh

pip install synspace

```

## Usage

Generate local chemical space given a SMILES string

```py

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

TODO

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