Group SELFIES

Installation

Python >= 3.8 is required.

RDKit is required to use this package. Once it is installed, clone this repository using

git clone https://github.com/aspuru-guzik-group/group-selfies

and run

pip install .

in the cloned folder.

Introduction

Group SELFIES extends SELFIES with the ability to represent groups with single tokens. This improves interpretability, compactness, and performance in generative models.

Encoding

Decoding

Usage

See tutorial.ipynb for details on usage. For key classes/functions, see below:

Class/Function	Description
`group_selfies.Group`	Class that represents groups.
`group_selfies.GroupGrammar`	Class that represents a grammar, which is a set of groups used for encoding and decoding.
`grammar.extract_groups`	Finds occurences of the grammar's defined set of groups in a molecule.
`grammar.encoder`	Encodes a molecule to its corresponding Group SELFIES representation. Requires extracted group occurences returned by `grammar.extract_groups`
`grammar.decoder`	Decodes a Group SELFIES string to its corresponding molecule.
`grammar.full_encoder`	Extracts groups from a molecule and encodes it, essentially a combination of `grammar.extract_groups` and `grammar.encoder`. Mainly for convenience.
`group_selfies.fragment_mols`	Fragments a set of molecules into a set of reasonable groups.