aspuru-guzik-group/group-selfies

Group SELFIES

https://arxiv.org/abs/2211.13322

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.