rxnutils documentation

rxnutils is a collection of routines for working with reactions, reaction templates and template extraction

Introduction

The package is divided into (currently) three sub-packages:

  • chem - chemistry routines like template extraction or reaction cleaning

  • data - routines for manipulating various reaction data sources

  • pipeline - routines for building and executing simple pipelines for modifying and analyzing reactions

  • routes - routines for handling synthesis routes

Auto-generated API documentation is available, as well as guides for common tasks. See the menu to the left.

Installation

For most users it is as simple as

pip install reaction-utils

For developers, first clone the repository using Git.

Then execute the following commands in the root of the repository

conda env create -f env-dev.yml
conda activate rxn-env
poetry install

the rxnutils package is now installed in editable mode.

Lastly, make sure to install pre-commits that are run on every commit

pre-commit install

Limitations

  • Some old RDKit wheels on pypi did not include the Contrib folder, preventing the usage of the rdkit_RxnRoleAssignment action

  • The pipeline for the Open reaction database requires some additional dependencies, see the documentation for this pipeline

  • Using the data piplines for the USPTO and Open reaction database requires you to setup a second python environment

  • The RInChI capabilities are not supported on MacOS