rdchiral_plus

Wrapper for RDKit's RunReactants to improve stereochemistry handling

This repository is a fork of rdchiral. It has been modified for improved performance while maintaining high consistency with the upstream library. These modifications provide speed that is marginally slower than the fast C++ version (rdchiral_cpp), but has the benefits of being written in Python. This library is pip installable cross platform.

Requirements

RDKit (version >= 2019)
Python (version >= 3.10)

Installation

Install rdchiral_plus from PyPI:

pip install rdchiral-plus

Or install rdchiral_plus with pip directly from this repo:

pip install git+https://github.com/denovochem/rdchiral_plus.git

This fork can be optionally compiled with mypyc. In our testing performance is not noticeably improved, as most of the computationally expensive work in this library is done with rdkit, which is already primarily written in C++.

For mypyc compilation:

RDCHIRAL_USE_MYPYC=1 pip install "git+https://github.com/denovochem/rdchiral_plus.git"

Basic usage

from rdchiral import rdchiralRun, rdchiralRunText, rdchiralReaction, rdchiralReactants

# Run directly from SMARTS and SMILES (slower than pre-initializing rdchiralReaction and rdchiralReactants when processing a large numbers of reactions)
reaction_smarts = '[C:1][OH:2]>>[C:1][O:2][C]'
reactant_smiles = 'OCC(=O)OCCCO'
outcomes = rdchiralRunText(reaction_smarts, reactant_smiles)
print(outcomes)

# Pre-initialize then run
rxn = rdchiralReaction(reaction_smarts)
reactants = rdchiralReactants(reactant_smiles)
outcomes = rdchiralRun(rxn, reactants)
print(outcomes)

# Get list of atoms that changed
outcomes, mapped_outcomes = rdchiralRun(rxn, reactants, return_mapped=True)
print(outcomes, mapped_outcomes)

Documentation

Full documentation is available here

Changes from upstream rdchiral

See the README for a full list of changes to template application, template extraction, and general improvements.

Consistency with the upstream library

See consistency for details on how consistency is measured against the original library and full details of what changes you can expect compared to the original rdchiral library.