rdchiral-plus 0.3.1

Wrapper for RDKit's RunReactants to improve stereochemistry handling

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, and is statically typed wherever possible so that it can be optionally compiled with mypyc for faster execution while maintaining consistency with the upstream library. These modifications provide comparable speed to the fast C++ version (rdchiral_cpp), with all of the benefits of being written in Python. This library is pip installable and cross platform.

This library has high consistency with the python rdchiral library, and can be used as a drop in replacement:

• rdchiralRun (1000 templates applied to 1000 reactants): 99.98% consistent
• rdchiralRunText (1000 templates applied to 100 reactants): 99.97% consistent
• rdchiralExtract (templates extracted from 50,016 mapped reactions): 94.99% consistent

See here for details on how consistency is measured against the original library.

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

For mypyc compilation:

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

Basic usage

from rdchiral import rdchiralRunText, rdchiralReaction, rdchiralReactants

# Run directly from SMARTS and SMILES strings
# This is slower than pre-initializing rdchiralReaction and rdchiralReactants when
# processing a large number 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

Contributing

• Feature ideas and bug reports are welcome on the Issue Tracker.
• Fork the source code on GitHub, make changes and file a pull request.

License

rdchiral_plus is licensed under the MIT license.

References

• Original rdchiral paper
• rdchiral repo
• rdchiral_cpp repo