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ChemKit

Package version


Documentation: http://chem-kit.metwork.science/

Source Code: https://github.com/metwork-project/chem-kit


ChemKit is a chemical toolbox based on RDKit with currently 2 main purposes :

  • Facilitate the usage of the RDKIt Python API with some more easy to use classes that can occasionally fix some bug (especially with Jupyter rendering).

  • Provide tailored methods for the MetWork project

Usage

Manipulate Molecules

    from chem_kit import Molecule
    mol = Molecule("CCO")

Manipulate Transformation

    from chem_kit import Transformation
    tsf = Transformation("[#6:1]-[#8:2]-[#1:3]>>[#6:1]-[#8:2]-[#6:3](-[#1])(-[#1])-[#1]")

More examples with Jupyter notebook

Install

Like RDKit, ChemKit needs Conda :

conda env create -f conda-env.yml
conda activate chem_kit

To manage other required Python packages, the better way is to use Poetry on top of Conda :

cd /path/to/chem_kit
poetry install

Poetry manipulate Python packages directly on Conda env.