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General Purpose > CGRtools

Toolkit for processing molecules, reactions and condensed graphs of reactions. Can be used for chemical standardization, MCS search, tautomers generation with backward compatibility to RDKit and NetworkX.

Package 51 stars GitHub

CGRTools

.. image:: https://zenodo.org/badge/14690494.svg :target: https://zenodo.org/badge/latestdoi/14690494

Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.

Basic operations:

  • Read/write/convert formats: MDL .RDF (RXN) and .SDF (MOL), .MRV, SMILES, INCHI (Linux and Windows), .XYZ, .PDB
  • Standardize molecules and reactions and valid structures checker.
  • Duplicate searching.
  • Tetrahedron, Allene and CIS-TRANS stereo checking.
  • Produce CGRs.
  • Perform subgraph search.
  • Build/edit molecules and reactions.
  • Produce template based reactions and molecules.
  • Atom-to-atom mapping checker and rule-based fixer.
  • Perform MCS search.
  • 2d coordinates generation (based on SmilesDrawer <https://github.com/reymond-group/smilesDrawer>_)
  • 2d/3d depiction.

Full documentation can be found here <https://cgrtools.readthedocs.io>_

INSTALL

Highly recommended to use python 3.8+. Python 3.6 and 3.7 deprecated.

Linux Debian based

  • Install python3.8, virtualenv and git::

    sudo apt install python3.8 python3.8-dev git python3-virtualenv

  • Create new environment and activate it::

    virtualenv -p python3.8 venv source venv/bin/activate

Mac

  • Install python3.8 and git using brew <https://brew.sh>_::

    brew install git brew install python3

  • Install virtualenv::

    pip install virtualenv

  • Create new environment and activate it::

    virtualenv -p python3.8 venv source venv/bin/activate

Windows

  • Install python3.8 and git using Chocolatey <https://chocolatey.org/>_::

    choco install git choco install python3

  • Install virtualenv::

    pip install virtualenv

  • Create new environment and activate it::

    virtualenv venv venv\Scripts\activate

General part

  • stable version available through PyPI::

    pip install CGRTools

  • Install CGRtools with MRV files parsing support::

    pip install CGRTools[mrv]

  • Install CGRtools with structures clean2d support (Note: install NodeJS into system, see details <https://github.com/sqreen/PyMiniRacer>_)::

    pip install CGRtools[clean2d]

  • Install CGRtools with optimized XYZ parser::

    pip install CGRtools[jit]

If you still have questions, please open issue within github.

PACKAGING

For wheel generation just type next command in source root::

python setup.py bdist_wheel

COPYRIGHT

CONTRIBUTORS

CITE THIS

CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing. Journal of Chemical Information and Modeling 2019 59 (6), 2516-2521. DOI: 10.1021/acs.jcim.9b00102

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