CGRTools

February 4, 2022 ยท View on GitHub

.. 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