CGRTools

Feature development in this repository has been discontinued. Further support and development of initial CGRTools is done by cimm-kzn group https://github.com/cimm-kzn/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]

• Install CGRtools library DEV version for features that are not well tested::

  pip install -U git+https://github.com/stsouko/CGRtools.git@master#egg=CGRtools

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

• 2014-2021 Ramil Nugmanov nougmanoff@protonmail.com main developer
• 2014-2019 Timur Madzhidov tmadzhidov@gmail.com features and API discussion
• 2014-2019 Alexandre Varnek varnek@unistra.fr base idea of CGR approach

CONTRIBUTORS

• Dinar Batyrshin batyrshin-dinar@mail.ru
• Timur Gimadiev timur.gimadiev@gmail.com
• Adelia Fatykhova adelik21979@gmail.com
• Tagir Akhmetshin tagirshin@gmail.com
• Ravil Mukhametgaleev sonic-mc@mail.ru

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