cgrtools-plus 4.1.35
Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach - Enhanced fork with modern Python support
Requires Python: >=3.8
Keywords: chemistry, chemoinformatics, reaction, molecule

CGRTools
========

**Fork Notice: This is a maintained fork of the original CGRtools project with updates for modern Python versions (3.10-3.14) and automated wheel builds for Linux (x86_64, ARM64) and macOS (Intel, Apple Silicon).
It fixes the issue with newer Cython versions, makes package PEP517-complient and provides precompiled wheels for easier installation.**

**[WIP] to fix your broken builds replace `cgrtools` with `cgrtools-plus` in your dependencies.**

.. 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-plus

* Install CGRtools with MRV files parsing support::

    pip install cgrtools-plus[mrv]
* Install CGRtools with structures `clean2d` support (Note: install NodeJS into system, see `details <https://github.com/sqreen/PyMiniRacer>`_)::

    pip install cgrtools-plus[clean2d]

* Install CGRtools with optimized XYZ parser::

    pip install cgrtools-plus[jit]

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

PACKAGING
=========

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

    python -m build

COPYRIGHT
=========

* 2014-2022 Timur Madzhidov tmadzhidov@gmail.com product owner, idea and development supervision
* 2014-2021 Ramil Nugmanov nougmanoff@protonmail.com main developer
* 2021-2022 Valentina Afonina valiaafo@yandex.ru development and support

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
* Valentina Afonina valiaafo@yandex.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