# CGRtools

**Repository Path**: dot23/CGRtools

## Basic Information

- **Project Name**: CGRtools
- **Description**: CGRs, molecules and reactions manipulation
- **Primary Language**: Unknown
- **License**: LGPL-3.0
- **Default Branch**: 4.1
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-01-13
- **Last Updated**: 2022-01-13

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

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

ACTUAL VERSION
==============

The latest version can be found `here <https://github.com/stsouko/CGRtools>`_