CGRTools
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)
- 2d/3d depiction.
Full documentation can be found here
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:
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:
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):
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
- 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