CGRtools: A Python repository from kingscolour

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]
```

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

kingscolour/CGRtools