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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

CONTRIBUTORS

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