jyarger/cgrtools

CGRs, molecules and reactions manipulation

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 [email protected] product owner, idea and development supervision
• 2014-2021 Ramil Nugmanov [email protected] main developer
• 2021-2022 Valentina Afonina [email protected] development and support

CONTRIBUTORS

• Dinar Batyrshin [email protected]
• Timur Gimadiev [email protected]
• Adelia Fatykhova [email protected]
• Tagir Akhmetshin [email protected]
• Ravil Mukhametgaleev [email protected]
• Valentina Afonina [email protected]

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