ldruizsan / 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 depiction.

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 (optimized version) [numba and numpy used]:

  pip install CGRtools[clean2djit]
  

• Install CGRtools with structures clean2d support slow version [without numba]:

  pip install CGRtools[clean2d]
  

• Install CGRtools library DEV version for features that are not well tested:

  pip install -U git+https://github.com/cimm-kzn/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

On Linux additionally do repairing of package:

pip install auditwheel
auditwheel repair dist/CGRtools-<version>-<python_version>-linux_x86_64.whl

COPYRIGHT

• 2014-2020 Ramil Nugmanov <[e-mail]> main developer
• 2014-2019 Timur Madzhidov <[e-mail]> features and API discussion
• 2014-2019 Alexandre Varnek <[e-mail]> base idea of CGR approach

CONTRIBUTORS

• Dinar Batyrshin <[e-mail]>
• Timur Gimadiev <[e-mail]>
• Adelia Fatykhova <[e-mail]>
• Tagir Akhmetshin <[e-mail]>
• Ravil Mukhametgaleev <[e-mail]>

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