tagirshin / chython

Library for processing molecules and reactions in python way

Chython [ˈkʌɪθ(ə)n]

Library for processing molecules and reactions in python way.

Features:

• Read/write/convert formats: MDL .RDF (.RXN) and .SDF (.MOL), .MRV, SMILES, INCHI (inchi-trust library), .XYZ, .PDB
• Standardize molecules and reactions and valid structures checker
• Supported python-magic
• Tetrahedron, Allene and CIS-TRANS stereo supported
• Perform subgraph search
• Build/edit molecules and reactions with Python API
• Produce template based reactions and molecules
• Atom-to-atom mapping, checking and rule-based fixing
• Perform MCS search
• 2d coordinates generation (based on SmilesDrawer)
• 2d/3d depiction with Jupyter support
• SMARTS parser with restrictions
• Protective groups remover
• Common reaction templates collection

Full documentation can be found here.

Chython is fork of CGRtools.

Install

Only python 3.8+.

Note: for using clean2d install NodeJS into system.

• stable version available through PyPI:

  pip install chython
  

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

  pip install -U git+https://github.com/chython/chython.git@master#egg=chython
  

Copyright

• 2014-2023 Ramil Nugmanov [email protected] main developer

Contributors

• Adelia Fatykhova [email protected]
• Aleksandr Sizov [email protected]
• Dinar Batyrshin [email protected]
• Dmitrij Zanadvornykh [email protected]
• Ravil Mukhametgaleev [email protected]
• Tagir Akhmetshin [email protected]
• Timur Gimadiev [email protected]
• Zarina Ibragimova