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chython

Library for processing molecules and reactions in python way

  • 1.78
  • PyPI
  • Socket score

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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 <https://github.com/reymond-group/smilesDrawer>_)
  • 2d/3d depiction with Jupyter support
  • SMARTS parser with restrictions
  • Protective groups remover
  • Common reaction templates collection

Full documentation can be found here <https://chython.readthedocs.io>_.

CGRtools

Chython is fork of CGRtools <https://github.com/stsouko/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

Contributors

CGRtools contributors are included too.

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