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

  • 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.

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

TESTS

Run unit tests:

git clone https://github.com/chython/chython.git && cd chython  # skip if already got sources
pip install -e .
pytest --pyargs chython

COPYRIGHT

CONTRIBUTORS

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (3.0.2)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for nougmanoff from gravatar.com nougmanoff

Credits

Author: Dr. Ramil Nugmanov

License

GNU Lesser General Public License v3 or later (LGPLv3+) (LGPLv3)

Requires

Python >=3.8

Classifiers

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3.0.2

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2.24

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2.22

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2.15.2a1

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