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Chython [ˈkʌɪθ(ə)n]

PyPI version Python versions License: LGPLv3 Documentation

Library for processing molecules and reactions in a Python way.

Features

File formats

  • Read/write/convert MDL RDF/RXN and SDF/MOL (V2000 & V3000, including atom parity and enhanced stereo), MRV, SMILES/SMARTS, InChI (inchi-trust library), XYZ, PDB
  • Compact binary (de)serialization and full pickle support

Toolkit interoperability

Conversions build the target structure directly from the graph, so atom order matches atoms() and stereo is carried over without needing a 2D layout.

Toolkit API Requires
RDKit to_rdkit() / MoleculeContainer.from_rdkit() extra rdkit
Open Babel to_openbabel() extra extra-clean2d
Indigo to_indigo() extra extra-clean2d
CDK to_cdk() extra extra-clean2d + cdk.jar (CDK_PATH)
CDPKit 3D conformers (conformer_engine = 'cdpkit') extra extra-clean3d

Allene stereo is not portable through any of these toolkits. Indigo additionally omits cis-trans, which it derives from 2D coordinates.

IUPAC names, both directions

from chython import iupac

mol = iupac('ethanol')   # name -> structure, via OPSIN
mol.iupac                # 'ethanol' -- structure -> name, via openclatura

iupac() needs JPype and opsin.jar (OPSIN_PATH); the .iupac property needs the iupac extra (Python >= 3.11) and returns None when the structure cannot be named.

Molecules

  • Build and edit molecules and reactions with a pure-Python API
  • Standardize, canonicalize, kekulize/aromatize, and check valences
  • Tautomer enumeration
  • Tetrahedral, allene, and cis/trans stereo
  • Morgan and linear fingerprints with Tanimoto similarity

Search

  • Subgraph isomorphism and maximum common substructure (MCS) search
  • SMARTS parser with chython-specific query semantics

Reactions

  • Condensed Graph of Reaction (CGR)
  • Atom-to-atom mapping (neural attention + rule-based fixing) and template-based mapping reconstruction
  • Template-based reaction application (Reactor, Transformer) and reaction enumeration
  • Functional and protective group detection and deprotection
  • Sticky fragment / linker enumeration for combinatorial reassembly

Depiction

  • 2D coordinate generation, default SmilesDrawer, switchable to RDKit/CDK/Open Babel/Indigo (clean2d_engine)
  • 3D conformer generation with RDKit or CDPKit (conformer_engine)
  • 2D/3D SVG depiction with Jupyter support

Full documentation can be found here.

Install

Only Python 3.10+.

pip install chython[racer-default]

Optional extras, combinable (chython[racer-default,rdkit,iupac]):

Extra Enables
racer-default JS engine for the default 2D layout backend
rdkit to_rdkit/from_rdkit, RDKit 2D layout and 3D conformers
mapping neural atom-to-atom mapping
iupac molecule.iupac name generation (Python >= 3.11)
extra-clean2d CDK, Open Babel and Indigo backends (CDK also needs cdk.jar)
extra-clean3d CDPKit conformer engine
png PNG output from depiction

CGRtools

Chython is a fork of CGRtools.

Copyright

Contributors

CGRtools contributors are included too.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

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

Credits

Author: Ramil Nugmanov

License

GNU Lesser General Public License v3 or later (LGPLv3+), Other/Proprietary License (LGPLv3)

Requires

Python >=3.10

Provides Extra

extra-clean2d extra-clean3d iupac mapping png racer-default racer-deprecated rdkit

Classifiers

Report project as malware

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Source Distributions

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chython-2.24-cp314-cp314-win_amd64.whl (1.5 MB view details)

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chython-2.24-cp314-cp314-manylinux_2_39_x86_64.whl (4.4 MB view details)

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chython-2.24-cp313-cp313-win_amd64.whl (1.4 MB view details)

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chython-2.24-cp312-cp312-win_amd64.whl (1.4 MB view details)

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chython-2.24-cp311-cp311-win_amd64.whl (1.4 MB view details)

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chython-2.24-cp310-cp310-win_amd64.whl (1.4 MB view details)

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2.24 This release

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2.15.2a1

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