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Chython [ˈkʌɪθ(ə)n]

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

2014-2026 Ramil Nugmanov nougmanoff@protonmail.com main developer

Contributors

CGRtools contributors are included too.

Adelia Fatykhova adelik21979@gmail.com
Aigul Khakimova
Aleksandr Sizov murkyrussian@gmail.com
Alexandre Varnek varnek@unistra.fr
Dinar Batyrshin batyrshin-dinar@mail.ru
Dmitrij Zanadvornykh zandmitrij@gmail.com
Philippe Gantzer
Ravil Mukhametgaleev sonic-mc@mail.ru
Tagir Akhmetshin tagirshin@gmail.com
Timur Gimadiev timur.gimadiev@gmail.com
Timur Madzhidov tmadzhidov@gmail.com
Zarina Ibragimova

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chython 2.22

Chython [ˈkʌɪθ(ə)n]

Features

Install

CGRtools

Copyright

Contributors

Project links

Key dates

1 maintainer

Credits

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