Library for processing molecules and reactions in a Python way.
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 openclaturaiupac() 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.
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 |
Chython is a fork of CGRtools.
- 2014-2026 Ramil Nugmanov nougmanoff@protonmail.com main developer
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