Library for processing molecules and reactions in python way.
- 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 supporting
- 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
- Produce CGRs (Condensed Graph of Reaction)
Full documentation can be found here.
Chython is fork of CGRtools.
Highly recommended to use python 3.8+. Python 3.6 and 3.7 deprecated.
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/[email protected]#egg=chython
Run unit tests:
git clone https://github.com/chython/chython.git && cd chython # skip if already got sources pip install -e . pytest --pyargs chython
- 2014-2021 Ramil Nugmanov [email protected] main developer