Cheminformatics Python Packages

rdkit

The official sources for the RDKit library

9.7M 4K 1K

pubchempy

Python wrapper for the PubChem PUG REST API.

5.4M 505 121

pdbeccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

307K 81 12

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

211K 398 128

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

119K 1K 219

thermo

Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

117K 764 134

rdkit-pypi

The official sources for the RDKit library

114K 4K 1K

datamol

Molecular Processing Made Easy.

79K 540 63

prolif

Interaction Fingerprints for protein-ligand complexes and more

48K 510 98

scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

30K 377 33

e3fp

3D molecular fingerprints

30K 144 34

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

30K 1K 478

dgllife

Python package for graph neural networks in chemistry and biology

29K 807 160

chematic

A pure-Rust cheminformatics library targeting RDKit feature parity — zero C/C++ by default.

27K 17 0

mols2grid

Interactive molecule viewer for 2D structures

15K 256 34

renkin

RENKIN is an open-source retrosynthesis engine for computer-aided synthesis planning (CASP) that automatically discovers optimal chemical reaction routes from a target molecule back to cheap, commercially available starting materials.

15K 3 0

molvs

Molecule Validation and Standardization

10K 187 57

stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

10K 286 52