Cheminformatics Python Packages

rdkit

The official sources for the RDKit library

pubchempy

Python wrapper for the PubChem PUG REST API.

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

rdkit-pypi

The official sources for the RDKit library

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

pysmiles

A lightweight python-only library for reading and writing SMILES strings

thermo

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

datamol

Molecular Processing Made Easy.

dgllife

Python package for graph neural networks in chemistry and biology

smsd

SMSD — exact substructure & MCS search for chemical graphs.

prolif

Interaction Fingerprints for protein-ligand complexes and more

e3fp

3D molecular fingerprints

scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

mols2grid

Interactive molecule viewer for 2D structures

fpsim2

Simple package for fast molecular similarity searches

cgrtools-plus

CGRs, molecules and reactions manipulation - maintained modern fork

aizynthfinder

A tool for retrosynthetic planning

stk

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

cirpy

Python wrapper for the NCI Chemical Identifier Resolver (CIR)

cosmolkit

COSMolKit is a Rust-native cheminformatics and structural biology toolkit for molecules, SMILES/SDF/MolBlock parsing, molecular graphs, conformers, coordinates, and AI-ready batch workflows.

molvs

Molecule Validation and Standardization

atomlite

Store your chemical data in a single file!

bingo-elastic

Universal cheminformatics toolkit, utilities and database search tools