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

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

thermo

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

chematic

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

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

renkin

Local and reproducible route auditing for AiZynthFinder, Syntheseus and RENKIN — plus a portable Rust retrosynthesis engine.

datamol

Molecular Processing Made Easy.

rdkit-pypi

The official sources for the RDKit library

scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

e3fp

3D molecular fingerprints

prolif

Interaction Fingerprints for protein-ligand complexes and more

openbabel

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

dgllife

Python package for graph neural networks in chemistry and biology

cosmolkit

Pure-Rust cheminformatics toolkit and RDKit-compatible alternative for SMILES/SMARTS, SDF, fingerprints, substructure search, ETKDG, UFF/MMFF, and Python workflows.

molvs

Molecule Validation and Standardization

mols2grid

Interactive molecule viewer for 2D structures

fpsim2

Simple package for fast molecular similarity searches

pysmiles

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

bofire

Experimental design and (multi-objective) bayesian optimization.

stk

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

cgrtools-plus

CGRs, molecules and reactions manipulation - maintained modern fork

atomlite

Store your chemical data in a single file!