PyPI Stats
  • Insights
  • PyPI
  • GitHub
  • Search
  • Compare
  • Advisories
  • Ecosystem
  • About
Home

Cheminformatics Python Packages

Python packages with the GitHub topic cheminformatics. Sorted by relevance, with stars and monthly downloads.
rdkit
rdkit

The official sources for the RDKit library

8.1M 3K 1K
mcs07
pubchempy

Python wrapper for the PubChem PUG REST API.

2.9M 497 121
PDBeurope
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

361K 79 12
rdkit
rdkit-pypi

The official sources for the RDKit library

287K 3K 1K
epam
epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

225K 386 123
mims-harvard
pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

108K 1K 211
pckroon
pysmiles

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

66K 160 24
CalebBell
thermo

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

61K 748 129
datamol-io
datamol

Molecular Processing Made Easy.

61K 534 62
awslabs
dgllife

Python package for graph neural networks in chemistry and biology

56K 801 159
asad
smsd

SMSD — exact substructure & MCS search for chemical graphs.

27K 48 0
chemosim-lab
prolif

Interaction Fingerprints for protein-ligand complexes and more

22K 497 99
keiserlab
e3fp

3D molecular fingerprints

21K 142 34
scikit-fingerprints
scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

21K 363 29
cbouy
mols2grid

Interactive molecule viewer for 2D structures

15K 253 34
chembl
fpsim2

Simple package for fast molecular similarity searches

11K 169 22
asiomchen
cgrtools-plus

CGRs, molecules and reactions manipulation - maintained modern fork

10K 0 0
MolecularAI
aizynthfinder

A tool for retrosynthetic planning

9K 826 175
lukasturcani
stk

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

8K 284 53
mcs07
cirpy

Python wrapper for the NCI Chemical Identifier Resolver (CIR)

8K 135 29
cosmol-studio
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.

7K 2 0
mcs07
molvs

Molecule Validation and Standardization

6K 183 57
lukasturcani
atomlite

Store your chemical data in a single file!

6K 12 1
epam
bingo-elastic

Universal cheminformatics toolkit, utilities and database search tools

5K 386 123
    • Data from PyPI, GitHub, ClickHouse, and BigQuery