Molecules Python Packages

datamol

Molecular Processing Made Easy.

biopandas

Working with molecular structures in pandas DataFrames

structure-clustering

Python package to cluster molecular structures into groups of similar ones.

nim-mmcif

mmCIF parser written in Nim with Python bindings

finalcif

CIF file editor

kgcnn

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

equiformer-pytorch

Equiformer - SE3/E3 Graph Attention Transformer for Molecules and Proteins

seqme

Metrics for evaluating biological sequence design

asciimol

Curses based ASCII molecule viewer for terminals.

scaffoldgraph

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

chelombus

Clustering and visualization of billions of molecules (or other high-dimensional data). 1 billion, 100K clusters, less than 3 hours, one GPU.

moldoc

Make better chemistry documentation!

molcraftdiffusion

A generative AI framework for 3D molecular generation and data-driven molecular design in computational chemistry.

molecule-attention-transformer

Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules

mlip-arena

🌟 [NeurIPS '25 Spotlight] Fair and transparent benchmark of machine learning interatomic potentials (MLIPs), beyond basic error metrics https://openreview.net/forum?id=SAT0KPA5UO

buildamol

A fragment-based molecular assembly toolkit

radient

Radient turns many data types (not just text) into vectors for similarity search, RAG, regression analysis, and more.

cebeconf

cebeconf: A package of machine-learning models for predicting 1s-core electron binding energies of CONF atoms in organic molecules.

st-speckmol

Streamlit component for for Speck molecule visualization.

scaffoldgraphdg

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

molstruct

Convert chemical molecule data CSV files to structured data formats

scaffoldgraphnew

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

mols2grid-to-image

Convert molecules to grid images using mols2grid and Playwright

geom3d

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023