Molecules Python Packages

datamol

Molecular Processing Made Easy.

biopandas

Working with molecular structures in pandas DataFrames

finalcif

A CIF file finalizer for small molecule crystallography with as much automation as possible.

structure-clustering

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

nim-mmcif

Parser for mmCIF files in Nim

kgcnn

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

equiformer-pytorch

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

molecule-attention-transformer

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

asciimol

An ASCII molecule viewer.

scaffoldgraph

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

geom3d

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

seqme

Metrics for evaluating biological sequence design

molcraftdiffusion

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

moldoc

Make better chemistry documentation!

buildamol

A fragment-based molecular assembly toolkit for python.

scaffoldgraphdg

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

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

chelombus

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

mols2grid-to-image

Convert CSV files with SMILES molecular data into grid PNG images using mols2grid and Playwright

st-speckmol

Streamlit component for for Speck molecule visualization.

radient

Turn unstructured data into vectors

cebeconf

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

scaffoldgraphnew

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