Molecules Python Packages

datamol

Molecular Processing Made Easy.

biopandas

Working with molecular structures in pandas DataFrames

xnns

Neural network interatomic potentials for chemistry and materials science

finalcif

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

structure-clustering

Python package for fast exact clustering of similar molecular structures through parameterized connectivity graphs.

scaffoldgraph

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

asciimol

Curses based ASCII molecule viewer for terminals.

nim-mmcif

Parser for mmCIF files in Nim

molcraft

A python package for building powerful GNN models for molecules.

moldoc

Make better chemistry documentation!

kgcnn

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

seqme

Metrics for evaluating biological sequence design

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

equiformer-pytorch

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

buildamol

A fragment-based molecular assembly toolkit

scaffoldgraphdg

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

radient

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

molcraftdiffusion

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

chelombus

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

st-speckmol

Streamlit Component for creating Speck molecular structures within Streamlit Web app.

molstruct

Convert chemical molecule data CSV files to structured data formats

cebeconf

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

mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

molecule-attention-transformer

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