Molecules Python Packages

datamol

Molecular Processing Made Easy.

biopandas

Working with molecular structures in pandas DataFrames

asciimol

Curses based ASCII molecule viewer for terminals.

structure-clustering

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

nim-mmcif

Parser for mmCIF files in Nim

finalcif

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

kgcnn

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

equiformer-pytorch

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

molecule-attention-transformer

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

buildamol

A fragment-based molecular assembly toolkit

seqme

Metrics for evaluating biological sequence design

scaffoldgraph

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

moldoc

Make better chemistry documentation!

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.

mols2grid-to-image

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

geom3d

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

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

radient

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

scaffoldgraphnew

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

mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers