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Molecules Python Packages

Python packages with the GitHub topic molecules. Sorted by relevance, with stars and monthly downloads.
datamol-io
datamol

Molecular Processing Made Easy.

61K 534 62
rasbt
biopandas

Working with molecular structures in pandas DataFrames

37K 751 117
photophys
structure-clustering

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

3K 1 1
lucidrains
nim-mmcif

mmCIF parser written in Nim with Python bindings

2K 7 0
dkratzert
finalcif

CIF file editor

2K 20 4
aimat-lab
kgcnn

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

1K 119 30
lucidrains
equiformer-pytorch

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

1K 289 31
szczurek-lab
seqme

Metrics for evaluating biological sequence design

842 14 1
dewberryants
asciimol

Curses based ASCII molecule viewer for terminals.

729 407 13
UCLCheminformatics
scaffoldgraph

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

659 195 40
afloresep
chelombus

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

614 5 2
lukasturcani
moldoc

Make better chemistry documentation!

590 15 0
pregHosh
molcraftdiffusion

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

529 15 2
lucidrains
molecule-attention-transformer

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

468 58 7
atomind-ai
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

432 99 9
NoahHenrikKleinschmidt
buildamol

A fragment-based molecular assembly toolkit

428 44 1
fzliu
radient

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

408 283 11
moldis-group
cebeconf

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

401 1 0
avrabyt
st-speckmol

Streamlit component for for Speck molecule visualization.

333 32 17
UCLCheminformatics
scaffoldgraphdg

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

266 195 40
lszeremeta
molstruct

Convert chemical molecule data CSV files to structured data formats

210 4 2
UCLCheminformatics
scaffoldgraphnew

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

167 195 40
N283T
mols2grid-to-image

Convert molecules to grid images using mols2grid and Playwright

155 3 0
chao1224
geom3d

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

150 130 15
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