molecules 开源项目推荐（165 个）

BioPandas /biopandas

Working with molecular structures in pandas DataFrames

datamol-io /datamol

Molecular Processing Made Easy.

HannesStark /EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

kjappelbaum /awesome-chemistry-datasets

overview of datasets for ML in chemistry

dewberryants /asciiMol

Curses based ASCII molecule viewer for terminals.

facebookresearch /all-atom-diffusion-transformer

Official implementation of All Atom Diffusion Transformers (ICML 2025)

lucidrains /equiformer-pytorch

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

gcorso /torsional-diffusion

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

fzliu /radient

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

jparkhill /TensorMol

Tensorflow + Molecules = TensorMol

vijaydwivedi75 /gnn-lspe

Source code for GNN-LSPE (Graph Neural Networks with Learnable Structural and Positional Representations), ICLR 2022

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.

pcko1 /Deep-Drug-Coder

A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.

virtualramblas /awesome-deep-learning-4-life-sciences

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

HannesStark /3DInfomax

利用分子的三维几何结构预训练GNNs，使自监督学习能够实现。已在DGL和Pytorch几何中实现。

senya-ashukha /simple-equivariant-gnn

A short and easy PyTorch implementation of E(n) Equivariant Graph Neural Networks

chao1224 /Geom3D

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

aimat-lab /gcnn_keras

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

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

samirelanduk /atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)