yanfeiguan

DECIMER-Image_Transformer

DECIMER: Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer

Awesome-Diffusion-Models

A collection of resources and papers on Diffusion Models

optuna

A hyperparameter optimization framework

mmpdb

A package to identify matched molecular pairs and use them to predict property changes.

ThinkMatch

A research protocol for deep graph matching.

cuda-quantum

C++ and Python support for the CUDA Quantum programming model for heterogeneous quantum-classical workflows

Indigo

Universal cheminformatics toolkit, utilities and database search tools

molplotly

add-on to plotly which show molecule images on mouseover!

HTMD-Adaptive-OpenMM

A set of scripts for running the High Throughput Molecular Dynamics adaptive sampling with OpenMM

Graph-Matching-Networks

PyTorch implementation of Graph Matching Networks, e.g., Graph Matching with Bi-level Noisy Correspondence (COMMON, ICCV 2023), Graph Matching Networks for Learning the Similarity of Graph Structured Objects (GMN, ICML 2019).

ogb

Benchmark datasets, data loaders, and evaluators for graph machine learning

build-your-own-x

Master programming by recreating your favorite technologies from scratch.

himp-gnn

Hierarchical Inter-Message Passing for Learning on Molecular Graphs

nglview

Jupyter widget to interactively view molecular structures and trajectories

biopython

Official git repository for Biopython (originally converted from CVS)

pytorch_geometric

Graph Neural Network Library for PyTorch

DBSTEP

DBSTEP: DFT-based Steric Parameters - python-based tool to extract molecular shape and steric descriptors from essentially any structure format

wSterimol

Generate Boltzmann-weighted Sterimol Steric Parameters for Conformationally-Flexible Substituents

presto

Python-based reactions in explicit solvent with trajectories via ONIOM

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

AaronTools.py

Python tools for automating routine tasks encountered when running quantum chemistry computations.

Pymol-script-repo

Collected scripts for Pymol

Freecurve_Labs_solvation_suite

QCFractal

A distributed compute and database platform for quantum chemistry.

autodE

automated reaction profile generation

kallisto

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

fireworks

The Fireworks Workflow Management Repo.

morfeus

A Python package for calculating molecular features

custodian

A simple, robust and flexible just-in-time job management framework in Python.

qgrid

An interactive grid for sorting, filtering, and editing DataFrames in Jupyter notebooks