Python Molecular-dynamics Resources

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

Intro Official implementation of "Learning Forward Dynamics Model and Informed Trajectory Sampler for Safe Quadruped Navigation" Robotics:Science and

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

DIGAN (ICLR 2022) Official PyTorch implementation of "Generating Videos with Dyn

bayesian_uncertainty This is my research project for the Irving Center for Cancer Dynamics/Azizi Lab, Columbia University. In this project I build a s

TorchMD-net TorchMD-Net provides state-of-the-art graph neural networks and equivariant transformer neural networks potentials for learning molecular

Direct Molecular Conformation Generation This repository contains the code for Direct Molecular Conformation Generation (DMCG). Dataset Download rdkit

Towards Representation Learning for Atmospheric Dynamics (AtmoDist) The prediction of future climate scenarios under anthropogenic forcing is critical

chem: collection of mostly python code for molecular visualization, QM/MM, FEP,

A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories.

Human Dynamics from Monocular Video with Dynamic Camera Movements Ri Yu, Hwangpil Park and Jehee Lee Seoul National University ACM Transactions on Gra

Boltzmann visualization - Visualize the Boltzmann distribution for simple quantum models of molecular motion

TUPÃ: Electric field analyses for molecular simulations What is TUPÃ? TUPÃ (pronounced as tu-pan) is a python algorithm that employs MDAnalysis engine

pybullet_sim_panda Pybullet simulation environment for Franka Emika Panda Dependency pybullet, numpy, spatial_math_mini Simple example (please check s

Video Tokneization Codebase for video tokenization, based on our paper Towards Tokenized Human Dynamics Representation. Prerequisites (tested under Py

Riemannian Geometry for Molecular Surface Approximation (RGMolSA) Introduction Ligand-based virtual screening aims to reduce the cost and duration of

Authors Marcus Lenler Garsdal, [email protected] Valdemar Søgaard, [email protected] Simon Moe Sørensen, [email protected] Introduction This repo contains the

Computational Design and Dynamics of Soft Systems · This is a repository that contains the source code for generating the lecture notes, handouts, exe

CFD Python Please cite as: Barba, Lorena A., and Forsyth, Gilbert F. (2018). CFD Python: the 12 steps to Navier-Stokes equations. Journal of Open Sour

The dynamics of representation learning in shallow, non-linear autoencoders The package is written in python and uses the pytorch implementation to ML

Bayesian Neural Networks Pytorch implementations for the following approximate inference methods: Bayes by Backprop Bayes by Backprop + Local Reparame

📃 About A simple MacOS menu bar app to display current coins from most popular

📃 About A simple MacOS menu bar app to display current coins from most popular Liquidity Pools on TinyMan.org

Notebooks A NASA MEaSUREs project to provide automated, low latency, global glacier flow and elevation change datasets This repository provides tools

Prescribed-time Control Prescribed-time control (PTC) blocks in Simulink environment, MATLAB R2020b. For more theoretical details, refer to the papers

pymbar Python implementation of the multistate Bennett acceptance ratio (MBAR) method for estimating expectations and free energy differences from equ

unit-converter-albert-ext Extension for converting units of length, mass, speed, temperature, time, current, luminosity, printing measurements, molecu

Curriculum Learning by Optimizing Learning Dynamics (DoCL) AISTATS 2021 paper: Title: Curriculum Learning by Optimizing Learning Dynamics [pdf] [appen

pyscreener A pythonic interface to high-throughput virtual screening software Overview This repository contains the source of pyscreener, both a libra

HyFactor Graph-based architectures are becoming increasingly popular as a tool for structure generation. Here, we introduce a novel open-source archit

Leaded Gradient Method (LGM) This repository contains the PyTorch implementation for paper Dynamics-aware Adversarial Attack of 3D Sparse Convolution

Occupancy Flow This repository contains the code for the project Occupancy Flow - 4D Reconstruction by Learning Particle Dynamics. You can find detail

Gala is a Python package for Galactic and gravitational dynamics. Documentation The documentation for Gala is hosted on Read the docs. Installation an

AERO - 421 Final Project Redevelopment Spacecraft Attitude, Dynamics, and Control: Simulation to determine and control a satellite's attitude in LEO.

Daphny_counter run command must be like this: /usr/bin/python3 /home/nmakagonov/Daphny/daphny_counter/Daphny_counter.py -o /home/nmakagonov/Daphny/out

MDAnalysis Repository README [*] MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale,

GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles This repository contains a method to generate 3D conformer ensembles direct

LitMatter A template for rapid experimentation and scaling deep learning models on molecular and crystal graphs. How to use Clone this repository and

ED2 Code for Environment Dynamics Decomposition (ED2). Installation Follow the installation in MBPO and Dreamer. Usage First follow the SD2 method for

Junction Tree Variational Autoencoder for Molecular Graph Generation Official implementation of our Junction Tree Variational Autoencoder https://arxi

Flexible Networks for Learning Physical Dynamics of Deformable Objects (2021) By Jinhyung Park, Dohae Lee, In-Kwon Lee from Yonsei University (Seoul,

Monitoring of lake dynamics This is a program that uses multi-source remote sensing data to monitor the dynamic changes of lakes. The detailed introdu

Ultra-Fast Force Fields (UF3) S. R. Xie, M. Rupp, and R. G. Hennig, "Ultra-fast interpretable machine-learning potentials", preprint arXiv:2110.00624

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures Code for the Multiplex Molecular Graph Neural Network (M

Knowledge-enhanced Contrastive Learning (KCL) Molecular Contrastive Learning with Chemical Element Knowledge Graph [ AAAI 2022 ]. We construct a Chemi

ReacNetGenerator An automatic reaction network generator for reactive molecular dynamics simulation. ReacNetGenerator: an automatic reaction network g

MoT - Molecular Transformer Large-scale Pretraining for Molecular Property Prediction Samsung AI Challenge for Scientific Discovery This repository is

Description Small wrapper around 3dmol.js and html2canvas for creating self-contained HTML files that display a 3D molecular representation. Double cl

Molecular Sets (MOSES): A benchmarking platform for molecular generation models Deep generative models are rapidly becoming popular for the discovery

Online Pseudo Label Generation by Hierarchical Cluster Dynamics for Adaptive Person Re-identification

Code of the paper "Deep Human Dynamics Prior" in ACM MM 2021. Figure 1: In the process of motion capture (mocap), some joints or even the whole human

Official code of APHYNITY Augmenting Physical Models with Deep Networks for Complex Dynamics Forecasting (ICLR 2021, Oral) Yuan Yin*, Vincent Le Guen*

Delve is a Python package for analyzing the inference dynamics of your PyTorch model.

Robotics Toolbox for Python A Python implementation of the Robotics Toolbox for MATLAB® GitHub repository Documentation Wiki (examples and details) Sy

Fluid Simulation Usage Download this repo and store it in your computer. Open a terminal and go to the root directory of this folder. Make sure you ha

Generating Videos with Scene Dynamics This repository contains an implementation of Generating Videos with Scene Dynamics by Carl Vondrick, Hamed Pirs

High Performance Molecular Dynamics Logging into CINECA's computer systems To logon to the M100 system use the following command from an SSH client ss

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

A Example for Calculating Robot Dynamics Using Pinocchio Library Developed by: Xinyang Tian. Platform: Linux + Pinocchio. In this work, i use Pinocchi

Hamiltonian Dynamics with Non-Newtonian Momentum for Rapid Sampling Code for the paper: Greg Ver Steeg and Aram Galstyan. "Hamiltonian Dynamics with N

README: GromacsWrapper A primitive Python wrapper around the Gromacs tools. The library is tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, and 2021

Likelihood-Free Inference in State-Space Models with Unknown Dynamics This package contains the codes required to run the experiments in the paper. Th

Official repository of the paper (UAI 2021) "A Variational Approximation for Analyzing the Dynamics of Panel Data", Mixed Effect Neural ODE. Panel dat

Molecular Orbital Transitions (MOT) Animate molecular orbital transitions using Psi4 and Blender Author: Maximilian Paradiz Dominguez, University of A

Molecular Sets (MOSES): A benchmarking platform for molecular generation models Deep generative models are rapidly becoming popular for the discovery

Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations This directory contains the model architectures and experimental

Python Rapid Artificial Intelligence Ab Initio Molecular Dynamics

MuJoCo Physics MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and develo

Helpdesk Application The project is a Helpdesk application (Helpdesk dynamics) where staff of an organization can raise and assign job/trouble tickets

pyHype: Computational Fluid Dynamics in Python pyHype is a Python framework for developing parallelized Computational Fluid Dynamics software to solve

Imitating Deep Learning Dynamics via Locally Elastic Stochastic Differential Equations This repo contains official code for the NeurIPS 2021 paper Imi

3D-Transformer: Molecular Representation with Transformer in 3D Space

PiSL A python implementation of Physics-informed Spline Learning for nonlinear dynamics discovery. Sun, F., Liu, Y. and Sun, H., 2021. Physics-informe

VectorNet Re-implementation This is the unofficial pytorch implementation of CVPR2020 paper "VectorNet: Encoding HD Maps and Agent Dynamics from Vecto

Robust, intersection-free, simulations of rigid bodies.

Automatic Differentiation Multipole Moment Molecular Forcefield Performance notes On a single gpu, using waterbox_31ang.pdb example from MPIDplugin wh

safe-control-gym Physics-based CartPole and Quadrotor Gym environments (using PyBullet) with symbolic a priori dynamics (using CasADi) for learning-ba

MolEncoder Molecular AutoEncoder in PyTorch Install $ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder $ python setup.py insta

DockStream Description DockStream is a docking wrapper providing access to a collection of ligand embedders and docking backends. Docking execution an

JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design This repository contains code for the paper: JA

Evidential Deep Learning for Guided Molecular Property Prediction and Discovery Ava Soleimany*, Alexander Amini*, Samuel Goldman*, Daniela Rus, Sangee

fluidnet_cxx: Accelerating Fluid Simulation with Convolutional Neural Networks. A PyTorch/ATen Implementation. This repository is based on the paper,

Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics This work will be published in Nature Biomedical

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.

Physics-aware Difference Graph Networks for Sparsely-Observed Dynamics This repository is the official PyTorch implementation of "Physics-aware Differ

Part of the 9th place solution for the Bristol-Myers Squibb – Molecular Translation challenge translating images containing chemical structures into I

VID-Fusion VID-Fusion: Robust Visual-Inertial-Dynamics Odometry for Accurate External Force Estimation Authors: Ziming Ding , Tiankai Yang, Kunyi Zhan

[PDF] | [Slides] The official implementation of Learning Gradient Fields for Molecular Conformation Generation (ICML 2021 Long talk) Installation Inst

BridgeWalk is a partially-observed reinforcement learning environment with dynamics of varying stochasticity. The player needs to walk along a bridge to reach a goal location. When the player walks off the bridge into the water, the current will move it randomly until it gets washed back on the shore. A good agent in this environment avoids this stochastic trap

MolRep: A Deep Representation Learning Library for Molecular Property Prediction Summary MolRep is a Python package for fairly measuring algorithmic p

The MDAkit for membrane curvature analysis is part of the Google Summer of Code program and it is linked to a Code of Conduct.

BMS-Molecular-Translation Introduction This is a pipeline for Bristol-Myers Squibb – Molecular Translation by Vadim Timakin and Maksim Zhdanov. We got

Memory In Memory Networks It is based on the paper Memory In Memory: A Predictive Neural Network for Learning Higher-Order Non-Stationarity from Spati

This repo contains code for our paper State-only Imitation with Transition Dynamics Mismatch published at ICLR 2020. The code heavily uses the RL mach

Contact and Human Dynamics from Monocular Video This is the official implementation for the ECCV 2020 spotlight paper by Davis Rempe, Leonidas J. Guib

SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks Molecular interaction networks are powerful resources for the discovery. While dee

PyDy, short for Python Dynamics, is a tool kit written in the Python programming language that utilizes an array of scientific programs to enable the study of multibody dynamics. The goal is to have a modular framework and eventually a physics abstraction layer which utilizes a variety of backends that can provide the user with their desired workflow

Few-shot Graph Learning for Molecular Property Prediction Introduction This is the source code and dataset for the following paper: Few-shot Graph Lea