Python Molecular-simulation Resources

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

Sionna: An Open-Source Library for Next-Generation Physical Layer Research Sionna™ is an open-source Python library for link-level simulations of digi

Viewer for MuJoCo in Python Interactive renderer to use with the official Python bindings for MuJoCo. Starting with version 2.1.2, MuJoCo comes with n

Fixing Malfunctional Objects With Learned Physical Simulation and Functional Prediction Figure 1. Teaser. Introduction This paper studies the problem

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

ICON: Implicit Clothed humans Obtained from Normals Yuliang Xiu · Jinlong Yang · Dimitrios Tzionas · Michael J. Black CVPR 2022 News 🚩 [2022/04/26] H

PWF 2021 Física Sin Fronteras es un proyecto del Centro Internacional de Física Teórica (ICTP) en Trieste Italia. El ICTP es un centro dedicado a fome

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

Phoenix-Drone-Simulation An OpenAI Gym environment based on PyBullet for learning to control the CrazyFlie quadrotor: Can be used for Reinforcement Le

This is the official implementation of our paper: Bowen Wen, Wenzhao Lian, Kostas Bekris, and Stefan Schaal. "CaTGrasp: Learning Category-Level Task-R

🦕 👨‍💻 nanosaur_gazebo nanosaur The smallest NVIDIA Jetson dinosaur robot, open-source, fully 3D printable, based on ROS2 & Isaac ROS. Designed & ma

solarSystemOrbitalSimulation graphical orbitational simulation of solar system planets with real values and physics implemented so you get a nice elli

PyMouseBot If you're from GT and annoyed with SGVPN idle timeouts while working on development laptop, You might find this useful. A python cli bot to

Shapeland Simulator Source code to accompany Defunctland's video "FASTPASS: A Complicated Legacy" Download the video at https://www.youtube.com/watch?

Conway's Game of Life The zero player Darwinism simulation game as described by Conway (demonstrates Turing Completeness). I created this script after

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

UMPNet: Universal Manipulation Policy Network for Articulated Objects Zhenjia Xu, Zhanpeng He, Shuran Song Columbia University Robotics and Automation

Ontologysim: a Owlready2 library for applied production simulation Ontologysim is an open-source deep production simulation framework, with an emphasi

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

Differentiable Simulation of Soft Multi-body Systems Yi-Ling Qiao, Junbang Liang, Vladlen Koltun, Ming C. Lin [Paper] [Code] Updates The C++ backend s

Devito-playbox A few of my adventures with Devito. This repository contains a few notebooks and scripts that will lead me in the road of learning this

Generate 3D Locomotion Data This module is intended to create 2D video trajector

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

Liquid Rocket Engine Cooling Simulation NASA CEA The implemented class calls NASA CEA via RocketCEA. INSTALL GUIDE In progress install instructions fo

Evolution Gym A large-scale benchmark for co-optimizing the design and control of soft robots. As seen in Evolution Gym: A Large-Scale Benchmark for E

This project uses the mosaik co-simulation framework, developed by the brilliant developers at the high-ranked Offis institue for computer science, Oldenburg, Germany, to simulate multidimensional LED matrices.

SSA Our implementation of Gillespie's Stochastic Simulation Algorithm (SSA) Requirements python =3.7 numpy pandas matplotlib pyyaml Command line usag

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

solsim is the Solana complex systems simulator. It simulates behavior of dynamical systems—DeFi protocols, DAO governance, cryptocurrencies, and more—built on the Solana blockchain

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

E2EDNA2 - An automated pipeline for simulation of DNA aptamers complexed with small molecules and short peptides

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

Modeling and Simulation of Satellite Servicing Manipulators Final Project for the course ENPM662: Introduction to Robot Modeling (Fall 2021). This pro

WATTS (Workflow and Template Toolkit for Simulation) provides a set of Python classes that can manage simulation workflows for multiple codes where information is exchanged at a coarse level.

Turtlebot-NavigationStack-Fixed-Waypoints fixed waypoint(pose) navigation for turtlebot simulation. Task Details Task Permformed using Navigation Stac

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

ProjetRIPlay v2 Simulation simplifiée du fonctionnement du protocole RIP par Eric Buonocore le 18/01/2022 Sur la base de l'exercice 5 du sujet zéro du

implementation of MM1 and MMC Queue on randomly generated data and evaluate simulation results then compare with analytical results and draw a plot curve for them, simulate some integrals and compare results and run monte carlo algorithm with them

Pytorch Implementation of Learning Mesh-based Simulation With Graph Networks This is the unofficial implementation of the approach described in the pa

PyElastica PyElastica is the python implementation of Elastica: an open-source project for simulating assemblies of slender, one-dimensional structure

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

StableSims is an open-source project aimed at simulating MakerDAO's Dai stablecoin system, initially used for researching optimal incentive parameters for Liquidations 2.0.

Aircraft design optimization made fast through modern automatic differentiation. Plug-and-play analysis tools for aerodynamics, propulsion, structures, trajectory design, and much more.

The Autonomous Driving Cookbook (Preview) NOTE: This project is developed and being maintained by Project Road Runner at Microsoft Garage. This is cur

MothPruning Scientific Overview Originally inspired by biological nervous systems, deep neural networks (DNNs) are powerful computational tools for mo

{ATAM} Active Transport Analytics Model Active Transport Analytics Model (“ATAM”

Free Unified Rendering in Python A software library for scientific visualization in Python. General Information • Key Features • Installation • How to

Trade Engine a library for demo trading | backtest and forward test simulation Features Limit/Market orders: you can place a Limit or Market order in

iGibson: A Simulation Environment to train Robots in Large Realistic Interactive Scenes iGibson is a simulation environment providing fast visual rend

What is it? Program for scientific research, which allows to simulate the phenomenon of self-focusing of different laser beams (including Gaussian, ri

PySDM PySDM is a package for simulating the dynamics of population of particles. It is intended to serve as a building block for simulation systems mo

msprime msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consis

Armer Driver Armer aims to provide an interface layer between the hardware drivers of a robotic arm giving the user control in several ways: Joint vel

Conway's Game of Life My PyGame implementation of Conway's Game of Life. This implementation involves treating all edges of the grid as stitched toget

ehtim (eht-imaging) Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This ve

Le problème de Monty Hall C'est un jeu télévisé où il y a trois portes sur le plateau de jeu. Seule une de ces portes cache un trésor. Il n'y a rien d

GAN-STEM-Conv2MultiSlice GAN method to help covert lower resolution STEM images generated by convolution methods to higher resolution STEM images gene

GHDL Interactive Simulation This is an interactive test bench for a simple VHDL adder. It uses GHDL to elaborate/run the simulation. It is coded in Py

Numerical Bric-a-Brac Collections of numerical techniques with Python and standard computational packages (Numpy, SciPy, Numba, Matplotlib ...). Diffe

3D-Lorenz-Attractor-simulation-with-python Animação 3D da trajetória do Atrator de Lorenz, implementada em Python usando o método de Runge-Kutta de 4ª

Monty Hall Problem Simulation monty_hall_sim is a brute-force method of determining the optimal strategy for the Monty Hall Problem. Usage Set boolean

CADLabs Ethereum Economic Model A modular dynamical-systems model of Ethereum's validator economics, based on the open-source Python library radCAD, a

MeerKATgen MeerKAT radio telescope simulation package. Designed with performance in mind and utilizes Just in time compile (JIT) and XLA backed vectro

A cool little repl-based simulation written in Python planned to integrate machine-learning into itself to have AI battle to the death before your eye

EIP: Elastic Interaction of Particles Code release for "Elastic Tactile Simulation Towards Tactile-Visual Perception", in ACMMM (Oral) 2021. By Yikai

################################################################################### #

PyBERT PyBERT is a serial communication link bit error rate tester simulator with a graphical user interface (GUI). It uses the Traits/UI package of t

Object oriented discrete event simulation and animation in Python. Includes process control features, resources, queues, monitors. statistical distrib

Jomini v0.1.4 Jomini creates military simulations by using mathematical combat models. Designed to be helpful for game developers, students, history e

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

PyDynamica PyDynamica is a pure python implementation of Sociodynamica, a virtual environment to simulate a simple economy with minimal dependencies.

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

ReaDDy (Reaction Diffusion Dynamics) is an open source particle based reaction-diffusion simulator that can be configured and run via Python. Currentl

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

NetKet NetKet is an open-source project delivering cutting-edge methods for the study of many-body quantum systems with artificial neural networks and

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

Python script to create a TOPAS-readable simulation file descriring a Multi-Leaf-Collimator. Builds the MLC using the data from a 3D .stl file.

topas-create-graphs A script to automatically plot the results of a topas simulation Works for percentage depth dose (pdd) and dose profiles (dp). Dep

topas-merge-simulations Python script to combine the statistical results of a TOPAS simulation that was split up into multiple batches At the top of t

RLBot Python bindings for rl_ball_sym 0.6 Prerequisites: Rust & Cargo Build Tools for Visual Studio RLBot - Verify that the file %localappdata%\RLBotG

gym-idsgame An Abstract Cyber Security Simulation and Markov Game for OpenAI Gym gym-idsgame is a reinforcement learning environment for simulating at

Blockchain-enabled Server-less Federated Learning Repository containing the files used to reproduce the results of the publication "Blockchain-enabled

OstrichRL This is the repository accompanying the paper OstrichRL: A Musculoskeletal Ostrich Simulation to Study Bio-mechanical Locomotion. It contain

PyNBoids A Python Boids Simulation This is a Boids simulation, written in Python3, with Pygame2 and NumPy. To use: Save the pynboids_sp.py file (and n

NeuralPDE NeuralPDE.jl is a solver package which consists of neural network solvers for partial differential equations using scientific machine learni

COSCO Framework COSCO is an AI based coupled-simulation and container orchestration framework for integrated Edge, Fog and Cloud Computing Environment

Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.

CONCEPT (COsmological N-body CodE in PyThon) is a free and open-source simulation code for cosmological structure formation. The code should run on any Linux system, from massively parallel computer clusters to laptops.

PythonPercolation Percolation simulation using python Exemple de percolation : Etude statistique sur le pourcentage de remplissage jusqu'à percolation

PyPowSyBl The PyPowSyBl project gives access PowSyBl Java framework to Python developers. This Python integration relies on GraalVM to compile Java co

Monte Carlo python simulation Install linux dependencies sudo apt update sudo apt install build-essential \ software-properties-commo

hooman ~ pygame for humans pip install hooman join discord: https://discord.gg/Q23ATve The package for clearer, shorter and cleaner PyGame codebases!

finitevolume2-python Finite Volume simulation of the Raleigh-Taylor Instability Create Your Own Finite Volume Fluid Simulation (With Python): Part 2 B

Neural Fluid Fields This is a small library for doing fluid simulation with neural fields. Check out our review paper, Neural Fields in Visual Computi

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

The devkit of the nuPlan dataset.

BIGDATA SIMULATION LIBRARY OF DREAM BY SANDMAN BOOKS ================= Solution Architecture Description In the realm of Dreaming, its ruler SANDMAN,

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

Simulation of moving particles under microscopic imaging Install scipy numpy scikit-image tiffile Run python simulation.py Read result https://imagej

SEE Injection Framework 2021 This repository contains two Single Event Effect (SEE) injection platforms. The first one is called BFSP - "Bitflip Fault