MDAnalysis/MDAKits

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Created over 2 years ago
Updated 2 months ago

MDAnalysis/MDAKits

MDAnalysis

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The MDAnalysis Toolkits Registry

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

WorkshopMDMLEdinburgh2022

Jupyter Notebook

solvation-analysis

A comprehensive tool for analyzing liquid solvation structure.

MDAnalysisCookbook

Examples and tutorials of using MDAnalysis

pmda

Parallel algorithms for MDAnalysis

WorkshopPrace2021

Materials for the 2021 PRACE Workshop @ SurfSARA

Jupyter Notebook

panedr

Reads Gromacs EDR file to populate a pandas dataframe

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

GridDataFormats

GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.

MDAPackmol

MDAnalysis wrapper around Packmol

UserGuide

User Guide for MDAnalysis

mdacli

Command line interface for MDAnalysis

MDAnalysis.github.io

MDAnalysis home page mdanalysis.org as GitHub pages.

MDAnalysisData

Access to data for workshops and extended tests of MDAnalysis.

WorkshopHackathon2018

Materials, issues and things for the 2018 Workshop and Hackathon

Jupyter Notebook

pytng

Python bindings for TNG file format

MDAnalysisMolSSIWorkshop-Intermediate2Day

Jupyter Notebook

MDAnalysisTutorial

Tutorial for MDAnalysis.

Jupyter Notebook

distopia

SIMD instructions for faster distance calculations.

stride

STRIDE: Protein secondary structure assignment from atomic coordinates

transport-analysis

A Python package to compute and analyze transport properties.

cookiecutter-mdakit

Cookiecutter for Python packages based on MDAnalysis

cellgrid

RotamerConvolveMD

Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.

MDAnalysisWorkshop-Intro0.5Day

Materials for 0.5-day MDAnalysis workshops

Jupyter Notebook

waterdynamics

Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.

mdahole2

An MDAKit implementing a Python interface for the HOLE program.

pystride

Python bindings to STRIDE

UGM2023

Materials for the 2023 MDAnalysis User Group Meeting

Jupyter Notebook

mdalint

Proof of concept for a MDAnalysis linter

binder-notebook

Notebooks for interactive use on https://mybinder.org/

Jupyter Notebook

dssp

DSSP - Secondary structure analysis

pyQuteMol

port of C++ QuteMol

RDKitConverter-benchmark

Benchmark for the RDKitConverter's inferring of bond orders and charges

scipy-2016

Accepted proposal for a talk at SciPy 2016

mdakits-whitepaper

MDAKits whitepaper (LaTeX sources).

MDAnalysisSandbox

testing reporsitory for workshops

benchmarks

Performance benchmarks of MDAnalysis provided by ASV.

MDAnalysisWorkshop-Intro1Day

Materials for 1-day MDAnalysis workshops

Jupyter Notebook

SPIDAL-MDAnalysis-Midas-tutorial

Tutorial for SPIDAL presentation at workshop, showing how to use Midas radical.pilot to analyze an ensemble of MD trajectories with Path Similarity Analysis (as implemented in MDAnalysis).

.github

MDAnalysis Org profile

mdanalysis-sphinx-theme

The official MDAnalysis Sphinx documentation theme.

mdgeomkit

Simple cookie-cutter based MDAKit (for Workshop teaching)

UGM2024

Materials for the 2024 MDAnalysis User Group Meeting

binder-env-userguide

Binder environment of the User Guide

mdanalysis-compatible-python

mda-xdrlib

Stand-alone XDRLIB module (from cpython 3.10.8)

get-latest-python-version