MDAnalysis/MDAKits

The MDAnalysis Toolkits Registry

Language: Python - Size: 80.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 18 - Forks: 30

MDAnalysis/stride

STRIDE: Protein secondary structure assignment from atomic coordinates

Language: C - Size: 315 KB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 8

MDAnalysis/WorkshopHackathon2018

Materials, issues and things for the 2018 Workshop and Hackathon

Language: Jupyter Notebook - Size: 84.4 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 14 - Forks: 24

MDAnalysis/UGM2023

Materials for the 2023 MDAnalysis User Group Meeting

Language: Jupyter Notebook - Size: 32.3 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 4 - Forks: 10

MDAnalysis/solvation-analysis

A comprehensive tool for analyzing liquid solvation structure.

Language: Python - Size: 43.5 MB - Last synced at: about 10 hours ago - Pushed at: 5 days ago - Stars: 53 - Forks: 13

MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day

Language: Jupyter Notebook - Size: 31.3 MB - Last synced at: about 21 hours ago - Pushed at: 5 days ago - Stars: 12 - Forks: 16

MDAnalysis/MDAnalysisWorkshop-Intermediate1Day

Materials for 1-day intermediate workshop

Language: Jupyter Notebook - Size: 12 MB - Last synced at: about 2 hours ago - Pushed at: 5 days ago - Stars: 4 - Forks: 1

MDAnalysis/mdanalysis-sphinx-theme

The official MDAnalysis Sphinx documentation theme.

Language: Sass - Size: 46.3 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 1

MDAnalysis/MDAnalysisWorkshop-Intro0.5Day

Materials for 0.5-day MDAnalysis workshops

Language: Jupyter Notebook - Size: 20.8 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 11 - Forks: 9

MDAnalysis/.github

MDAnalysis Org profile

Size: 5.86 KB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 0

MDAnalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Language: Python - Size: 514 MB - Last synced at: 7 days ago - Pushed at: 10 days ago - Stars: 1,444 - Forks: 718

MDAnalysis/UserGuide

User Guide for MDAnalysis

Language: Python - Size: 561 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 28 - Forks: 42

MDAnalysis/GridDataFormats

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

Language: Python - Size: 14.9 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 31 - Forks: 19

MDAnalysis/MDAnalysis.github.io

MDAnalysis home page mdanalysis.org as GitHub pages.

Language: CSS - Size: 91.8 MB - Last synced at: 8 days ago - Pushed at: 15 days ago - Stars: 15 - Forks: 48

MDAnalysis/pypi-deployment

Reusable github action to package, deploy and and check code to PyPi & TestPyPi

Size: 30.3 KB - Last synced at: 3 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

MDAnalysis/benchmarks

Performance benchmarks of MDAnalysis provided by ASV.

Language: Shell - Size: 599 MB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 1

MDAnalysis/mdacli

Command line interface for MDAnalysis

Language: Python - Size: 7.15 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 8

MDAnalysis/MDAnalysisData

Access to data for workshops and extended tests of MDAnalysis.

Language: Python - Size: 7.12 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 18 - Forks: 5

MDAnalysis/distopia

SIMD instructions for faster distance calculations.

Language: C++ - Size: 2.12 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 20 - Forks: 7

MDAnalysis/MDAPackmol

MDAnalysis wrapper around Packmol

Language: Python - Size: 28.3 KB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 33 - Forks: 9

MDAnalysis/MDAnalysisWorkshop-Intro1Day

Materials for 1-day MDAnalysis workshops

Language: Jupyter Notebook - Size: 3.56 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

MDAnalysis/WorkshopMDMLEdinburgh2022

Language: Jupyter Notebook - Size: 68.6 MB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 65 - Forks: 14

MDAnalysis/mdahole2

An MDAKit implementing a Python interface for the HOLE program.

Language: Python - Size: 15.7 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 7 - Forks: 2

MDAnalysis/panedr

Reads Gromacs EDR file to populate a pandas dataframe

Language: Python - Size: 29.7 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 33 - Forks: 8

MDAnalysis/transport-analysis

A Python package to compute and analyze transport properties.

Language: Python - Size: 4.58 MB - Last synced at: 8 days ago - Pushed at: 12 months ago - Stars: 13 - Forks: 2

MDAnalysis/membrane-curvature

MDAnalysis tool to calculate membrane curvature.

Language: Python - Size: 42.3 MB - Last synced at: 8 days ago - Pushed at: 11 months ago - Stars: 32 - Forks: 9

MDAnalysis/waterdynamics

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

Language: Python - Size: 11.2 MB - Last synced at: 3 days ago - Pushed at: 8 months ago - Stars: 7 - Forks: 4

MDAnalysis/helanal

A package to characterise the geometry of protein helicies.

Language: Python - Size: 794 KB - Last synced at: about 13 hours ago - Pushed at: 5 months ago - Stars: 1 - Forks: 2

MDAnalysis/WorkshopPrace2021

Materials for the 2021 PRACE Workshop @ SurfSARA

Language: Jupyter Notebook - Size: 34.8 MB - Last synced at: 8 days ago - Pushed at: over 3 years ago - Stars: 30 - Forks: 5

MDAnalysis/imd-workshop-2024

Materials for the virtual 2024 MDAnalysis IMD streaming workshop.

Language: Jupyter Notebook - Size: 25.5 MB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 7 - Forks: 1

MDAnalysis/PathSimAnalysis

An MDAKit that calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff or Fréchet distances.

Language: Python - Size: 10.7 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1

MDAnalysis/mda-openbabel-converter

MDAnalysis-OpenBabel Converter

Language: Python - Size: 1.21 MB - Last synced at: 4 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1

MDAnalysis/mda-xdrlib

Stand-alone XDRLIB module (from cpython 3.10.8)

Language: Python - Size: 55.7 KB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

MDAnalysis/pystride

Python bindings to STRIDE

Language: Python - Size: 725 KB - Last synced at: 3 days ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 1

MDAnalysis/scipy-2016

Accepted proposal for a talk at SciPy 2016

Language: TeX - Size: 32.2 MB - Last synced at: 3 days ago - Pushed at: about 9 years ago - Stars: 4 - Forks: 1

MDAnalysis/mdanalysis-compatible-python

Language: Python - Size: 28.3 KB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

MDAnalysis/pmda

Parallel algorithms for MDAnalysis

Language: Python - Size: 6.71 MB - Last synced at: 3 days ago - Pushed at: 12 months ago - Stars: 31 - Forks: 23

MDAnalysis/cookiecutter-mdakit

Cookiecutter for Python packages based on MDAnalysis

Language: Python - Size: 6.33 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 7 - Forks: 5

MDAnalysis/branding

Resources for MDAnalysis branding

Size: 4.08 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 0 - Forks: 2

MDAnalysis/UGM2024

Materials for the 2024 MDAnalysis User Group Meeting

Language: Jupyter Notebook - Size: 78.7 MB - Last synced at: 9 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 2

MDAnalysis/pytng

Python bindings for TNG file format

Language: C - Size: 17.4 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 13 - Forks: 5

MDAnalysis/RDKitConverter-benchmark

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

Language: HTML - Size: 75.1 MB - Last synced at: 3 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 0

MDAnalysis/mdaencore

Ensemble overlap comparison software for molecular data.

Language: Python - Size: 12.2 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

MDAnalysis/omnireader

Language: Cython - Size: 126 KB - Last synced at: 3 days ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

MDAnalysis/distopia_2_the_highway_warrior 📦

Language: C++ - Size: 170 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

MDAnalysis/mdgeomkit

Simple cookie-cutter based MDAKit (for Workshop teaching)

Language: Python - Size: 51.8 KB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 2

MDAnalysis/mdakit-cookie

Size: 97.7 KB - Last synced at: 3 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

MDAnalysis/RotamerConvolveMD

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

Language: Python - Size: 9.12 MB - Last synced at: 3 days ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 4

MDAnalysis/install-mdanalysis

Action to install MDAnalysis

Size: 15.6 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

MDAnalysis/MDAnalysisSandbox

testing reporsitory for workshops

Language: Python - Size: 87.9 KB - Last synced at: 8 days ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 21

MDAnalysis/scipy_proceedings Fork of scipy-conference/scipy_proceedings

SciPy conference proceedings: MDAnalysis paper

Language: TeX - Size: 123 MB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 4

MDAnalysis/hole2 Fork of osmart/hole2 📦

Source code for HOLE program.

Language: Fortran - Size: 2.34 MB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

MDAnalysis/get-latest-python-version

Language: Python - Size: 11.7 KB - Last synced at: 3 days ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

MDAnalysis/mdakits-whitepaper

MDAKits whitepaper (LaTeX sources).

Language: TeX - Size: 411 KB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

MDAnalysis/mdanalysistests-feedstock Fork of conda-forge/mdanalysistests-feedstock

A conda-smithy repository for mdanalysistests.

Size: 82 KB - Last synced at: 3 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

MDAnalysis/griddataformats-feedstock Fork of conda-forge/griddataformats-feedstock

A conda-smithy repository for griddataformats.

Size: 52.7 KB - Last synced at: 3 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

MDAnalysis/mdanalysis-feedstock Fork of conda-forge/mdanalysis-feedstock

A conda-smithy repository for mdanalysis.

Size: 138 KB - Last synced at: 3 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

MDAnalysis/mdalint

Proof of concept for a MDAnalysis linter

Language: Python - Size: 14.6 KB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 0

MDAnalysis/mda-bot Fork of obsproject/obs-bot

Source code for the MDAnalysis Discord bot

Language: Python - Size: 393 KB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

MDAnalysis/binder-env-userguide

Binder environment of the User Guide

Size: 5.86 KB - Last synced at: 3 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

MDAnalysis/pyqcprot Fork of synapticarbors/pyqcprot

Python implementation of the fast rmsd and optimal rotation matrix method by Douglas Theobald and Pu Liu

Language: Python - Size: 247 KB - Last synced at: 3 days ago - Pushed at: over 10 years ago - Stars: 3 - Forks: 1

MDAnalysis/dssp

DSSP - Secondary structure analysis

Language: C++ - Size: 49.8 KB - Last synced at: 3 days ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 3

MDAnalysis/binder-notebook

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

Language: Jupyter Notebook - Size: 821 KB - Last synced at: 3 days ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 8

MDAnalysis/docsearch-configs Fork of algolia/docsearch-configs

DocSearch - Configurations

Language: Shell - Size: 11.3 MB - Last synced at: 3 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

MDAnalysis/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).

Language: Python - Size: 3.47 MB - Last synced at: 3 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 2

MDAnalysis/pyQuteMol

port of C++ QuteMol

Language: Python - Size: 219 KB - Last synced at: 8 days ago - Pushed at: almost 10 years ago - Stars: 3 - Forks: 2

MDAnalysis/numfocus Fork of numfocus/numfocus

NumFOCUS Foundation Documents

Size: 180 KB - Last synced at: 3 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

MDAnalysis/mmtf-python-feedstock Fork of conda-forge/mmtf-python-feedstock

A conda-smithy repository for mmtf-python.

Language: Shell - Size: 30.3 KB - Last synced at: 3 days ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1

MDAnalysis/pmda-feedstock Fork of conda-forge/pmda-feedstock

A conda-smithy repository for pmda.

Language: Shell - Size: 19.5 KB - Last synced at: 3 days ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

MDAnalysis/mdanalysisdata-feedstock Fork of conda-forge/mdanalysisdata-feedstock

A conda-smithy repository for mdanalysisdata.

Language: Shell - Size: 9.77 KB - Last synced at: 3 days ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

MDAnalysis/cellgrid

Language: Python - Size: 610 KB - Last synced at: 3 days ago - Pushed at: about 7 years ago - Stars: 7 - Forks: 6

MDAnalysis/gsoc Fork of numfocus/gsoc

Numfocus Google Summer of Code Materials

Language: TeX - Size: 4.66 MB - Last synced at: 3 days ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1

MDAnalysis/rotamerconvolvemd-feedstock Fork of conda-forge/rotamerconvolvemd-feedstock

A conda-smithy repository for rotamerconvolvemd.

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