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https://github.com/bio-phys/pydiffusion

Analyse Rotational Diffusion Tensor from MD Simulations

https://github.com/bio-phys/pydiffusion

Science Score: 23.0%

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    Found 1 DOI reference(s) in README
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    Links to: acs.org
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    Low similarity (9.2%) to scientific vocabulary

Keywords

brownian-dynamics diffusion mdanalysis molecular-dynamics python rotation simulation
Last synced: 5 months ago · JSON representation

Repository

Analyse Rotational Diffusion Tensor from MD Simulations

Basic Info
  • Host: GitHub
  • Owner: bio-phys
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 564 KB
Statistics
  • Stars: 17
  • Watchers: 4
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Topics
brownian-dynamics diffusion mdanalysis molecular-dynamics python rotation simulation
Created about 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.rst 

=============
 PyDiffusion
=============

.. image:: https://travis-ci.org/bio-phys/pydiffusion.svg?branch=master
   :target: https://travis-ci.org/bio-phys/pydiffusion

.. image:: https://mybinder.org/badge.svg
   :target: https://mybinder.org/v2/gh/bio-phys/pydiffusion/master?filepath=example%2FAnalysis.ipynb

PyDiffusion is a python library to analyze the rotational and translational
diffusion of molecules in molecular dynamics simulation or rigid body simulations.

INSTALL
=======
**Note**: You need cython, numpy and setuptools to install pydiffusion

.. code::
   pip install .

If you want to install the library locally for your user then append the ``-e``
flag.

For reference the requirements.txt shows the dependencies we used to run the testsuite

Usage
=====

Please refer to the `example notebook `_.

References
==========

 | M. Linke, J. Köfinger, G. Hummer: Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry Part B `(2018, in print)  `_


DEVELOPMENT
===========

To install the library in development mode and it's own venv use

.. code::
   make develop

This will create a python-package-symlink to this folder and every change you
make is directly applied to your installed package.

Owner

  • Name: bio-phys
  • Login: bio-phys
  • Kind: organization

GitHub Events

Total
  • Issues event: 2
  • Watch event: 4
  • Push event: 1
  • Pull request event: 2
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 4
  • Push event: 1
  • Pull request event: 2
  • Fork event: 1
  • Create event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 58
  • Total Committers: 3
  • Avg Commits per committer: 19.333
  • Development Distribution Score (DDS): 0.069
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Max Linke m****e@g****e 54
Max Linke k****e 3
Max Linke m****8@g****m 1
Committer Domains (Top 20 + Academic)
gmx.de: 1

Issues and Pull Requests

Last synced: about 2 years ago

All Time
  • Total issues: 4
  • Total pull requests: 1
  • Average time to close issues: 1 day
  • Average time to close pull requests: less than a minute
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 3.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • akvasan2 (1)
  • sperezconesa (1)
  • sobuelow (1)
  • kain88-de (1)
Pull Request Authors
  • kain88-de (2)
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Dependencies

binder/environment.yml conda
  • cython
  • matplotlib
  • mdanalysis
  • numba
  • scipy
setup.py pypi
  • MDAnalysis >=0.17.0
  • joblib *
  • numba *
  • numpy *
  • scipy >=0.19
  • six *