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

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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 and numpy to install pydiffusion

.. code::

python setup.py install

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

Usage

Please refer to the example notebook <https://github.com/bio-phys/pydiffusion/blob/master/example/Analysis.ipynb>_.

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) <https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b11988>_

DEVELOPMENT

To install the library in development mode use

.. code:: python setup.py develop --user

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