PyDiffusion is a python library to analyze the rotational and translational diffusion of molecules in molecular dynamics simulation or rigid body simulations.
Note: You need cython, numpy and setuptools to install pydiffusion
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
Please refer to the example notebook.
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)
To install the library in development mode and it's own venv use
This will create a python-package-symlink to this folder and every change you make is directly applied to your installed package.