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Welcome to the Pynoramix wiki!

Info:

Download the tar.gz here: https://github.com/dprada/Pynoramix

The program is able to reproduce the analysis proposed in the paper: J. Phys. Chem. B, 2010, 114 (47), pp 15598–15604.

Kickstart example

For the impatient, some simple code to start with.

First, fire-up your python shell:

$ ipython

then, load the libraries:

>>> from pyn_cl_set import *
>>> from pyn_cl_unit import *
>>> from pyn_cl_net import *

Create the system topology from the pdb file:

>>> wbox=cl_set('tip4p_ew.pdb')

Apply the analysis over the trajectory:

>>> wbox.water_analysis(traj_name='md_test.xtc')

Extract from the system wbox the network as a new object:

>>> net=wbox.get_network()

From net, create a symmetric network:

>>> net_symm=net.symmetrize()

To obtain the gradient clusters from this network:

>>> net_symm.gradient_clusters()