Module dist

source code

``analysis.plugins.dist`` --- Helper Class for ``g_dist``
=========================================================

:mod:`dist` contains helper classes for other analysis plugins that
want to make use of the Gromacs command ``g_dist``.


Overview
--------

The task we are solving is to analyze output from ::

   g_dist -f md.xtc -s md.tpr -n cys_ow.ndx -dist 1.0 | bzip2 -vc > mindist_C60_OW_1nm.dat.bz2 

and produce a histogram of minimum contact distances. This should
provide an estimate for water accessibility of the atom (here: SG of
Cys60).

File format
-----------
  
``g_dist`` with the ``-dist CUTOFF`` option writes to stdout the
identity of all atoms within the cutoff distance and the distance
itself::

   Selected 22: 'CYSH_CYSH_60_&_SG'
   Selected 25: 'OW'
   ....
   t: 184  6682 SOL 35993 OW  0.955138 (nm)
   t: 184  10028 SOL 46031 OW  0.803889 (nm)
   t: 185  6682 SOL 35993 OW  0.879949 (nm)
   t: 185  10028 SOL 46031 OW  0.738299 (nm)
   t: 186  6682 SOL 35993 OW  0.897016 (nm)
   t: 186  10028 SOL 46031 OW  0.788268 (nm)
   t: 187  6682 SOL 35993 OW  0.997688 (nm)
   ....
   

Classes
-------

.. autoclass:: Mindist
   :members: histogram, hist, dist, edges, midpoints, plot
.. autoclass:: GdistData
   :members: __iter__