Class CysAccessibility

source code

 object --+    
          |    
core.Plugin --+
              |
             CysAccessibility

*CysAccessibility* plugin.

For each frame of a trajectory, the shortest distance of all water oxygens
to all cysteine sulphur atoms is computed. For computational efficiency,
only distances smaller than a cutoff are taken into account. A histogram of
the distances shows how close water molecules can get to cysteines. The
closest approach distance should be indicative of the reactivity of the SH
group with crosslinking agents.

.. class:: CysAccessibility(cysteines, [cys_cutoff[, name[, simulation]]])

:Arguments:
    name : string
        plugin name (used to access it)
    simulation : instance
        The :class:`gromacs.analysis.Simulation` instance that owns the plugin.
    cysteines : list
        list of *all* resids (eg from the sequence) that are used as
        labels or in the form 'Cys<resid>'. (**required**)
    cys_cutoff : number
        cutoff in nm for the minimum S-OW distance [1.0]

Note that *all* Cys residues in the protein are analyzed. Therefore, the
list of cysteine labels *must* contain as many entries as there are
cysteines in the protein. There are no sanity checks.