Class _HelixBundle

Set up HelixBundle analysis.

:Keywords:
   *helixtable*
       reST table with columns "name", "top", "bottom",
       "kink"; see :mod:`gromacs.analysis.plugins.helixbundle`
       for details
   *offset*
       add the *offset* to the residue numbers in *helixtable* [0]
   *helixndx*
       provide a index file with the appropriate groups
       instead of the table; also requires *na*
   *na*
       number of helices
   *with_kinks*
       take kinks into account [True]
   *name*
       plugin name [HelixBundle]
   *simulation*
       The :class:`gromacs.analysis.Simulation` instance that
       owns the plugin [None]

Overrides: object.__init__

Build g_bundle index file from a record array.

:Keywords:
  *force*
      - ``None`` does nothing if the index file already exists
      - ``False`` raises exception if it exists
      - ``True`` always rebuild index file

Format of the index table:
- must contain columns name, top, bottom, kink
- a row corresponds to one helis
- name contains the name of the helix e.g. 'TM5'
- a entry is a *string* of residues which is split on white space; 
  entries in the same column must have the same number of residues 
  (limitation of g_bundle)

Analyze trajectory and write HelixBundle files.

:Arguments:
  - *force*: ``True`` does analysis and overwrites existing files
  - *gmxargs*: additional keyword arguments for :func:`gromacs.g_bundle` 

.. Note:: The plugin default is *z* = ``True``, i.e. the tilt is computed
          relative to the box z-axis.

Overrides: core.Worker.run

Collect output xvg files as :class:`gromacs.formats.XVG` objects.

:Returns:  a dictionary of the results and also sets ``self.results``.

Overrides: core.Worker.analyze

Parameters:

• figure -
  • True: save figures in the given formats
  • "name.ext": save figure under this filename (ext -> format)
  • False: only show on screen
• formats (sequence) - sequence of all formats that should be saved [('png', 'pdf')]
• plotargs - keyword arguments for pylab.plot()

Overrides: core.Worker.plot