Module helixbundle

source code

Helix bundle analysis
=====================

Analysis of helix bundles with :func:`gromacs.g_bundle`.

.. SeeAlso:: HELANAL does some things better than g_bundle, in
              particular it can find kinks automatically.

Plugin class
------------

.. autoclass:: HelixBundle
   :members: worker_class
   :undoc-members:

Example
~~~~~~~

.. Warning:: Note that the helices should be sorted in ascending order
             because all indices are sorted that way. If they are in
             mixed order then the correspondence between the name
             column and the helices is lost. This is a shortcoming of
             :program:`make_ndx` that is not easy to rectify.

Define helices in a reST table (use column names as shown!), set up
the plugin, and add it to a simulation instance::

   helixtable = '''
        Table[helices]: helices top = N-term, bot = C-term; kink
        =====  ================ ================ ===============
        name   top              bottom           kink
        =====  ================ ================ ===============
        TM1    G28  P29  F30    T53  S54  S55    I41  Q42  V43
        TM2    Q57  V58  W59    I84  R85  W86    F78  T79  Q80
        TM3    R101 G102 S103   L135 L136 T137   F116 W117 F118
        TM4    L142 P143 L144   T157 F158 Y159   F149 G150 A151
        TM6    F209 S210 T211   D229 I230 V231   G219 W220 I221
        TM7    E243 G244 Q245   L277 V278 G279   V261 P262 A263
        TM8    P297 M298 A299   C327 S328 T329   N314 P315 A316
        TM9    F336 K337 T338   L348 L349 M350   V342 S343 A344
        =====  ================ ================ ===============
        '''
   hb = HelixBundle(helixtable=helixtable, offset=-9)
   S = Simulation(....)
   S.add_plugin(hb)


Worker class
------------

The worker class performs the analysis.

.. autoclass:: _HelixBundle
   :members: