gromacs.analysis.plugins

Package plugins

:mod:`analysis.plugins` -- Plugin Modules ========================================= Classes for :class:`gromacs.analysis.core.Simulation` that provide code to analyze trajectory data. New analysis plugins should follow the API sketched out in :mod:`gromacs.analysis.core`; see an example for use there. List of plugins --------------- Right now the number of plugins is limited. Feel free to contribute your own by sending it to the `package author`_. You will be acknowledged in the list below. .. _`package author`: oliver.beckstein@bioch.ox.ac.uk .. table:: Plugins for analysis. ========================== ========= ======================================== plugin author description ========================== ========= ======================================== :class:`CysAccessibility` [#OB]_ estimate accessibility of Cys residues by water :class:`HelixBundle` [#OB]_ g_bundle analysis of helices :class:`Distances` [#OB]_ time series of distances :class:`MinDistances` [#OB]_ time series of shortest distances :class:`COM` [#OB]_ time series of centres of mass :class:`Dihedrals` [#OB]_ analysis of dihedral angles :class:`RMSF` [#OB]_ calculate root mean square fluctuations :class:`RMSD` [#OB]_ calculate root mean square distance :class:`Energy` [#OB]_ terms from the energy file ========================== ========= ======================================== .. table:: Plugins for trajectory manipulation and status queries. ========================== ========= ======================================== plugin author description ========================== ========= ======================================== :class:`Trajectories` [#OB]_ write xy-fitted trajectories :class:`StripWater` [#OB]_ remove solvent (and optionally fit to reference) :class:`ProteinOnly [#OB]_ remove all atoms except the Protein (and optionally fit to reference) :class:`Ls` [#OB]_ simple :program:`ls` (for testing) ========================== ========= ======================================== .. rubric:: Footnotes .. [#OB] Oliver Beckstein <oliver.beckstein@bioch.ox.ac.uk> Plugin classes -------------- .. autoclass:: CysAccessibility :members: .. autoclass:: HelixBundle :members: .. autoclass:: Distances :members: .. autoclass:: MinDistances :members: .. autoclass:: COM :members: .. autoclass:: Dihedrals :members: .. autoclass:: RMSF :members: .. autoclass:: RMSD :members: .. autoclass:: Energy :members: .. autoclass:: Trajectories :members: .. autoclass:: StripWater :members: .. autoclass:: ProteinOnly :members: .. autoclass:: Ls :members: Developer notes --------------- In principle all that needs to be done to automatically load plugins is to add their name to :data:`__plugins__`. See the source code for further comments and how the auto loading of plugins is done. .. autodata:: __plugins__ .. autodata:: __plugin_classes__

Submodules

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gromacs.analysis.plugins.com: Centre of mass ==============
gromacs.analysis.plugins.cysaccessibility: CysAccessibility plugin =======================
gromacs.analysis.plugins.dihedrals: Dihedrals plugin ================
gromacs.analysis.plugins.dist: ``analysis.plugins.dist`` --- Helper Class for ``g_dist`` =========================================================
gromacs.analysis.plugins.distances: Distance plugin ===============
gromacs.analysis.plugins.energy: Various terms from the energy (edr) file ========================================
gromacs.analysis.plugins.gridmatmd: :mod:`gromacs.analysis.plugins.gridmatmd` --- Lipid bilayer analysis helper ===========================================================================
gromacs.analysis.plugins.helixbundle: Helix bundle analysis =====================
gromacs.analysis.plugins.ls: ls plugin =========
gromacs.analysis.plugins.mindistances: MinDistance plugin ===============
gromacs.analysis.plugins.proteinonly: ProteinOnly ===========
gromacs.analysis.plugins.rmsd: RMSD calculation ================
gromacs.analysis.plugins.rmsf: RMSF calculation ================
gromacs.analysis.plugins.stripwater: StripWater ==========
gromacs.analysis.plugins.template_plugin: Template for a plugin ======================
gromacs.analysis.plugins.trajectories: Trajectories ============

Variables

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__plugins__ = ['CysAccessibility', 'Distances', 'MinDistances'...
All available plugin names are listed here.

__plugin_classes__ = dict([(p, M.__dict__ [p]) for p, M in _mo...
Gives access to all available plugin classes (or use the module __dict__)

Variables Details

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plugins

All available plugin names are listed here. Because this is used to automatically set up imports a module file must be named like the plugin class it contains but in all lower case. For example, the Distances plugin class is contained in the module distances (the file plugins/distances.py).

Value:

['CysAccessibility', 'Distances', 'MinDistances', 'Dihedrals', 'COM', 
'RMSF', 'RMSD', 'Energy', 'HelixBundle', 'Trajectories', 'StripWater',
 'ProteinOnly', 'Ls',]

__plugin_classes__

Gives access to all available plugin classes (or use the module __dict__)

Value:

dict([(p, M.__dict__ [p]) for p, M in _modules.items()])