Modules and submodules of the bioen Python package
==================================================

.. toctree::
   :maxdepth: 2


bioen
-----

.. automodule:: bioen
   :members:
   :undoc-members:


.. TODO: add other modules


bioen.version
-------------

.. automodule:: bioen.version
   :members:
   :undoc-members:


bioen.analyze
-------------

.. automodule:: bioen.analyze
   :members:
   :undoc-members:


bioen.analyze.procedure
-----------------------

.. automodule:: bioen.analyze.procedure
   :members:
   :undoc-members:


bioen.analyze.run_bioen
-----------------------

.. automodule:: bioen.analyze.run_bioen
   :members:
   :undoc-members:


bioen.analyze.utils
-------------------

.. automodule:: bioen.analyze.utils
   :members:
   :undoc-members:


bioen.analyze.observables
-------------------------

.. automodule:: bioen.analyze.observables
   :members:
   :undoc-members:


bioen.analyze.observables.observables
-------------------------------------

.. automodule:: bioen.analyze.observables.observables
   :members:
   :undoc-members:


bioen.analyze.observables.deer
------------------------------

.. automodule:: bioen.analyze.observables.deer
   :members:
   :undoc-members:


bioen.analyze.observables.deer.deer
-----------------------------------

.. automodule:: bioen.analyze.observables.deer.deer
   :members:
   :undoc-members:


bioen.analyze.observables.generic
---------------------------------

.. automodule:: bioen.analyze.observables.generic
   :members:
   :undoc-members:


bioen.analyze.observables.generic.generic
-----------------------------------------

.. automodule:: bioen.analyze.observables.generic.generic
   :members:
   :undoc-members:


bioen.analyze.observables.scattering
------------------------------------

.. automodule:: bioen.analyze.observables.scattering
   :members:
   :undoc-members:


bioen.analyze.observables.scattering.scattering
-----------------------------------------------

.. automodule:: bioen.analyze.observables.scattering.scattering
   :members:
   :undoc-members:


bioen.analyze.show_plot
-----------------------

.. automodule:: bioen.analyze.show_plot
   :members:
   :undoc-members:


bioen.analyze.show_plot.show_plot
---------------------------------

.. automodule:: bioen.analyze.show_plot.show_plot
   :members:
   :undoc-members:


bioen.optimize
-----------------------

.. automodule:: bioen.optimize
   :members:
   :undoc-members:


bioen.optimize.minimize
-----------------------

.. automodule:: bioen.optimize.minimize
   :members:
   :undoc-members:


bioen.optimize.log_weights
--------------------------

.. automodule:: bioen.optimize.log_weights
   :members:
   :undoc-members:


bioen.optimize.forces
---------------------

.. automodule:: bioen.optimize.forces
   :members:
   :undoc-members:


bioen.optimize.util
-------------------

.. automodule:: bioen.optimize.util
   :members:
   :undoc-members:


bioen.optimize.ext.c_bioen
--------------------------

.. automodule:: bioen.optimize.ext.c_bioen
   :members:
   :undoc-members:
