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.. 
    === UCSF ChimeraX Copyright ===
    Copyright 2016 Regents of the University of California.
    All rights reserved.  This software provided pursuant to a
    license agreement containing restrictions on its disclosure,
    duplication and use.  For details see:
    http://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
    This notice must be embedded in or attached to all copies,
    including partial copies, of the software or any revisions
    or derivations thereof.
    === UCSF ChimeraX Copyright ===

.. _ChimeraX Python Modules:

Python Modules
==============

Atomic Structures
-----------------

.. toctree::
   :maxdepth: 1
              
   modules/atomic/atomic.rst

   modules/mmcif/mmcif.rst

   modules/atomic/pdbio.rst

ChimeraX Core
-------------

These modules are in chimerax.core.

Commands and Tools

.. toctree::
    :maxdepth: 1

    modules/core/commands/commands.rst

    modules/core/tools.rst

    modules/core/toolshed.rst

Data
  
.. toctree::
    :maxdepth: 1

    modules/core/models.rst

    modules/core/objects.rst

    modules/core/session.rst

Files

.. toctree::
    :maxdepth: 1

    modules/core/fetch.rst

    modules/core/history.rst

    modules/core/safesave.rst

    modules/core/serialize.rst

    modules/core/settings.rst

Notifications

.. toctree::
    :maxdepth: 1

    modules/core/data_events.rst

    modules/core/logger.rst

    modules/core/tasks.rst

    modules/core/triggerset.rst

Utility

.. toctree::
    :maxdepth: 1

    modules/core/orderedset.rst

    modules/core/utils.rst

Generic I/O
-----------

.. toctree::
    :maxdepth: 1

    modules/io/io.rst

Geometry
--------
  
.. toctree::
    :maxdepth: 1

    modules/geometry/geometry.rst


Graphics
--------
  
.. toctree::
    :maxdepth: 1

    modules/graphics/graphics.rst

Open and Save
-------------

.. toctree::
    :maxdepth: 1

    modules/open_command/open.rst

    modules/save_command/save.rst
    

Surfaces
--------

.. toctree::
    :maxdepth: 1

    modules/surface/surface.rst

    
User Interface
--------------

.. toctree::
    :maxdepth: 1

    modules/ui/gui.rst

    modules/scheme_mgr/scheme_mgr.rst

    modules/toolbar/toolbar.rst
    
Volume Data
-----------

.. toctree::
    :maxdepth: 1

    modules/map/map.rst

    modules/map_fit/fitmap.rst

    modules/segment/segment.rst