.. _app :

Application Layer
=================

Loaders and Setup
~~~~~~~~~~~~~~~~~
.. autosummary::
    :toctree: generated/
    :template: class.rst

{% for fileclass in fileclasses %}
    ~{{ fileclass }}
{% endfor %}


Representation and Manipulation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. autosummary::
    :toctree: generated/
    :template: class.rst

    ~simtk.openmm.app.topology.Topology
    ~simtk.openmm.app.topology.Chain
    ~simtk.openmm.app.topology.Residue
    ~simtk.openmm.app.topology.Atom
    ~simtk.openmm.app.modeller.Modeller

Simulation
~~~~~~~~~~
.. autosummary::
    :toctree: generated/
    :template: class.rst

    ~simtk.openmm.app.forcefield.ForceField
    ~simtk.openmm.app.simulation.Simulation


Reporting Output
~~~~~~~~~~~~~~~~
.. autosummary::
    :toctree: generated/
    :template: class.rst

{% for reporter in reporters %}
    ~{{ reporter }}
{% endfor %}


Extras
~~~~~~
.. autosummary::
    :toctree: generated/
    :template: class.rst

    {% for extra in app_extras %}
    ~{{ extra }}
    {% endfor %}

Units
~~~~~~
.. autosummary::
    :toctree: generated/
    :template: class.rst
    :nosignatures:

    {% for unit in units %}
    ~{{ unit }}
    {% endfor %}