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

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

    ~simtk.openmm.app.pdbfile.PDBFile
    ~simtk.openmm.app.pdbxfile.PDBxFile
    ~simtk.openmm.app.gromacsgrofile.GromacsGroFile
    ~simtk.openmm.app.gromacstopfile.GromacsTopFile
    ~simtk.openmm.app.amberinpcrdfile.AmberInpcrdFile
    ~simtk.openmm.app.amberprmtopfile.AmberPrmtopFile
    ~simtk.openmm.app.charmmpsffile.CharmmPsfFile
    ~simtk.openmm.app.charmmcrdfiles.CharmmRstFile
    ~simtk.openmm.app.charmmparameterset.CharmmParameterSet
    ~simtk.openmm.app.desmonddmsfile.DesmondDMSFile


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

    ~simtk.openmm.app.topology.Topology
    ~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 %}
    ~simtk.openmm.app.dcdfile.DCDFile