.. _app :

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

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


    ~simtk.openmm.app.amberinpcrdfile.AmberInpcrdFile

    ~simtk.openmm.app.amberprmtopfile.AmberPrmtopFile

    ~simtk.openmm.app.charmmcrdfiles.CharmmCrdFile

    ~simtk.openmm.app.charmmparameterset.CharmmParameterSet

    ~simtk.openmm.app.charmmpsffile.CharmmPsfFile

    ~simtk.openmm.app.charmmcrdfiles.CharmmRstFile

    ~simtk.openmm.app.dcdfile.DCDFile

    ~simtk.openmm.app.desmonddmsfile.DesmondDMSFile

    ~simtk.openmm.app.gromacsgrofile.GromacsGroFile

    ~simtk.openmm.app.gromacstopfile.GromacsTopFile

    ~simtk.openmm.app.pdbfile.PDBFile

    ~simtk.openmm.app.pdbxfile.PDBxFile



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


    ~simtk.openmm.app.checkpointreporter.CheckpointReporter

    ~simtk.openmm.app.dcdreporter.DCDReporter

    ~simtk.openmm.app.pdbreporter.PDBReporter

    ~simtk.openmm.app.pdbreporter.PDBxReporter

    ~simtk.openmm.app.statedatareporter.StateDataReporter



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

    
    ~simtk.openmm.app.internal.charmm.exceptions.CharmmPSFWarning
    
    ~simtk.openmm.app.element.Element
    

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

    
    ~simtk.unit.basedimension.BaseDimension
    
    ~simtk.unit.baseunit.BaseUnit
    
    ~simtk.unit.quantity.Quantity
    
    ~simtk.unit.unit.ScaledUnit
    
    ~simtk.unit.prefix.SiPrefix
    
    ~simtk.unit.unit.Unit
    
    ~simtk.unit.unit.UnitSystem