.. _Reference:

.. |C_alpha| replace:: C\ :sub:`α`

Module Reference
################

.. Undocumented modules
     __pkginfo__
     AtomEnvironment
     CCPNDataModel
     ComplexEnvironment
     CrystalEnvironment
     Database
     GroupEnvironment
     Features
     ForceFields.Amber.AmberData
     ForceFields.BondedInteractions
     ForceFields.ForceField
     ForceFields.NonBondedInteractions
     ForceFields.MMForceField
     MoleculeEnvironment
     NormalModes.Core
     PDBML
     ProteinEnvironment
     PyMOL
     surfm
     tess
     Skeleton
     ThreadManager
     Tk
     Tk.ProteinVisualization
     Utility

MMTK
=====
.. automodule:: MMTK

MMTK.Biopolymers
================ 
.. automodule::  MMTK.Biopolymers 
 
MMTK.Bonds
==========
.. automodule::  MMTK.Bonds 
 
MMTK.ChargeFit
==============
.. automodule::  MMTK.ChargeFit

MMTK.ChemicalObjects
====================
.. automodule::  MMTK.ChemicalObjects  
  
MMTK.Collections
================
.. automodule::  MMTK.Collections 

MMTK.ConfigIO
=============
.. automodule::  MMTK.ConfigIO 

MMTK.DCD
========
.. automodule::  MMTK.DCD
   :exclude-members: writePDB, writeDCD

MMTK.Deformation
================
.. automodule::  MMTK.Deformation

MMTK.Dynamics
=============
.. automodule::  MMTK.Dynamics

MMTK.Environment
================
.. automodule::  MMTK.Environment

MMTK.Field
==========
.. automodule::  MMTK.Field

MMTK.ForceFields
================

MMTK.ForceFields.AmberForceField
--------------------------------
.. automodule:: MMTK.ForceFields.Amber.AmberForceField 
   :no-members:

MMTK.ForceFields.Amber94ForceField
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autoclass:: MMTK.ForceFields.Amber.Amber94ForceField 

MMTK.ForceFields.Amber99ForceField
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autoclass:: MMTK.ForceFields.Amber.Amber99ForceField 

MMTK.ForceFields.OPLSForceField
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autoclass:: MMTK.ForceFields.Amber.OPLSForceField 

MMTK.ForceFields.AnisotropicNetworkForceField
---------------------------------------------
.. autoclass:: MMTK.ForceFields.ANMFF.AnisotropicNetworkForceField

MMTK.ForceFields.CalphaForceField
--------------------------------------
.. autoclass:: MMTK.ForceFields.CalphaFF.CalphaForceField

MMTK.ForceFields.DeformationForceField
--------------------------------------
.. autoclass:: MMTK.ForceFields.DeformationFF.DeformationForceField

MMTK.ForceFields.HarmonicForceField
-----------------------------------
.. autoclass:: MMTK.ForceFields.BondFF.HarmonicForceField

MMTK.ForceFields.LennardJonesForceField
---------------------------------------
.. autoclass:: MMTK.ForceFields.LennardJonesFF.LennardJonesForceField

MMTK.ForceFields.SPCEForceField
-------------------------------
.. autoclass:: MMTK.ForceFields.SPCEFF.SPCEForceField

MMTK.ForceFields.ForceFieldTest
------------------------------- 
.. automodule::  MMTK.ForceFields.ForceFieldTest 
 
MMTK.ForceFields.Restraints
---------------------------
.. automodule::  MMTK.ForceFields.Restraints

MMTK.FourierBasis
=================
.. automodule::  MMTK.FourierBasis  

MMTK.Geometry
=============
.. automodule::  MMTK.Geometry 

MMTK.InternalCoordinates
========================
.. automodule::  MMTK.InternalCoordinates
   :show-inheritance:

MMTK.Minimization
=================
.. automodule::  MMTK.Minimization

MMTK.MolecularSurface
=====================
.. automodule::  MMTK.MolecularSurface

MMTK.MoleculeFactory
====================
.. automodule::  MMTK.MoleculeFactory 

MMTK.NormalModes
================
.. automodule::  MMTK.NormalModes

MMTK.NormalModes.BrownianModes
------------------------------
.. automodule::  MMTK.NormalModes.BrownianModes 

MMTK.NormalModes.EnergeticModes
-------------------------------
.. automodule::  MMTK.NormalModes.EnergeticModes 
 
MMTK.NormalModes.VibrationalModes
---------------------------------
.. automodule::  MMTK.NormalModes.VibrationalModes 

MMTK.NucleicAcids
=================
.. automodule::  MMTK.NucleicAcids 
 
MMTK.PDB
========
.. automodule::  MMTK.PDB 
 
MMTK.PDBMoleculeFactory
-----------------------
.. automodule::  MMTK.PDBMoleculeFactory 
 
MMTK.ParticleProperties
=======================
.. automodule::  MMTK.ParticleProperties 
 
MMTK.ProteinFriction
====================
.. automodule::  MMTK.ProteinFriction 
 
MMTK.Proteins
=============
.. automodule::  MMTK.Proteins 

MMTK.Random
===========
.. automodule::  MMTK.Random

MMTK.Solvation
==============
.. automodule::  MMTK.Solvation

MMTK.Subspace
=============
.. automodule::  MMTK.Subspace

MMTK.Trajectory
===============
.. automodule::  MMTK.Trajectory  

MMTK.Units
==========
.. automodule::  MMTK.Units  

MMTK.Universe
=============
.. automodule::  MMTK.Universe  

MMTK.Visualization
==================
.. automodule::  MMTK.Visualization 
 
MMTK.XML
========
.. automodule::  MMTK.XML
