Documentation
=============

You can find here documentation for most of the modules that HTMD provides. One can either explore the tree of contents
or, if looking for a particular module/class/function, use the search box on the sidebar.

Contents:

.. toctree::
    :maxdepth: 2

    Molecule <../moleculekit/moleculekit.molecule.rst>
    Building <building>
    MD Simulations <simulation>
    Simulation List <htmd.simlist>
    Projections <projections>
    Dimensionality Reduction <dimreduction>
    Clustering <clustering>
    Markov state models <htmd.model>
    Kinetics <htmd.kinetics>