.. _notebooks/static_code:

Static Code Examples
====================

These static code examples can also help you with your EncoderMap endeavors.

Cube Example
------------

This is the classic EncoderMap example. In this example, EncoderMap is used to project a 3D cube into 2D and back.

.. dropdown:: Cube Example

    .. literalinclude:: ../../../encodermap/examples/cube.py
        :language: python


Cube Distance Analysis
----------------------

In this example a way of visualizing the mapping of high-dimensional differences to low-dimensional distances is introduced.


.. dropdown:: Cube Distance Analysis

    .. literalinclude:: ../../../encodermap/examples/cube_distance_analysis.py
        :language: python


Trp Cage
--------

In this example, you can work with actual MD data from simulations of the Trp-cage protein.


.. dropdown:: Trp Cage

    .. literalinclude:: ../../../encodermap/examples/trp_cage.py
        :language: python


Dihedral to Cartesian diUbi
---------------------------

In this example, you can work with MD data from simulations of the M1-linked diUbi protein.

.. dropdown:: Data Generation

    .. literalinclude:: ../../../encodermap/examples/dihedral_to_cartesian_diubi.py
        :language: python


.. dropdown:: Data Analysis

    .. literalinclude:: ../../../encodermap/examples/dihedral_to_cartesian_diubi_analysis.py
        :language: python