mdance.cluster
======================

mdance.cluster.nani
--------------------------

.. automodule:: mdance.cluster.nani
   :members:
   :undoc-members:
   :show-inheritance:

mdance.cluster.equal
--------------------------
.. automodule:: mdance.cluster.equal
   :members:
   :undoc-members:
   :show-inheritance:

mdance.cluster.helm
--------------------------
.. automodule:: mdance.cluster.helm
   :members:
   :undoc-members:
   :show-inheritance:

mdance.cluster.shine
--------------------------
.. automodule:: mdance.cluster.shine
   :members:
   :undoc-members:
   :show-inheritance:


mdance.cli
====================

mdance.cli.prime_sim
-----------------------

.. automodule:: mdance.cli.prime_sim
   :members:
   :undoc-members:
   :show-inheritance:

mdance.cli.prime_rep
-----------------------

.. automodule:: mdance.cli.prime_rep
   :members:
   :undoc-members:
   :show-inheritance:

mdance.data
====================

mdance.data.top
---------------

Sample topology files for testing Molecular Dynamics systems. Works with ``mdance.data.traj``.

mdance.data.traj
----------------

Sample trajectory files for testing Molecular Dynamics systems. Works with ``mdance.data.top``.

mdance.data.sim_traj_numpy
--------------------------

Numpy array of sample trajectory data for testing Molecular Dynamics systems. Extracted from ``mdance.data.top`` and ``mdance.data.traj``.

mdance.data.cc_sim
---------------------

Complementary similarity of sample trajectory data for testing Molecular Dynamics systems. 

mdance.data.trimmed_sim
---------------------

Trimmed outliers of sample trajectory data for testing Molecular Dynamics systems.

mdance.data.blob_disk
---------------------

2D dataset with the multiple blobs shaped of a disk for testing 2D systems.

mdance.data.diamonds
---------------------
2D dataset shape of nine diamonds for testing 2D systems.

mdance.data.ellipses
---------------------
2D dataset shape of multiple ellipses for testing 2D systems.

mdance.inputs
=====================

mdance.inputs.preprocess
-------------------------------

.. autofunction:: mdance.inputs.preprocess.gen_traj_numpy
.. autofunction:: mdance.inputs.preprocess.normalize_file



mdance.outputs
======================

mdance.outputs.postprocess
---------------------------------

.. automodule:: mdance.outputs.postprocess
   :members:
   :undoc-members:
   :show-inheritance:


mdance.prime
====================

mdance.prime.sim\_calc
-----------------------------

.. automodule:: mdance.prime.sim_calc
   :members:
   :undoc-members:
   :show-inheritance:


mdance.prime.rep\_frames
-------------------------------

.. automodule:: mdance.prime.rep_frames
   :members:
   :undoc-members:
   :show-inheritance:


mdance.tools
====================

mdance.tools.bts
-----------------------

.. automodule:: mdance.tools.bts
   :members:
   :undoc-members:
   :show-inheritance:

mdance.tools.isim
---------------------------------

.. automodule:: mdance.tools.isim
   :members:
   :undoc-members:
   :show-inheritance:

mdance.tools.esim
---------------------------------

.. automodule:: mdance.tools.esim
   :members:
   :undoc-members:
   :show-inheritance: