:orphan: true

.. _fpocket-pocket-prediction:

###############################################################
Pocket prediction
###############################################################
The main program of the `FPocket <https://github.com/Discngine/fpocket>`_ package is fpocket and it is 
integrated in scipion-chem-fpocket as a protocol.

.. image:: ../../../../_static/images/plugins/fpocket/pocket-prediction/protocol.png
   :alt: Pocket prediction protocol
   :height: 400
   :align: center

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This protocol takes a ``AtomStruct`` as an input and predicts its pockets based on its concavities (based on alpha-spheres) and electrostatics. 
The parameters in the form control the alpha-spheres creation and their posterior clustering.

Input
----------------------------------------
.. include:: ../../../templates/plugins/input-help.rst

If you need more information we recommend you to check the `FPocket documentation <https://github.com/Discngine/fpocket/blob/master/doc/MANUAL.md>`_.

.. image:: ../../../../_static/images/plugins/fpocket/pocket-prediction/form.png
   :alt: Pocket prediction protocol
   :height: 400
   :align: center

|

The result of this protocol is a ``SetOfStructROIs`` object, containing the predicted pockets. You can inspect this pockets
using the **Analyze results** button or if you want to directly see the related files you will be able to find them
in the protocol's folder.

.. |testCommand| replace:: fpocket.tests.test_fpocket.TestFPocket
.. include:: ../../../templates/plugins/protocol-test.rst

Viewer
================================
The viewer for fpocket results include the Pymol General Viewer for ``SetOfStructROIs`` objects plus an specific viewer of
the alpha-spheres over the protein structure using VMD.

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|viewer|  |vmd|

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.. |viewer| image:: ../../../../_static/images/plugins/fpocket/pocket-prediction/viewer.png
   :alt: fpocket viewer
   :width: 50%

.. |vmd| image:: ../../../../_static/images/plugins/fpocket/pocket-prediction/vmd.png
   :alt: fpocket vmd
   :width: 45%

As for the rest of the Scipion object, you can also check **Table view** to visualize the stored parameters for each of
the items in the set.