:orphan: true

.. _pwchem-sasa-calculation:

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SASA calculation
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This protocol uses `BioPython <https://biopython.org/>`_ to calculate the `SASA <https://en.wikipedia.org/wiki/Accessible_surface_area>`_
(Solvent-Accessible Surface Area) for each residue in an ``AtomStruct``.

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

.. image:: ../../../../../_static/images/plugins/pwchem/virtual-drug-screening/sasa-calculation/form_1.png
   :alt: SASA calculation form 1
   :height: 400
   :align: center

|

.. image:: ../../../../../_static/images/plugins/pwchem/virtual-drug-screening/sasa-calculation/form_2.png
   :alt: SASA calculation form 2
   :height: 400
   :align: center

|

The result of this protocol is an ``AtomStruct`` containing the SASA value for each reside of the receptor, which can be
visualized in the Analyzed results window.

.. image:: ../../../../../_static/images/plugins/pwchem/virtual-drug-screening/sasa-calculation/output_1.png
   :alt: SASA calculation output 1
   :align: center

|

Additionally, the protocol can also output a ``SetOfSequenceROIs`` with those residues with SASA values higher/lower than a
threshold. The user can preview the SASA values in the protocol to define the threshold.

.. image:: ../../../../../_static/images/plugins/pwchem/virtual-drug-screening/sasa-calculation/output_2.png
   :alt: SASA calculation output 2
   :align: center

|

.. |testCommand| replace:: pwchem.tests.tests_attributes.TestCalculateSASA
.. include:: ../../../../templates/plugins/protocol-test.rst