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entropy tutorial updated
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Pranavkhade authored Apr 4, 2023
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Expand Up @@ -5,11 +5,11 @@ Entropy Analysis API
====================
This tutorial familiarises users with the Application Programming Interface (API) of the Entropy Analysis. The same functionality is also available in the PACKMAN CLI ( :ref:`tutorials_entropy_cli` ) and GUI (:ref:`tutorials_gui`).

PACKMAN Entropy Analysis Web Server: <link>
PACKMAN Entropy Analysis Web Server: https://packing-entropy.bb.iastate.edu/

How to cite::

Paper Under Review.
Pranav M. Khade and Robert L. Jernigan. Entropies Derived from the Packing Geometries within a Single Protein Structure. ACS Omega 2022 7 (24), 20719-20730 DOI: 10.1021/acsomega.2c00999

There are two ways the entropy can be calculated. The second way is when the user explicitly wants to leave specific atoms/residues out of the entropy calculation. Chain exclusion can be done via the first method as well. Also, the user has access to the extra get, set, and calculate methods of the Entropy objects using the second way.

Expand Down Expand Up @@ -118,4 +118,4 @@ Step 3
~~~~~~
Please note that the get_entropy (This step) is just a retrieval method. The way entropy is calculated defined in Step 2.

The entropy can be retrieved using the same procedure explained in Step 3 of the first way. However, the PackingEntropy also has get, set, and calculate methods that can be used. Please check the :mod:`packman.entropy.PackingEntropy` for more details.
The entropy can be retrieved using the same procedure explained in Step 3 of the first way. However, the PackingEntropy also has get, set, and calculate methods that can be used. Please check the :mod:`packman.entropy.PackingEntropy` for more details.

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