Merge pull request #54 from Pranavkhade/dev

documentation changes 1
Pranavkhade · Oct 9, 2023 · b9827ce · b9827ce
2 parents ffa102b + f791284
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diff --git a/docs/source/rd-anm_run.rst b/docs/source/rd-anm_run.rst
diff --git a/docs/source/tutorials/GNM.rst b/docs/source/tutorials/GNM.rst
@@ -10,6 +10,7 @@ How to cite::
     - For original GNM: Tirion, M.M. (1996). "Large amplitude elastic motions in proteins from a single-parameter, atomic analysis". Phys. Rev. Lett. 77 (9): 1905-1908.
     - For using GNM with this package: Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics, Bioinformatics Advances, 2022;, vbac007, https://doi.org/10.1093/bioadv/vbac007
     - For 7.8 Angstrom cutoff: Yang, L., Song, G. & Jernigan, R. L. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A 106, 12347-52 (2009).
+    - For PACKMAN molecule API: Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python toolbox for structural bioinformatics, Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac007, https://doi.org/10.1093/bioadv/vbac007
 
 Note: If PACKMAN is not installed, please follow the link: https://github.com/Pranavkhade/PACKMAN
 

diff --git a/docs/source/tutorials/alpha_shape.rst b/docs/source/tutorials/alpha_shape.rst
@@ -4,7 +4,11 @@ Calculate Alpha Shape of the Protein
 ====================================
 
 This tutorial is to show how an API user can get the alpha shape of a protein.
+
+Citation::
     
+    Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python toolbox for structural bioinformatics,
+    Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac007, https://doi.org/10.1093/bioadv/vbac007
 
 Step 1
 ------

diff --git a/docs/source/tutorials/bond_rotate.rst b/docs/source/tutorials/bond_rotate.rst
@@ -4,7 +4,11 @@ Rotate specific bonds
 =====================
 
 This tutorial helps users how to rotate specific bonds using Molecule submodule
+
+Citation::
     
+    Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python toolbox for structural bioinformatics,
+    Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac007, https://doi.org/10.1093/bioadv/vbac007
 
 Step 1
 ------

diff --git a/docs/source/tutorials/dci_cli.rst b/docs/source/tutorials/dci_cli.rst
@@ -10,7 +10,9 @@ PACKMAN DCI Analysis Web Server:
 
 How to cite::
 
-    Paper Under Review.
+    Kumar, A., Khade, P. M., Dorman, K. S., & Jernigan, R. L. (2022). Coarse-graining protein structures into their 
+    dynamic communities with DCI, a dynamic community identifier. 
+    Bioinformatics, 38(10). https://doi.org/10.1093/bioinformatics/btac159
 
 
 CLI INSTRUCTIONS

diff --git a/docs/source/tutorials/entropy_api.rst b/docs/source/tutorials/entropy_api.rst
@@ -9,7 +9,8 @@ PACKMAN Entropy Analysis Web Server: https://packing-entropy.bb.iastate.edu/
 
 How to cite::
 
-    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
+    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.
 

diff --git a/docs/source/tutorials/entropy_cli.rst b/docs/source/tutorials/entropy_cli.rst
@@ -10,7 +10,8 @@ PACKMAN Entropy Analysis Web Server: * Packing Entropy: https://packing-entropy.
 
 How to cite::
 
-    Paper Under Review.
+    Khade, P. M., & Jernigan, R. L. (2022). Entropies Derived from the Packing Geometries within a Single Protein Structure. 
+    ACS Omega, 7(24). https://doi.org/10.1021/acsomega.2c00999
 
 
 CLI INSTRUCTIONS

diff --git a/docs/source/tutorials/molecule.rst b/docs/source/tutorials/molecule.rst
@@ -5,8 +5,9 @@ Using 'Molecule' to load and manupulate molecular structures. (Basics)
 
 This module is base for all the algorithms and programs written in the PACKMAN. This tutorial aims to give an idea about the information flow and hierarchy in the objects. Once the object's basic understanding is developed, all the objects' advanced special features can be explored on their object documentation page.
 
-Citation:
-    Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics, Bioinformatics Advances, 2022;, vbac007, https://doi.org/10.1093/bioadv/vbac007
+Citation::
+        Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics,
+        Bioinformatics Advances, 2022;, vbac007, https://doi.org/10.1093/bioadv/vbac007
 
 .. image:: ../../_static/gallary/molecule_graph.png
 

diff --git a/packman/anm/__init__.py b/packman/anm/__init__.py
@@ -1,25 +1,7 @@
 # -*- coding: utf-8 -*-
-# Author: Pranav Khade, Iowa State University
-# Please read the project licence file for the Copyrights.
-
-"""The 'packman.anm' module is a collection of anm methods and applications built on packman.molecule API.
-
-Notes:
-    * Current apps list: - packman.anm.ANM, packman.anm.RDANM
-    * Cite the following paper:
-        
-
-Example:
-    * Review the packman.bin.PACKMAN.py file for the app use.
-
-Todo:
-    * Add new features
-    * Add citations in the note
-    * Use ``sphinx.ext.todo`` extension
-    * Clean the code
-    * Redesign print statements
-    * Add Tutorial Link
-
+# Author: Pranav Khade
+"""The 'packman.anm' module is a collection of Anisotropic Network Model (ANM) based methods and applications built on packman.molecule API.
 """
+
 from .anm import ANM
 from .hd_anm import hdANM