Merge pull request #32 from Pranavkhade/GNM

GNM

README.md

@@ -52,6 +52,7 @@ WEB SERVERS
 * [Hinge Prediction Web Server](https://packman.bb.iastate.edu/)
 * [hd-ANM Web Server](https://hdanm.bb.iastate.edu/)
 * [Packing Entropy Web Server](https://packing-entropy.bb.iastate.edu/)
+* [DCI web server](https://dci.bb.iastate.edu/)
 
 RELATED RESEARCH ARTICLES
 -------------------------
@@ -60,6 +61,7 @@ RELATED RESEARCH ARTICLES
 * [Compliance](https://doi.org/10.1002/prot.25968)
 * [hd-ANM](https://doi.org/10.1016/j.bpj.2021.10.017)
 * [Packing Entropy](coming_soon)
+* [DCI](https://doi.org/10.1093/bioinformatics/btac159)
 
 ACKNOWLEDGEMENTS
 ----------------

docs/source/index.rst

@@ -25,13 +25,15 @@ Web Servers
 - `Hinge Prediction <https://packman.bb.iastate.edu/>`_
 - `hdANM <https://hdanm.bb.iastate.edu/>`_
 - `Packing Entropy <https://packing-entropy.bb.iastate.edu/>`_
+- `DCI <https://dci.bb.iastate.edu/>`_
 
 Publications
 ------------
 - PACKMAN-molecule (https://doi.org/10.1093/bioadv/vbac007)
 - Hinge Prediction (https://doi.org/10.1016/j.jmb.2019.11.018)
 - Structural Compliance (https://doi.org/10.1002/prot.25968)
 - hdANM (https://doi.org/10.1016/j.bpj.2021.10.017)
+- DCI (https://doi.org/10.1093/bioinformatics/btac159)
 
 Project Goal
 ------------

docs/source/tutorials/GNM.rst

@@ -0,0 +1,96 @@
+.. _tutorials_gnm_api:
+
+Using Gaussian Network Model (GNM)
+==================================
+
+This tutorial aims to get the user to familiarize with the concept of GNM API. GNM is available only in API.
+
+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).
+
+Note: If PACKMAN is not installed, please follow the link: https://github.com/Pranavkhade/PACKMAN
+
+
+Step 1: Loading Structure
+-------------------------
+
+In this section, we load the file containing the molecular structure. To understand in dept about the :mod:`packman.molecule` object, pelase visit :ref:`tutorials_molecule`
+
+Code Example::
+
+    from packman import molecule
+
+    #File loading 
+    mol = molecule.load_structure('1prw.cif')
+    #OR
+    #mol = molecule.load_structure('1prw.pdb')
+
+    #If the c-alpha atoms of the ALL the chains need to be studied,
+    #calpha = [i for i in mol[0].get_calpha()  if i is not None]
+
+    #If the c-alpha atoms of the specific chain 'A' needs to be studied,
+    calpha = [i for i in mol[0]['A'].get_calpha() if i is not None]
+
+
+Step 2: Loading the GNM
+------------------------
+
+The GNM object has one required argument (set of atoms) and several optional arguments that can be changed according to the user's needs. Please check :mod:`packman.gnm.GNM` for more details.
+
+Code Example::
+
+    from packman.gnm import GNM
+    model = GNM(calpha)
+
+
+Step 3: Calculating Kirchhoff's Matrix
+--------------------------------------
+
+Please refer to the publication mentioned at the top of this page for more details.
+
+In future, we will allow users to provide amino acid residue specific molecular masses, atom specific atomic masses, or any other type of weights that needs to be assigned to the atoms/residues. To give custom residue-specific values as mass to the method, simply create a standard python dictionary with 20 standard amino acids as keys and assign corresponding values to it (mass_type parameter).
+
+Code Example::
+
+    model.calculate_kirchhoff()
+    kirchhoff = model.get_kirchhoff()
+    print(kirchhoff)
+
+
+Step 4: Eigenvalue decomposition
+--------------------------------
+
+The Eigenvalue decomposition is carried out using the Kirchhoff's matrix and mass matrix to calculate eigenvalues and eigenvectors.
+
+Code Example::
+
+    model.calculate_decomposition()
+
+Eigenvalues and Eigenvectors. can be obtained by::
+
+	model.get_eigenvalues()
+	model.get_eigenvectors()
+
+Respectively. Other calculated attributes and properties of the hd-ANM built can be obtained by its 'get' methods. Please refer to :mod:`packman.gnm.GNM` documentation for more details.
+
+
+Step 6: Getting other data from GNM
+-----------------------------------
+
+This step demonstrates how one can obtain other data from GNM.
+
+
+Code Example::
+
+    model.calculate_fluctuations()
+    print(model.get_fluctuations())
+
+    model.calculate_crosscorrelation()
+    print(model.get_pseudoinverse())
+
+    from matplotlib import pyplot as plt
+    plt.imshow( model.get_crosscorrelation(), cmap='hot')
+    plt.show()

docs/source/tutorials/main.rst

@@ -26,6 +26,7 @@ Application Programming Interface (API)
 #. :ref:`tutorials_compliance`
 #. :ref:`tutorials_hdANM`
 #. :ref:`tutorials_entropy_api`
+#. :ref:`tutorials_gnm_api`
 
 Utilities (API)
 ---------------

docs/source/tutorials/molecule.rst

@@ -11,7 +11,7 @@ Citation:
 .. image:: ../../_static/gallary/molecule_graph.png
 
 
-Figure 1. The object hierarchy of the :mod:`packman.molecule` submodule.
+Figure 1. The object hierarchy of the :mod:`packman.molecule` submodule. (Figure taken from the paper cited at the top)
 
 
 Downloading & Loading

packman/__init__.py

@@ -15,4 +15,4 @@
 
 
 #VERSION CHANGE HERE CHANGES IT IN docs AND setup.py
-__version__='1.4.4'
+__version__='1.4.5'

packman/anm/anm.py

@@ -50,12 +50,7 @@ class ANM:
             gamma (float, optional): Spring Constant Value.                                      Defaults to 1.0.
             dr (float, optional)   : Distance Cutoff.                                            Defaults to 15.0.
             power (int, optional)  : Power of distance (mainly useful in non-parametric mode).   Defaults to 0.
-            pf (None, optional)    : Parameter free model?.                                      Defaults to None.
-        
-        Raises:
-            Exception: [description]
-            Exception: [description]
-            Exception: [description]
+            pf (None, optional)    : Parameter free model. (Check the dr and power params)       Defaults to None.
         """
 
     def __init__(self, atoms, gamma=1.0, dr=15.0, power=0, pf=None):

packman/bin/GUI.py

@@ -347,28 +347,28 @@ def write_hng_file():
 
                     select_count += 1
                     if(ALL_RESIDUES[ChainOfHinge][0]!=hinge_res_ids[0]):
-                        fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(ALL_RESIDUES[ChainOfHinge][0])+':'+str(hinge_res_ids[0]-1)+'\n' )
-                        fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'H'+str(select_count) +'\t'+ str(hinge_res_ids[0])+':'+str(hinge_res_ids[-1])+'\n' )
+                        fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(ALL_RESIDUES[ChainOfHinge][0])+':'+str(hinge_res_ids[0]-1)+'\n' )
+                        fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'H'+str(select_count) +'\t'+ str(hinge_res_ids[0])+':'+str(hinge_res_ids[-1])+'\n' )
                     else:
-                        fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'H'+str(select_count) +'\t'+ str(hinge_res_ids[0])+':'+str(hinge_res_ids[-1])+'\n' )
+                        fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'H'+str(select_count) +'\t'+ str(hinge_res_ids[0])+':'+str(hinge_res_ids[-1])+'\n' )
                     last_hinge_end = hinge_res_ids[-1]
                 elif( i.get() ):
                     hinge_res_ids = sorted([j.get_id() for j in current_hinge.get_elements()])
                     select_count += 1
-                    fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(last_hinge_end+1)+':'+str(hinge_res_ids[0]-1)+'\n' )
-                    fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'H'+str(select_count) +'\t'+ str(hinge_res_ids[0])+':'+str(hinge_res_ids[-1])+'\n' )
+                    fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(last_hinge_end+1)+':'+str(hinge_res_ids[0]-1)+'\n' )
+                    fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'H'+str(select_count) +'\t'+ str(hinge_res_ids[0])+':'+str(hinge_res_ids[-1])+'\n' )
                     last_hinge_end = hinge_res_ids[-1]
                 try:
                     if(ChainOfHinge != All_Hinges[numi+1].get_elements()[0].get_parent().get_id() ):
                         select_count += 1
-                        fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(last_hinge_end+1)+':'+str(ALL_RESIDUES[ChainOfHinge][-1])+'\n' )
+                        fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(last_hinge_end+1)+':'+str(ALL_RESIDUES[ChainOfHinge][-1])+'\n' )
                         last_hinge_end = 0
                 except:
                     None
 
             if(last_hinge_end != ALL_RESIDUES[ChainOfHinge][-1]):
                 select_count += 1
-                fh.write(self.Box1.get()+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(last_hinge_end+1)+':'+str(ALL_RESIDUES[ChainOfHinge][-1])+'\n' )
+                fh.write(self.Box1.get().split('/')[-1].replace(' ','+')+'_'+ChainOfHinge +'\t'+ 'D'+str(select_count) +'\t'+ str(last_hinge_end+1)+':'+str(ALL_RESIDUES[ChainOfHinge][-1])+'\n' )
             fh.flush()
             fh.close()
             showinfo('Notification',self.output_filename.get()+' file saved!')

packman/gnm/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# Author: Pranav Khade, Iowa State University
+# Please read the project licence file for the Copyrights.
+
+"""The 'packman.gnm' module is a collection of anm methods and applications built on packman.molecule API.
+
+Notes:
+    * Current apps list: - packman.gnm.GNM
+    * 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
+
+"""
+from .gnm import GNM