Added example script for version 0.2.1

examples/example_script_v0.2.1.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+#Purpose     : To show basic usage of correlationplus Python package on a Unix system.#              
+#              The script has been tested  with 0.2.1 version of correlationplus on
+#              CentOS 7 and MacOS Catalina.
+#              Please visit https://correlationplus.readthedocs.io/en/latest/quickstart.html
+#              for the most uptodate usage information and more examples. 
+#Prerequisite: You must have installed correlationplus. Otherwise, try 'pip install correlationplus'.
+#Author      : Mustafa Tekpinar
+#Email       : [email protected]
+#Date        : August 9, 2021
+#Licence     : LGPL v3
+
+#We recommend to run it in a completely empty folder.
+#The script will try to download a monomer of apo SARS-CoV-2 main protease pdb file 6y2e.pdb
+#with curl. If you have wget, try to replace curl with wget.
+
+#Step 0: Download 6y2e.pdb with curl or wget.
+#If you want, you can download your own pdb as well.
+#In this case, do not forget to comment wget and curl lines.
+#In addition, correct the protein variable in the following line.
+protein="6y2e"
+
+
+#wget https://files.rcsb.org/download/${protein}.pdb
+curl https://files.rcsb.org/download/${protein}.pdb -o ${protein}.pdb
+
+if test -f "${protein}.pdb"
+then
+    echo "${protein}.pdb was downloaded successfully."
+
+    #Step 1: Calculate normalized LMI matrix from CG-ANM
+    echo "Calculating normalized LMI matrix from CG-ANM."
+    correlationplus calculate -p ${protein}.pdb -t nlmi
+
+    #Step 2: Visualize the normalized LMI matrix
+    echo "Visualizing normalized LMI matrix"
+    echo "Only high correlations (>=0.75) will be projected onto the protein!"
+    correlationplus visualize -p ${protein}.pdb -i nLMI.dat -t nlmi -o nlmi -v 0.75
+
+    #Step 3: Network analysis of the normalized LMI matrix
+    echo "Analyzing dynamical network from the normalized LMI matrix"
+    correlationplus analyze -p ${protein}.pdb -i nLMI.dat -t nlmi -o network
+
+    #Voila! You have many pml and tcl files.
+    #You can open pml files as
+    #pymol network_eigenvector.pml
+
+    #If you are a VMD person
+    #vmd -e network_eigenvector.tcl
+
+    #Please note that pymol or vmd has to be in your path to run these commands.
+    #Any other problem?
+    #Read the documentation at https://correlationplus.readthedocs.io/en/latest/quickstart.html
+    #Or email me at [email protected]!
+
+else    
+        echo "ERROR: ${protein}.pdb file is not in the directory!"
+	echo "wget or curl failed to download the protein!"
+fi