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//	Protein Contact Matrix Generator (PCMGen)
//Command line application to generate 2D contact matrices from 3D protein structures
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0. Table of Contents - $Date: 2015/25/06 (Updated 2018/23/11)
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0. Table of Contents
1. Protein Contact Map/ Matrix - Introduction
2. Installation / Usage
3. License Agreement

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1 Protein Contact Map/ Matrix - Introduction
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Thank you for downloading PCMGen 1.0

A protein contact matrix is 2D representation of the distances between amino acid
residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a
command line tool which takes protein 3D structures (PDB format files) as input
and computes contact distances between two chains (from single or two different
proteins). These matrix files can be further visualised as Contact Maps using other
visualization tools/ programs (like R-heatmaps).

Contact Maps can be used to understand protein's :
1. Secondary structures
2. Conformational arrangements
3. Surface interactions
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Arguments of PCMGen 1.0

1. PDB format protein files to be loaded (maximum files 2)
   Input comma separated PDB files with complete path
2. Enter chain number to be loaded as chain 1 (for first protein loaded)
3. Enter chain number to be loaded as chain 2 (for second protein -in case of two PDB files)
4. Default PCMGen parameters include Atom type = 'CA' , Distance cutoff = '8.0'
   If you wish to change the parameters they can be changed at this step
5. PCMGen can generate three types of matrix outputs;
	 1: Contact Distance Matrix (default)
	 2: Contact Matrix
	 3: Contact Score Matrix
   You can give input as 1,2 or 3 otherwise default (i.e. 1) is selected
6. Finally you can give output file into which you wish to store the matrix

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The package has been tested
	on the following JDK:
	    * >= JDK 1.6
	on the following OS:
	    * Linux

Developed by
- Sanket Desai { desai.sanket12@outlook.com }

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2. Installation / Usage
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- Download the JAR file (PCMGen1.0.jar)
- Use the following command to execute JAR file:

$ java -jar PCMGen1.0.jar

The output file contains a matrix, which can be imported in any visualization tools
to generate the graphical result or the Contact Map of the proteins.

For example using R (http://www.r-project.org/) following command generates a Contact Map
- contmap.out being the output file from PCMGen

> heatmap(as.matrix(read.table("contmap.out")), Rowv=NA, Colv=NA, col = heat.colors(3))

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3. License Agreement
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This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

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Cheers!

Sanket Desai {desai.sanket12@outlook.com}