Software suite for the prediction of physical interactions within protein complexes.
Version: 1.0

Web:      http://www.bio.ifi.lmu.de/Complexes/ProCope/
Contact:  Caroline Friedel (Caroline.Friedel@web.de)

Getting started
===============
After unpacking the download archive to a directory of your choice you can run
the command line tool by typing

java -jar substructures.jar

The following parameters are used (invoking without parameters prints this list):
Required parameters
  -n      Complete interaction network
  -m      Method
    mst   Maximum spanning tree method only
    emst  Extended maximum spanning tree method
    con   Baseline method calculating connected network

Optional parameters
  -a      Parameter alpha for extending the maximum spanning trees (default: alpha=1)
  -c      Protein complexes, if not given method will be applied to the complete network
  -sub    Options for finding subcomplexes (default: no subcomplex finding)
     false   no subcomplex finding
     true    use subcomplex finding

Input/Output options
  -o      Output file for the final network
  -omst   Output file for mst network (if given the mst network will be printed additionally for the emst method)
  -d      Output directory for complex networks (Networks written for each complex separately)



Requirements
============
This tool requires the Java 5.0 Runtime Environment or later which is freely 
available at http://www.java.com

This software package is based on the ProCope library, which is provided with
this release.


Package structure
=================

substructures.jar      Compiled binary 
README.txt             This file
lib/                   Library files containing the ProCope library (version 1.2)
src/                   Source codes


Copyright 2009, Teaching and Research Unit Bioinformatics, LMU Munich