ProtCon: Contact Map Trajectory Viewing Tool
author: Corban Rivera <cgrivera@vt.edu> (Graduate Student at Virginia Tech)
project supervision: Alexey Onufriev <alexey@cs.vt.edu> (Virginia Tech)

Requirements:
at least JAVA JRE version 1.4.2

Running the Example:
change directories to the location where you unzipped this tool, and type the command:
java -jar ProtCon.jar

FAQ:
Q:How do i change the axis label?
A:change the axisLabel atribute in the graphProperties file. If a graphProperties file doesn't exist, make one.  Then, add a line axisLabel=yourLabel

Q: My atom names are not being recognized by the trajectory viewer.
A: Add the mapping between your atom names and atom types to the atomName file. The program will try to associate atom names with atom types by looking for the first instance of an atom type in an atom name

Q: When i change a parameter using the legend *nothing happens*, what is going on?
A: After you change a parameter in the text field, it is necessary to press enter for your change to register.

Q: What are all of these .contact files, are they necessary?
A: They are necessary, but don't worry if some get deleted.  They will be regenerated if they are not present.  The .contacts files are speed optimizations. By preprocessing the contacts in files, the tool can process trajectories more quickly.

Q: What are the I, D and V checkboxes for?
A: The I checkbox shows contacts that intersect with the other
trajectories.  The D option only shows contacts that are different
from contacts in other directories.  The V option decides if a
trajectory is visible.

Q: What is contact_map_awk executable? 
A: This is simple script that computes the contacts from structure files 
in PQR format. Example: contact_map.awk < /pdb_examples/2mb5.pqr 
will produce the corresponding contact matrix that looks like: 
1   3  2.66144
1   137  2.17114
1   7  2.51797
.   .  .....
Where the 3rd number is the minimal distance between two residues in contact. 
