Computes various statistics about a left or right handed beta helix
Java
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README
Reader3.class
Reader3.ctxt
Reader3.java
bluej.pkg
bluej.pkh
pdbConvert.class
pdbConvert.ctxt
pdbConvert.java

README

This was a project that I completed in the Summer of 2006 while doing an undergrad research project with Prof. Daniel Cox at UC: Davis. The results were later published in Prion: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634523/?tool=pubmed. I have not touched the code in years but decided to put it up on GitHub where it might find some love and I might have a chance to get back into it again.

/*
 * Reader3
 * Written by: Scott Clark, Oregon State University, University of California: Davis
 * (C) 2006
 *
 * This program reads in a *.pdb file for a left or right handed beta helix and computes various statistics about it including
 * The volume (total both approximated with a cylinder and Monte Carlo integration)
 * The volume of internal side chains
 * The hydrophobisity of the side chains that point in, as well as those that point out
 * As well as the hydrophobisity of the burried (non top, bottom, or loop residues)
 * The Ramachandran Plot of the helix (Phi-Psi angles)
 * The Ramachandran statistics (how many beta etc)
 * The Stacking information (what residues lie directly above and below eachother)
 * Possible sites of Hydrogen bonding
 *
 * It writes all of this information out to the terminal
 * And then makes a *.dat file called stats.dat with the information in it
 * along with the orientation of the individual resiudes
 * And in RAM.dat there is the plot if the phi-psi angles in the form:
 * residueNumber PHI PSI
 */