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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 */