001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package demo; 022 023import java.io.IOException; 024import java.util.List; 025 026import org.biojava.nbio.structure.Structure; 027import org.biojava.nbio.structure.StructureException; 028import org.biojava.nbio.structure.align.util.AtomCache; 029import org.biojava.nbio.structure.secstruc.SecStrucElement; 030import org.biojava.nbio.structure.secstruc.SecStrucCalc; 031import org.biojava.nbio.structure.secstruc.SecStrucTools; 032 033/** 034 * Demonstration on how to use the Secondary Structure Prediction (DSSP) 035 * implementation in BioJava and obtain different SS representations and 036 * outputs. 037 * 038 * @author Aleix Lafita 039 * 040 */ 041public class DemoSecStrucCalc { 042 043 public static void main(String[] args) throws IOException, 044 StructureException { 045 046 String pdbID = "5pti"; 047 048 AtomCache cache = new AtomCache(); 049 050 // Load structure without any SS assignment 051 Structure s = cache.getStructure(pdbID); 052 053 // Predict and assign the SS of the Structure 054 SecStrucCalc ssp = new SecStrucCalc(); 055 ssp.calculate(s, true); 056 057 // Print the DSSP output 058 System.out.println("******DSSP output: "); 059 System.out.println(ssp.printDSSP()); 060 061 // Print the FASTA sequence of SS 062 System.out.println("\n******FASTA output: "); 063 System.out.println(ssp.printFASTA()); 064 065 // Print the Helix Summary 066 System.out.println("\n******Helix Summary: "); 067 System.out.println(ssp.printHelixSummary()); 068 069 // Obtain and print the SS elements of the Structure 070 List<SecStrucElement> sse = SecStrucTools.getSecStrucElements(s); 071 System.out.println("\n******SecStrucElements: "); 072 for (SecStrucElement e : sse) 073 System.out.println(e); 074 075 } 076}