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The protein structure modules of BioJava.

There is a newer version: 7.1.3

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package demo;


import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.StructureIO;


/** Example of how to load PDB files using the AtomCache class.
 *
 * @author Andreas Prlic
 *
 */
public class DemoAtomCache {
	public static void main(String[] args){
		demoAtomCache();
		demoStructureIO();

	}

	@SuppressWarnings("unused")
	private static void demoStructureIO()  {


		try {
			Structure s1 = StructureIO.getStructure("4hhb");

			Structure bioAssembly = StructureIO.getBiologicalAssembly("1stp",1);

			// do something with them...
		} catch (Exception e){
			e.printStackTrace();
		}

	}

	private static void demoAtomCache() {
		AtomCache cache = new AtomCache();

		FileParsingParameters params = cache.getFileParsingParams();

		params.setAlignSeqRes(true);
		params.setHeaderOnly(false);
		params.setParseCAOnly(false);
		params.setParseSecStruc(false);

		String[] pdbIDs = new String[]{"4hhb", "1cdg","5pti","1gav", "WRONGID" };

		for (String pdbID : pdbIDs){

			try {
				Structure s = cache.getStructure(pdbID);
				if ( s == null) {
					System.out.println("could not find structure " + pdbID);
					continue;
				}
				// do something with the structure
				System.out.println(s);

			} catch (Exception e){
				// something crazy happened...
				System.err.println("Can't load structure " + pdbID + " reason: " + e.getMessage());
				//e.printStackTrace();
			}
		}

	}
}