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The protein structure modules of BioJava.

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/*
 *                    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.Chain;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.cif.CifStructureConverter;

import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;

/**
 * An example of how to convert mmCIF file to PDB file
 *
 * @author Jose Duarte
 */
public class DemoMmcifToPdbConverter {
	public static void main(String[] args) throws Exception {
		File inFile = new File(args[0]);
		File outFile = new File(args[1]);
		convert(inFile, outFile);
	}

	public static void convert(File inFile, File outFile) throws IOException {
		// now get the protein structure.
		Structure cifStructure = CifStructureConverter.fromPath(inFile.toPath());

		// and write it out as PDB format
		PrintWriter pr = new PrintWriter(outFile);
		for (Chain c : cifStructure.getChains()) {
				// we can override the chain name, the mmCIF chain names might have more than 1 character
				c.setName(c.getName().substring(0, 1));
				pr.print(c.toPDB());
				pr.println("TER");
		}

		pr.close();
	}
}