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 */ 021 022package demo; 023 024import org.biojava.nbio.structure.Chain; 025import org.biojava.nbio.structure.Structure; 026import org.biojava.nbio.structure.io.mmcif.MMcifParser; 027import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer; 028import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser; 029 030import java.io.BufferedReader; 031import java.io.File; 032import java.io.FileInputStream; 033import java.io.IOException; 034import java.io.InputStreamReader; 035import java.io.PrintWriter; 036 037/** 038 * An example of how to convert mmCIF file to PDB file 039 * 040 * @author Jose Duarte 041 * 042 */ 043public class DemoMmcifToPdbConverter 044{ 045 046 public static void main(String[] args) throws Exception { 047 048 File inFile = new File(args[0]); 049 File outFile = new File(args[1]); 050 convert(inFile, outFile); 051 } 052 053 054 055 public static void convert(File inFile, File outFile) throws IOException { 056 057 MMcifParser parser = new SimpleMMcifParser(); 058 059 SimpleMMcifConsumer consumer = new SimpleMMcifConsumer(); 060 parser.addMMcifConsumer(consumer); 061 parser.parse(new BufferedReader(new InputStreamReader(new FileInputStream(inFile)))); 062 063 // now get the protein structure. 064 Structure cifStructure = consumer.getStructure(); 065 066 // and write it out as PDB format 067 PrintWriter pr = new PrintWriter(outFile); 068 for (Chain c : cifStructure.getChains()) { 069 // we can override the chain name, the mmCIF chain names might have more than 1 character 070 c.setName(c.getName().substring(0, 1)); 071 pr.print(c.toPDB()); 072 pr.println("TER"); 073 } 074 075 pr.close(); 076 077 078 } 079}