New demo for mmcif to pdb conversion

josemduarte · josemduarte · commit f596afbe3965 · 2017-12-06T22:07:35.000-08:00
diff --git a/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java b/biojava-structure/src/main/java/demo/DemoMmcifToPdbConverter.java
@@ -0,0 +1,79 @@
+/*
+ *                    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.mmcif.MMcifParser;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+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 {
+				 
+        MMcifParser parser = new SimpleMMcifParser();
+ 
+        SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();       
+        parser.addMMcifConsumer(consumer);
+        parser.parse(new BufferedReader(new InputStreamReader(new FileInputStream(inFile))));
+        
+        // now get the protein structure.
+        Structure cifStructure = consumer.getStructure();
+
+        // 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();
+		
+
+	}
+}
