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Protein Data Bank PDB File Reading in Java Tool Example Code




Protein Data Bank PDB File Reading in Java Tool Example Code biojava api integration

package pdb;

import java.util.Map;
import org.biojava.bio.structure.AminoAcid;
import org.biojava.bio.structure.Chain;
import org.biojava.bio.structure.Group;
import org.biojava.bio.structure.GroupIterator;
import org.biojava.bio.structure.HetatomImpl;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.io.PDBFileReader;

/**
 *
 * @author Usman
 */
public class PDBInfo {

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
       // also works for gzip compressed files
 String ProjectPath= System.getProperties().getProperty("user.dir");
 String filename =  ProjectPath+"/SamplePDB/12E8.pdb" ;

 PDBFileReader pdbreader = new PDBFileReader();

 try{
     Structure struc = pdbreader.getStructure(filename);
   
     System.out.println(struc);

     GroupIterator gi = new GroupIterator(struc);

     while (gi.hasNext()){

           Group g = (Group) gi.next();
       
           if ( g instanceof AminoAcid ){
                System.out.println("Group********************************************");
               AminoAcid aa = (AminoAcid)g;
               Map sec = aa.getSecStruc();
               Chain  c = g.getParent();
               System.out.println("Chain name : "+c.getName() + " Group: " + g.getAtoms() + " Sec Strucure:" + sec);
           }
             if ( g instanceof HetatomImpl ){
                System.out.println("Group********************************************");
               HetatomImpl aa = (HetatomImpl)g;
         
               Chain  c = g.getParent();
               System.out.println("Chain name : "+c.getName() + " Group: " + g.getAtoms());
           }
     }

 } catch (Exception e) {
     e.printStackTrace();
 }
    }

}

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  • Title : Protein Data Bank PDB File Reading in Java Tool Example Code
  • Posted by :
  • Date : 04:16
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