PDB Alignment Java Code Example with Biojava | Structural alignment tools

 PDB Alignment Java Code Example with Biojava | Structural alignment tools online run in java

package pdb;

import java.io.FileOutputStream;
import java.io.PrintStream;
import javax.swing.JOptionPane;
import org.biojava.bio.structure.Structure;

import org.biojava.bio.structure.align.ClusterAltAligs;
import org.biojava.bio.structure.align.StructurePairAligner;
import org.biojava.bio.structure.align.pairwise.AlternativeAlignment;
import org.biojava.bio.structure.io.PDBFileReader;


/**
 *
 * @author Usman
 */
public class Alignment {
public static void main(String[] args){
 try{
            PDBFileReader pdbr = new PDBFileReader();
            String ProjectPath= System.getProperties().getProperty("user.dir");

            pdbr.setPath(ProjectPath+"/SamplePDB/");
           
           
            String pdb1 = "12E8";
            String pdb2 = "tnf";          
            String outputfile = "SamplePDB/alig_"+pdb1+"_"+pdb2+".pdb";
         

            // NO NEED TO DO CHANGE ANYTHING BELOW HERE...
           
            StructurePairAligner sc = new StructurePairAligner();          
           
            // step1 : read molecules
           
            System.out.println("aligning " + pdb1 + " vs. " + pdb2);
           
            Structure s1 = pdbr.getStructureById(pdb1);
            Structure s2 = pdbr.getStructureById(pdb2);                      
            // of course you do not have to use the full structures
            // you could also just use any set of atoms of your choice

            // step 2 : do the calculations
            sc.align(s1,s2);

            // if you want more control over the alignment parameters
            // use the StrucAligParameters
            //StrucAligParameters params = new StrucAligParameters();
            //params.setFragmentLength(8);    
            //sc.align(s1,s2,params);

         
           
            AlternativeAlignment[] aligs = sc.getAlignments();
           
            //cluster similar results together
            ClusterAltAligs.cluster(aligs);
           
           // print the result:
           // the AlternativeAlignment object gives  access to rotation matrices / shift vectors.
           for (int i=0 ; i< aligs.length; i ++){
               AlternativeAlignment aa = aligs[i];
               System.out.println(aa);            
           }


           
                     
            // convert AlternativeAlignment 1 to PDB file, so it can be opened with a viewer of your choice
            //(e.g. Jmol, Rasmol)
           
            if ( aligs.length > 0) {
                AlternativeAlignment aa1 =aligs[0];
                String pdbstr = aa1.toPDB(s1,s2);
               
                System.out.println("writing alignment to " + outputfile);
                FileOutputStream out= new FileOutputStream(outputfile);
                PrintStream p =  new PrintStream( out );
         JOptionPane.showMessageDialog(null, "Align Sucess");
                p.println (pdbstr);

                p.close();
                out.close();
            }
           
         
        } catch (Exception e){
            e.printStackTrace();
        }

}
}