[Biojava-l] Biojava goes 3D

[Andreas Prlic]

Hi everybody!

I am working at the Sanger Centre to extend the DAS protocol toward 
protein structures. Biojava so far did not contain many tools for 
protein structure bioinformatics, so I am trying to commit a few things...

Biojava now contains a PDB file parser and a few classes to represent 
three dimensional biological objects like protein structures, or DNA 
structures.

See: org.biojava.bio.structure


This is some example code:


Q: How can I parse a PDB file ?


import org.biojava.bio.structure.*;
import org.biojava.bio.structure.io.*;

public class simplePDB {
      public static void main(String args[]){
    String filename = "path/to/pdbfile.ent" ;
    PDBFileReader pdbreader = new PDBFileReader();

    try{
        Structure struc = pdbreader.getStructure(filename);
        System.out.println(struc);
    } catch (Exception e){
        e.printStackTrace();
    }

   }
}



Regards,
Andreas

-- 
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Andreas Prlic      Wellcome Trust Sanger Institute
                   Hinxton, Cambridge CB10 1SA, UK