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