How To Convert Pdb.Gz To Pdb Directly In In Java

Question

[potassiumiodide0990]

import java.util.Map; 
import javax.swing.text.Position; 
import org.biojava.bio.structure.*; 
import org.biojava.bio.structure.io.PDBFileReader; 
public class PDBFile {
    public PDBFile()     {
         Parser parserObj = new Parser();     String PDBID = parserObj.passPDBID();
      {     
         PDBFileReader pdbreader = new PDBFileReader();
         pdbreader.setAlignSeqRes(true);
         pdbreader.setAutoFetch(true);

     try{
        Structure struc = pdbreader.getStructureById(PDBID);
         }  catch (Exception e)    {
  e.printStackTrace();
}   }  } }

This code directly downloads a pdb file from the protein data bank, but the file obtained is in pdb.gz , in a zip file. how do i extract the pdb file using java or biojava? is there any method that would directly download the pdb file alone and not in pdb.gz format? please help..

Answer 1

[Nikolay Vyahhi]

You can use GZIPInputStream to read gzipped files in Java.

More info here: http://www.javamex.com/tutorials/compression/gzip.shtml

Answer 2

[Reyhaneh]

I use C# and I do the same thing. You need to download the files and then unzip them. the code i use in c# is:

void DecompressFiles(string pdbCode, string chain)
         {
            //location of where zip pdb files are saved.
             var file = Path.Combine(Program.current_pdbFilesLocation, pdbCode + ".gz");
             using (FileStream fInStream = new FileStream(file, FileMode.Open, FileAccess.Read))
             {
                 using (GZipStream zipStream = new GZipStream(fInStream, CompressionMode.Decompress))
                 {
                     var newname = file.Replace(".gz", "-"+chain.ToUpper()+".pdb");

                     using (FileStream fOutStream = new FileStream(newname, FileMode.Create, FileAccess.Write))
                     {
                         byte[] tempBytes = new byte[4096];
                         int i;
                         while ((i = zipStream.Read(tempBytes, 0, tempBytes.Length)) != 0)
                         {
                             fOutStream.Write(tempBytes, 0, i);
                         }
                     }
                 }
             }
             // delete the zip file
             File.Delete(file);
         }