[Biojava-l] PdbToXMLConverter with PDBConverter

[jon portuondo murguiondo]

Hello, I have the first output! The problem I had was that PdbToXMLConverter doesn't have main method. 
This is the program that Matthew gave me, called PDBConverter.java:

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package org.biojava.bio.program;
import java.io.*; 
  import org.biojava.bio.program.*; 
  public class PDBConverter { 
  public static void main(String[] args) 
  throws Exception { 
  StringBuffer sbuf = new StringBuffer(); 
  BufferedReader in = new BufferedReader( 
  new FileReader( 
  new File(args[0]) ) ); 
  for( 
  String line = in.readLine(); 
  line != null; 
  line = in.readLine() 
  ) { 
  sbuf.append(line); 
                } 
  PdbToXMLConverter converter = 
  new PdbToXMLConverter(sbuf.toString()); 
  converter.convert(); 
        } 
  } 

--------------------------------------------------------------------------------------------------

With this program I finally get an output from PdbToXMLConverter, but it is really odd:

------------------------------------------------------------------------------------------------
<?xml version="1.0"?>
no protocol: HEADER    LIGASE                                  08-SEP-00   1FS1              TITLE     INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF             TITLE    2 THE SKP1-SKP2 COMPLEX                                                COMPND    MOL_ID: 1;                                                            COMPND   2 MOLECULE: CYCLIN A/CDK2-ASSOCIATED P19;                              COMPND   3 CHAIN: A, C;                                                         COMPND   4 FRAGMENT: RESIDUES 101-153;                                          COMPND   5 SYNONYM: SKP2 F-BOX;                                                 COMPND   6 ENGINEERED: YES;                                                     COMPND   7 MOL_ID: 2;                                                           COMPND   8 MOLECULE: CYCLIN A/CDK2-ASSOCIATED P45;                              COMPND   9 CHAIN: B, D;                                                         COMPND  10 FRAGMENT: RESIDUES 1-147;              
                              COMPND  11 SYNONYM: SKP1;                                                       COMPND  12 ENGINEERED: YES                                                      SOURCE    MOL_ID: 1;                                                            SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   SOURCE   3 ORGANISM_COMMON: HUMAN;                                              SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 SOURCE   5 EXPRESSION_SYSTEM_COMMON: BACTERIA;                                  SOURCE   6 MOL_ID: 2;                                                           SOURCE   7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   SOURCE ---------------------------------------------------------------------------------------------------
There is no change of line and I am sure that would be more defects on that expected XML.

To get it run I typed:
java org.biojava.bio.program.PDBConverter /home/jon/1FS1.pdb

I would like to understand why the output is so odd and how can I get the expected structured XML.
Thanks for all!