[Biojava-dev] PDBFileParser pdb_TITLE_Handler bug

[Steve Darnell]

Greetings,

There is a small bug in PDBFileParser.pdb_TITLE_Handler().  It is working on the assumption that the title text occupies columns 10 to 70; the PDB format states it is from 10 to 80.  Consequently, long titles get truncated.

>From 3NHE:
'TITLE     HIGH RESOLUTION STRUCTURE (1.26A) OF USP2A IN COMPLEX WITH UBIQUITIN  '

Output from Structure.getPDBHeader().toPDB():
'TITLE     HIGH RESOLUTION STRUCTURE (1.26A) OF USP2A IN COMPLEX    '
'TITLE    2 WITH U                                                  '

Output from Structure.getPDBHeader().getTitle():
'HIGH RESOLUTION STRUCTURE (1.26A) OF USP2A IN COMPLEX WITH U'

Regards,
Steve

________________________________________
From: Susanne Schaller 
Sent: Tuesday, January 25, 2011 1:27 PM
To: Steve Darnell
Subject: Java source and pdb files

If you say structures.getPDBHeader().getTitle() it cuts off the last letters.

I've looked through the source code (look for PDBFileParser.java) of biojava3 and I think I've found the problem:

There are only character from 11-70 allowed.

Here is the source code from PDBFileParser.java:

/** Handler for
    TITLE Record Format

     COLUMNS        DATA TYPE       FIELD          DEFINITION
    ----------------------------------------------------------------------------------
    1 -  6        Record name     "TITLE "
    9 - 10        Continuation    continuation   Allows concatenation of multiple records.
    11 - 70        String          title          Title of the experiment.


     */
   private void pdb_TITLE_Handler(String line) {
        String title;
        if ( line.length() > 69)
            title = line.substring(10,70).trim();
        else
           title = line.substring(10,line.length()).trim();

        String t= (String)header.get("title") ;
        if ( (t != null) && (! t.equals("")))
            t += " ";
        t += title;
        header.put("title",t);
        pdbHeader.setTitle(t);
    }