[Biojava-l] SITE records in PDBFileReader

[Amr AL-Hossary]

Dear all,

Please, some body revise the attached code & checks it in if it is OK, or contact me back for any inquiry.

This submitted updates handle dealing with "SITE" records to a sufficient degree (but didn't handle REMARK 800 yet)

to achieve this goal I had to create a new bean called "Residue". It is implemented as a static inner class inside PDBSite (and it can be extracted to be a top level class if needed).

Why I created it? because I couldn't use any of the subclasses of Group class (e.g. HOH is  neither an amino acid, nor a neucleotide). in case some body has another idea, let's open the discussion about it.

Regards

Amr


  From: Andreas Prlic 
  Sent: Tuesday, August 17, 2010 8:04 PM
  To: Amr AL-Hossary 
  Cc: Steve Darnell ; biojava-l at lists.open-bio.org 
  Subject: Re: [Biojava-l] SITE records in PDBFileReader


  Hi Amr,

  thanks for taking this on.  For a first time contributor, it is probably best to post your patches to the list, so somebody else can take a look at them first and commit them for you.

  Andreas



  On Tue, Aug 17, 2010 at 10:36 AM, Amr AL-Hossary <amr_alhossary at hotmail.com> wrote:

    I'll see it in a couple of days. I have first to be able to check out & in the source code.
    All I found till now is anonymous access.

    Amr

    --------------------------------------------------
    From: "Steve Darnell" <darnells at dnastar.com>
    Sent: Tuesday, August 17, 2010 6:00 PM
    To: "Andreas Prlic" <andreas at sdsc.edu>; "Amr AL-Hossary" <amr_alhossary at hotmail.com>
    Cc: <biojava-l at lists.open-bio.org>
    Subject: RE: [Biojava-l] SITE records in PDBFileReader


      Andreas and Amr,

      Thank you very much for agreeing  to add this feature.  May I make one additional refinement to my request?

      REMARK 800 provides a very useful SITE_DESCRIPTION for each SITE_IDENTIFIER code in use in the SITE records.  Could the site name also be associated with the site identifier and residues?  There is precedence for parsing REMARK records in BioJava (e.g. experiment type, resolution), but this is a special case where REMARK 800 and SITE records are dependent on one another and physically separated in the header.

      Regards,
      Steve

      ________________________________________
      From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
      Sent: Monday, August 16, 2010 6:59 PM
      To: Amr AL-Hossary
      Cc: Steve Darnell; biojava-l at lists.open-bio.org
      Subject: Re: [Biojava-l] SITE records in PDBFileReader


      - Take a look at PDBFileParser.java and athttp://www.wwpdb.org/documentation/format32/sect7.html 

      - It needs a new Handler method for the Site records that builds up the data containers.
      - Create a new bean that will contain the data for the SITE record

      - Instead of having fields for insertion code residue nr and chain IDs, you can use the newPDBResidueNumber.java class to group this together. 

      - Add a get/set method for the Site beans to the Structure class
      - Create a junit test that make sure the parsing works ok.

      Hope that makes sense...
      Andreas


      -
      On Mon, Aug 16, 2010 at 4:48 PM, Amr AL-Hossary <amr_alhossary at hotmail.com> wrote:
      If you like It would be my pleasure to do it for you,
      Just tell me where to start (in the code).

      Amr






  -- 
  -----------------------------------------------------------------------
  Dr. Andreas Prlic
  Senior Scientist, RCSB PDB Protein Data Bank
  University of California, San Diego
  (+1) 858.246.0526
  -----------------------------------------------------------------------
-------------- next part --------------
A non-text attachment was scrubbed...
Name: SITE-specific commits.zip
Type: application/x-zip-compressed
Size: 34069 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20100827/7926d6c9/attachment-0002.bin>