[Biojava-l] SITE records in PDBFileReader

[Steve Darnell]

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 at http://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 new PDBResidueNumber.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