[Biojava-l] SITE records in PDBFileReader

[Amr AL-Hossary]

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

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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
>
>