[Biojava-l] SITE records in PDBFileReader

[Amr AL-Hossary]

I sent the updated code as an attachment to the group, as well as to Andreas 
Prlic<andreas at sdsc.edu>; Steve Darnell<darnells at dnastar.com>; 
jacobsen at ebi.ac.uk<jacobsen at ebi.ac.uk>; to be reviewed for submission.

It seems that the group daemon prevents attachments whatever small is their 
size.
Please feed me back if it wasn't delivered correctly.

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).

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 nucleotide).

I guess this should be discussed on the biojava-dev mail list if any body is 
interested and if it suits the list policy.
I also have some comments on the already present code that needs to be 
discussed. to whom shall I address my comments?

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






-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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