I sent the updated code as an attachment to the group, as well as to Andreas
Prlic<[email protected]>; Steve Darnell<[email protected]>;
[email protected]<[email protected]>; 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 ; [email protected]
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 <[email protected]>
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" <[email protected]>
Sent: Tuesday, August 17, 2010 6:00 PM
To: "Andreas Prlic" <[email protected]>; "Amr AL-Hossary"
<[email protected]>
Cc: <[email protected]>
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: [email protected] [mailto:[email protected]] On Behalf Of
Andreas Prlic
Sent: Monday, August 16, 2010 6:59 PM
To: Amr AL-Hossary
Cc: Steve Darnell; [email protected]
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 <[email protected]>
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
-----------------------------------------------------------------------
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