[Biojava-l] SITE records in PDBFileReader

[jitesh dundas]

Hi,

Thanks & nice work.I think you need to tell your module lead about that..


Hibernate inclusion isnot a good idea for BioJava.It is slow & XML
based, thus big data files will be affected.
I think we need a plugin framework with better features that deploy
functionalities ,which biologists look for..

I have been doing analysis on the BioJava 3 proposal and have some
concerns on this, besides the other analysis that is present. I will
be sending it to my lead, Andreas Sir (not Andreas Prilic) on this.

Regards,
JD

On 8/27/10, Amr AL-Hossary <amr_alhossary at hotmail.com> wrote:
> 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
>
>
>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
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