[Biojava-l] SITE records in PDBFileReader

[Andreas Prlic]

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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