[Biojava-l] SITE records in PDBFileReader

[Andreas Prlic]

- Take a look at PDBFileParser.java and at
http://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 new PDBResidueNumber.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
>
>
> --------------------------------------------------
> From: "Andreas Prlic" <andreas at sdsc.edu>
> Sent: Tuesday, August 17, 2010 12:49 AM
> To: "Steve Darnell" <darnells at dnastar.com>
> Cc: <biojava-l at lists.open-bio.org>
> Subject: Re: [Biojava-l] SITE records in PDBFileReader
>
>
>  Hi Steve,
>>
>> thanks for the feature request. I will probably be able to add this at
>> some
>> point in September. If you need it already before that, I will be happy to
>> commit a patch if somebody else provides it...
>>
>> Andreas
>>
>>
>> On Mon, Aug 16, 2010 at 3:26 PM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>>
>>  I'm sorry for reposting this message.  I accidentally sent the previous
>>> one
>>> as HTML.
>>>
>>> ________________________________________
>>> From: Steve Darnell
>>> Sent: Monday, August 16, 2010 5:19 PM
>>> To: 'biojava-l at lists.open-bio.org'
>>> Subject: SITE records in PDBFileReader
>>>
>>> Greetings,
>>>
>>> I am interested in parsing SITE records from a PDB file.  I looked over
>>> the
>>> org.biojava.bio.structure API, but I was unable to find reference to this
>>> functionality.  Does the PDBFileReader in BioJava extract SITE record
>>> information?  If not, would it be possible to add this capability to
>>> PDBFileReader and the Structure class?
>>>
>>> SITE record format at wwPDB:
>>> http://www.wwpdb.org/documentation/format32/sect7.html
>>>
>>> Regards,
>>> Steve Darnell
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>


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