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
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