Re: SITE records in PDBFileReader
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l