- 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 <[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 > > > -------------------------------------------------- > From: "Andreas Prlic" <[email protected]> > Sent: Tuesday, August 17, 2010 12:49 AM > To: "Steve Darnell" <[email protected]> > Cc: <[email protected]> > 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 <[email protected]> >> 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: '[email protected]' >>> 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 - [email protected] >>> 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 - [email protected] >> 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 - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
