Hi, Thanks & nice work.I think you need to tell your module lead about that..
Hibernate inclusion isnot a good idea for BioJava.It is slow & XML based, thus big data files will be affected. I think we need a plugin framework with better features that deploy functionalities ,which biologists look for.. I have been doing analysis on the BioJava 3 proposal and have some concerns on this, besides the other analysis that is present. I will be sending it to my lead, Andreas Sir (not Andreas Prilic) on this. Regards, JD On 8/27/10, Amr AL-Hossary <[email protected]> wrote: > I sent the updated code as an attachment to the group, as well as to Andreas > Prlic<[email protected]>; Steve Darnell<[email protected]>; > [email protected]<[email protected]>; to be reviewed for submission. > > It seems that the group daemon prevents attachments whatever small is their > size. > Please feed me back if it wasn't delivered correctly. > > This submitted updates handle dealing with "SITE" records to a sufficient > degree (but didn't handle REMARK 800 yet) > > to achieve this goal I had to create a new bean called "Residue". It is > implemented as a static inner class inside PDBSite (and it can be extracted > to be a top level class if needed). > > I created it because I couldn't use any of the subclasses of Group class > (e.g. HOH is neither an amino acid, nor a nucleotide). > > I guess this should be discussed on the biojava-dev mail list if any body is > interested and if it suits the list policy. > I also have some comments on the already present code that needs to be > discussed. to whom shall I address my comments? > > Regards > > Amr > From: Andreas Prlic > Sent: Tuesday, August 17, 2010 8:04 PM > To: Amr AL-Hossary > Cc: Steve Darnell ; [email protected] > Subject: Re: [Biojava-l] SITE records in PDBFileReader > > > 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
