Hi Brendan, I just committed the patches to CVS so BioJava can now parse the SSBond records.
Andreas On 14 Nov 2007, at 16:28, Brendan Duggan wrote: > Hi Andreas > > Thanks for the quick response. I submitted a bug > request (#2400) as suggested by Richard. Parsing the > SSBOND records is indeed what I was talking about. I > want to identify the disulfides then calculate their > torsions, dihedrals and bond lengths, all of which I > believe can be implemented with the existing code. If > you could implement this parsing in a few days that > would be great! > > Thanks > > Brendan > > > --- Andreas Prlic <[EMAIL PROTECTED]> wrote: > >> Hi Brendan, >> >> SSBOND lines are currently not parsed. If this is >> what you need, >> I can add this over the next couple of days. >> >> If you want to compute the bonds yourself, the >> framework can >> e.g. calculate distances between the sulphur atoms >> for you. - >> >> Andreas >> >> >> >> >> >> On 14 Nov 2007, at 00:48, Brendan Duggan wrote: >> >>> Greetings >>> >>> I'm trying to mine some information on disulfides >> in >>> the PDB and was hoping there might be a way of >>> obtaining this information with the BioJava PDB >>> parser. However, I haven't been able to see >> anything >>> like this mentioned in the API docs. If it is >>> currently not possible to extract disulfide >>> information from PDB files are there any plans to >>> implement this? >>> >>> Thanks! >>> >>> Brendan >>> >>> >>> Make the switch to the world's best email. >> Get the new Yahoo! >>> 7 Mail now. >> http://au.yahoo.com/worldsbestmail/viagra/index.html >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - >> [email protected] >>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> > ---------------------------------------------------------------------- > - >> >> Andreas Prlic Wellcome Trust Sanger Institute >> Hinxton, Cambridge >> CB10 1SA, UK >> +44 (0) 1223 49 6891 >> >> > ---------------------------------------------------------------------- > - >> >> >> >> -- >> The Wellcome Trust Sanger Institute is operated by >> Genome Research >> Limited, a charity registered in England with >> number 1021457 and a >> company registered in England with number 2742969, >> whose registered >> office is 215 Euston Road, London, NW1 2BE. >> > > > Brendan M. Duggan, PhD > > [EMAIL PROTECTED] > (858) 692-2298 > > > Make the switch to the world's best email. Get the new Yahoo! > 7 Mail now. http://au.yahoo.com/worldsbestmail/viagra/index.html > > ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
