[Biojava-l] Newbie struggling with secondary structure

[Tamas Horvath]

Hi!I have the needed modifications of PDBFileParser to read secondary structuredata.The code is not final, there maybe some changes before it is added to cvs.(And I need Andreas to be around for that... )But if you need the file right now, I can send it to you, and you canrecompile your biojava. alternatively I can send u my compiledbiojava.jaras well. It's not the most current cvs, but not too lateeither...
On 2/13/06, Tamas Horvath <hotafin at gmail.com> wrote:>> You are right.... the secondary structure is not yet parsed. But it's> quite easy, so if Andreas is around today, we may add the needed code...>> On 2/13/06, Tjaart de Beer <tjaart at tuks.co.za> wrote:> >> > Thanks for help! But I still have problems. Here is my code, please see> > if you can find anything wrong....> >> >> > import org.biojava.bio.structure.*;> > import org.biojava.bio.structure.io.*;> > .> > .> > .> > PDBFileReader file = new PDBFileReader();> > Structure structure = file.getStructure (filename); //I used 1eye.pdb> > Chain chain = structure.getChain(0); //Only get 1st chain> > ArrayList s = chain.getGroups("amino"); //Get amino acids> > AminoAcidImpl a  = (AminoAcidImpl)s.get(28); //Make object of element 28> >> > Map secStruc = a.getSecStruc(); -> This returns an empty map...> > ???> >> >> > My chain variable contains the specifed chain and I can get a specific> > value for element 28. When I check the class of a element in the> > ArrayList it says "class org.biojava.bio.structure.AminoAcidImpl". Thus> > I now want to use the getSecStruc method on that element. Typing> > "System.out.println(s.get(28).getSecStruc())" does not give me anyhting> > but an empty array.> >> > Any help would be appreciated...> >> >> > Tamas Horvath wrote:> > > It's very easy really. Especially if you use cvs BioJava.> > >> > > You parse a PDB file using PDBFileParser.> > > That gives you a structure object.> > > Than you need to iterate through all models (if there are more than 1)> > > and all chains in them.> > > Once you have a chain object, you can iterate through it.> > > for example you can say findChain("A")> > > that gives you the "A" chain.> > > then you can say getGroups("amino").> > > That gives you a list of the aminoacids.> > > And every aminoacid object has a secondary structure attribute.> > >> > > On 2/12/06, *Tjaart de Beer* <tjaart at tuks.co.za> > > <mailto:tjaart at tuks.co.za>> wrote:> > >> > >     Hi> > >> > >     Thanks for all the suggstions. Currently I just want to extract> > the> > >     secondary structure as specified in the PDB file. I am having> > trouble> > >     understanding how to utilize the AminoAcid class (after having> > >     looked at> > >     the source...). Does anyone have an example of extracting the> > secondary> > >     structure from a PDB file using the AminoAcid class in Biojava? Or> > any> > >     example using the AminoAcid class to extract info from a PDB file?> >> > >> > >     Any help would be greatly appreciated!> > >> > >     Martin Heusel wrote:> > >      > Hi Tjaart,> > >      > you can use DSSP to determine the secondary structure from a> > PDB.> > >      > http://swift.cmbi.ru.nl/gv/dssp/ <> > http://swift.cmbi.ru.nl/gv/dssp/>> > >      > or maybe better use Christoph's SecondaryStructure_Predictor> > with> > >     biojava> > >      >> > >     http://www.charite.de/bioinf/strap/biojavaInAnger_SecondaryStructure_Predictor.html> >> > >     <> > http://www.charite.de/bioinf/strap/biojavaInAnger_SecondaryStructure_Predictor.html> > >> > >      > bye> > >      > Martin> > >      > _______________________________________________> > >      > Biojava-l mailing list  -  Biojava-l at biojava.org> > >     <mailto: Biojava-l at biojava.org>> > >      > http://biojava.org/mailman/listinfo/biojava-l> > >      >> > >> > >     --> > >     Tjaart de Beer> > >> > >> > >     ---------> > >     The software required "Windows XP or better" ... so I installed> > Linux> > >     _______________________________________________> > >     Biojava-l mailing list  -  Biojava-l at biojava.org> > >     <mailto:Biojava-l at biojava.org>> > >     http://biojava.org/mailman/listinfo/biojava-l> > >> > >> >> > --> > Tjaart de Beer> > Bioinformatics and Computational Biology Unit> > Department Biochemistry> > FABI Square/Bioinformatics building> > Faculty of Natural Sciences> > University of Pretoria> > Lynwood rd> > Pretoria> > South Africa> > 0001> >> > Tel:    +27 12 420 5802> > Cell:   +27 83 504 7914> > Fax:    +27 12 420 5800> > Email:  tjaart at tuks.co.za> >         tdebeer at gmail.com> >> > ---------> > The software required "Windows XP or better" ... so I installed Linux> >>>