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 <[EMAIL PROTECTED]> 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
<[EMAIL PROTECTED]> 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 c!
lass 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* <[EMAIL PROTECTED]>
> > <mailto:[EMAIL PROTECTED]>> wrot!
e:> > >> > > 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_P!
redictor.html> >> > > <> >
http://www.charite.de/bioinf/strap/biojavaInAnger_SecondaryStructure_Predictor.html>
> >> > > > bye> > > > Martin> > > >
_______________________________________________> > > > Biojava-l mailing
list - Biojava-l@biojava.org> > > <mailto: Biojava-l@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@biojava.org> > > <mailto:Biojava-l@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> > So!
uth Africa> > 0001> >> > Tel: +27 12 420 5802> > Cell: +27 83 504 7914> >
Fax: +27 12 420 5800> > Email: [EMAIL PROTECTED]> > [EMAIL
PROTECTED]> >> > ---------> > The software required "Windows XP or better" ...
so I installed Linux> >>>
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