On Thu, 2006-08-24 at 09:39 +0200, Egon Willighagen wrote:
> On Wednesday 23 August 2006 19:25, Rajarshi Guha wrote:
> > Hi, I'm using ProteinBuilderTool to create a peptide sequence like
> >
> > BioPolymer pepseq = ProteinBuilderTool.createProtein("ACDEFGH");
> >
> > However, when I do
> >
> > Collection aas = peptide.getMonomerNames();
> >
> > and then print out the monomer names I get an extra blank entry. Is this
> > supposed to be the case?
>
> Yes, I think so. This blank entry is a container for all atoms that do not
> belong to a residue (e.g. ligands, water, metals...)
A few more questions regarding the use of IBioPolymer:
Currently I have some test code that generates a peptide sequence using
ProteinBuilderTool via the one letter codes.
However if I read in a PDB file I get a PDBPolymer - now in a PDB (at
least for sequences other than DNA's and RNA's) the PDB will contain the
3-letter codes.
When I access the monomer names, do I get the 3 letter codes? Or the 1
letter codes? If one or the other (depending on the source of the data)
could this be standardized internally?
Also the IBioPolymer class has a a method to get the monomer names.
However there is no method that would give me the all the monomer's
themselves. Is there a reason for this absence?
I see that PDBPolymer has a method to get all the monomers in sequential
order. But in my code I am assuming that I might get a hand built
peptide sequence or a sequence obtained from a PDB file. So should there
not be a method to get all the monomers in IBioPolymer?
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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