[Biojava-l] Structure.getChains()

[Andreas Prlic]

Hi Dmitry,

The object model reflects the organization of data in PDB files
http://www.wwpdb.org/docs.html.

Chains can contain a mix of different groups of atoms.  As such the
BioJava object model allows you to distinguish between amino acids
nucleotides and hetatoms on the Group level, rather than on the chain
level.

Andreas

On Thu, Aug 28, 2008 at 2:14 AM, Dmitry Repchevsky
<dmitry.repchevski at bsc.es> wrote:
> Hello!
>
> I have a PDB (1pio) with 2 chains and 1 HETATM solvent (water).
> A Structure object contains "models" and "compounds".
> "models" contains ALL elements (aminoacid chains AND solvents) and
> "compaunds" only aminoacids.
> The method Structure.getChains() returns me ALL elements... is it ok? I mean
> that when I'm asking for a "chain" I do not expect to get a solvent...
>
> Just a curiosity,
>
> Dmitry
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