[Biojava-l] PDBFileParser and identifying atoms in ligands

[Andreas Prlic]

Hi Andy,

You don't need to process TERs to build up the representation of a
structure.  The BioJava data model will work fine even if the file
does not contain any amino acids. (e.g.  check 2KQO )

Ligands will get represented as Hetatom groups in the datamodel.
Check the Hetatom or Group javadocs for how to access their atoms.

For your last question: Check out the Chain.getAtomGroups() and
Chain.getSeqResGroups() methods...

If it does not work the way you expect for a particular PDB ID, please
let me know the ID, so I can take a look at the details.

Andreas


On Thu, May 6, 2010 at 9:50 AM, Andy Thomas-Cramer
<thomascramera at dnastar.com> wrote:
> >From a PDB file, I can identify which atoms are in ligands, and which
> are in residues in the chain. The chain atoms end with the TER record.
>
>
>
> >From the BioJava API, I can distinguish as well -- if it's an amino
> sequence and the automatic alignment between SEQRES and ATOM sequences
> is successful.
>
>
>
> Is there a way through the API to identify atoms in ligands, when the
> chain is not an amino sequence or alignment fails? It looks like the TER
> record is ignored by PDBFileParser.
>
>
>
>
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