[Biojava-dev] Biojava3 structure

[Andreas Prlic]

Hi Scooter,

at the present the structure modules depend on the alignment module and on
the (old) core module.  This is for aligning ATOM and SEQRES residues in the
PDB files, and for the Smith Waterman alignment based 3D structure
superposition. If we target a release of biojava 3 in about a month, I don't
think it will be possible to break this out, mainly because the alignment
module is still based on the biojava 1 code base. Overall I think that the
core module probably should still be part of the BioJava 3 release. Any
opinions on that?

Andreas

On Sun, Mar 28, 2010 at 3:06 PM, Scooter Willis <HWillis at scripps.edu> wrote:

> Andreas
>
> I needed to do some work with a PDB file so started to use the structure
> library. It looks like it depends on all the old biojava code. Mainly the
> structure exceptions that extend bioexception is the first thing tripping me
> up. Should the biojava3-structure module have any external dependencies or
> am I working with the wrong package?
>
> Thanks
>
> Scooter