[Biojava-l] structure alignment seems slow ...

[Andreas Prlic]

glad to hear that it works now. I agree with your initial assumption
about the StructureTool class. The getAtomCAArray should only consider
model 0. I will change it to behave accordingly...

Andreas



On Wed, Jan 19, 2011 at 3:12 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Fixed my problem, the issue was that i had multiple models in my structures,
> and I assumed biojava was only using the first one.
>
> To fix it , if you replace
>
>
>         Atom[] ca2 = StructureTools.getAtomCAArray(s2);
>
>      with
>
>         Atom[] ca2 = StructureTools.getAtomCAArray(s2.getModel(0).get(0));
>
> The CE alignmenbt is blazing fast. ~0 seconds
>
> --
> Jay Vyas
> MMSB/UCHC
>