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
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