> Use specialized CompileAutomorphismQuery again since it is much faster. It 
> wasn't working before since it was using unmasked symmetry classes which are 
> obviously different leading to incorrect matches (or no matches at all in 
> most cases)

Wow. That went from a timeout (>1500 s) for the align test to 0.47s on my Mac.

One test failure down. :-)

Cheers,
-Geoff
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