Feature/performance improvements

[HenriettaHolze]

Hi,

Thanks for developing this very useful tool.
AlphaJudge crashed my laptop when using 8 cores with big AF3 models, so I tried to optimize.

1. Keeping PAE matrices as numpy arrays gives ~3x memory improvement and is ~2x faster.
2. I added an option to only return the QC metrics and not calculate the biophysical metrics which is ~20x faster.

Hope this is useful :)

Best,
Henrietta