printed structure does not obey --use-reflections about rmsd

[Jellby]

Just realized that this might actually be a fixed bug in the rmsd printed with --use-reflections in the older version. Apologies if that's the case.

[charnley]

Hi @Jellby, I finally found some time to look at this. The bug is 1.3.2 specific. It seems by default the reorder method was enabled by default. So not only did you check reflections, you checked reflections while reordering the atoms. To get the 0.3 RMSD in 1.4.0 use

calculate_rmsd a.xyz b.xyz --use-reflections --reorder

The default --reorder-method is the same for both version, e.i. Hungarian-Distance.

However, can confirm that reflections are not contained in the -p flag, as they should be. I have started the fix #80. Will need to add better tests for --print output, and merge ASAP.

[charnley]

Fixed in master