[Performance] Pruning energy-sorted ensembles

[ntampellini]

If energies are provided (and therefore also a maximum energy difference that structure must have to be considered similar) the ensemble is energy-sorted before pruning, so that energetically similar structures are more likely to be grouped together early and pruned as soon as possible, reducing the total number of evaluate_sim calls.

The ConformerEnseble XYZ reader can now read energies from structures comment lines.

[codecov]

Codecov Report

❌ Patch coverage is 76.00000% with 12 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
prism_pruner/pruner.py	68.18%	7 Missing ⚠️
prism_pruner/conformer_ensemble.py	81.81%	2 Missing ⚠️
prism_pruner/utils.py	75.00%	2 Missing ⚠️
prism_pruner/torsion_module.py	50.00%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!

[ntampellini]

Tried exiting early from rotationally_corrected_rmsd_and_max as soon as a global RMSD value below the desired one is found. That was unfortunately slower, as it increased the number of calls to rmsd_and_max and had a very low success rate in exiting early from the function. Idea scrapped for now.