Merge pull request #5659 from RosettaCommons/roccomoretti/speed_up_scoring Speed up PDB loading by improving the ResidueTypeFinder. Rosetta 3.13 is about 30% slower than Rosetta 3.12 when doing a plain rescoring of a large number of PDBs. I tracked that down to PDB file loading, specifically extra time in the ResidueTypeFinder, in large part due to patching. I was able to rearrange some things to reduce wasted effort and make things more efficient. I my hands, we're now about twice as fast as Rosetta 3.13 when doing plain re-scoring. It still looks like the ResidueTypeFinder is a substantial factor in the runtime (as measured by perf), but not necessarily in an easily fixable way.