Merge pull request #6343 from RosettaCommons/roccomoretti/avoid_atomtree_updates
Speed up PDB loading by deferring AtomTree updates.
Benchmarking indicates that ~10-15% of the time for PDB loading is due to AtomTree::update_sequence_numbering(), which is called for each residue addition.
This is completely unnecessary, as we can just call setup_atom_tree() after we're all done adding the residues. To enable this we create a new Conformation function which takes a list of residues to append and does the addition all at once.
A quick test shows we do save ~10-15% of the time with this approach, and as far as I can tell we don't lose anything by the rearrangement.