Merge pull request #6345 from RosettaCommons/roccomoretti/pdb_loading_small_tweaks
A set of small efficiency tweaks for PDB Loading
Small inefficiencies I found when looking into PDB loading speeds. Mostly doing work we don't really have to do (refolding, creating new objects which aren't used). These probably account for a ~2% speedup in my test set.
fixing broken unit test (#6384)
* editing "correct" pdb file to have the right chemistry. Pushing to get help.
* copied the output of the test (build/test/debug/macos/11.6/64/arm/clang/13.0/default/PDB_w_glycans_IO_cxxtest.pdb._tmp_) to replace the old, wrong `test/core/io/5FYL_correct_output.pdb`. The PDB_w_glycans_IO unit test now passes.
Merge pull request #6367 from RosettaCommons/JackMaguire-cartmd-vrt-fix
Remove divide-by-zero in CartesianMD
There's a snippet of code in the run_rattle1() function that divides some numbers by the mass of each atom. This PR just adds a check to skip loop iterations where that mass is zero.
Thanks Frank for the help and the review!
Merge pull request #6306 from RosettaCommons/LDM_fix
Fix to my previous merge that threw errors on post0merge tests. Also addresses an issue introduced in protocols/ligand_docking/HighResDocker.cc where a variable was erroneously initially declared as true (and should have been false).
Merge pull request #6295 from RosettaCommons/rhiju/no_reload_rna_suite_potential
use ScoringManager to prevent re-loading lots of copies of rna_suite_potential in RNA_SuiteEnergy.cc