Fix CA_rmsd warning message
Meiler lab Powercoding with Alyssa Lokits
Make it such that CA_rmsd(pose1,pose2) doesn't print a warning message
for missing CA atom (e.g. ligand residues or virtual residues). Explicit
range CA_rmsd will still print a warning.
Also fix/remove bb_rmsd_*() functions, which weren't actually using
all their parameters.
Fixes bug 0000337
Integration test changes expected as warnings are no longer printed:
membrane_relax
relax_w_allatom_cst
mr_protocols
hybridization
density_refine
metalloprotein_abrelax
density_refine_symm
readin_dna_rna_protein