fixed very subtle errors in BackboneMutator, RotamerMutator, and Peptide
the error had to do with a problem in Peptide.replaceResidueType as well as
some other subtle things.  Also added detailed debugging message capability
to Residue and added scripts to minimize a bunch of peptides in TINKER
simultaneously.  Figured out that an OPLS energy of 100000 or less per atom
is enough to get reasonable TINKER geometries.  If the atoms aren't closer
than about 1.00 A (maybe slightly less) the energy will be less than 100000.
These are set in Settings.