Merge pull request #4871 from RosettaCommons/dimaio/dna_phil_modes
A few general fixes for DNA.
- Enabling (plus fix a few deriv discontinuities) in Phil's dna_dihedral_* terms.
- Fix cart_bonded for DNA
- Change default of -excluded_dna_dna to true.
- Adding some utility functions (from Phil) for minimizing DNA with a zig-zag atom tree
Integration test changes are due to: a) changes to cart_bonded database (and consequent changes in summation order of cart_bonded terms); b) integration tests that print EnergyMethodOptions or HbondOptions (which have had defaults changed).