Fixed bugs with ChiralMover and TryRotamers optimal connection point
ChiralMover now updates backbone oxygens on upper terminus.
Also, properly handles orienting functional group for residues that do
not have three side chain residues to orient.
Added case of D-Proline in NtermTruncation patch
Updated atom connection points in optimal_connection_point function.
This is used by TryRotamers for automatic fold tree creation and was
failing to create properly aligned rotamers for HIS, LEU and ILE.
Updated optimal atom based on a fixed atom in the terminal chi angle.
Unit tests: pass
Integration tests: ld_converter has minor coordinate changes due to the
update to ChiralMover and cosmetic output changes.