Merge pull request #903 from RosettaCommons/aleaverfay/fix_lcaa_nbr_radii
Modifying the neighbor radii of the canonical amino acids.
The neighbor radii must represent the maximum distance from a
residue's neighbor atom to its furthest heavy atom under all
dihedral angle assignments. Their purpose is to provide a
geometry-independent bound on the reach of a residue so long as you
know where the neighbor atom (e.g. CBeta) is. The radii are used
by the score function and by the packer to avoid unnecessary
residue-pair energy calculations where possible.
I originally measured these maximum distances by building the
Dunbrack rotamers for a particular phi/psi. In this new calculation,
I've sweept all chi angle combinations at 5 degree increments.
For a handful of residue types, this resulted in an increase for
the neighbor radius. In the case of valine, it looks like the
original neighbor radius was never set to the default c-beta-to-
backbone-heavyatom distance (valine's c-beta-to-sc-heavyatom
distance is a meager 1.5A).
For HIS_D, the radius calculated by building rotamers was never applied,
so that Phil's original guess at HIS and HIS_D's radius was left; but
HIS's radius was updated. This meant that HIS and HIS_D ended up with
different radii. This discrepancy was initialy uncovered by Andrew Ban in
2009 and has reared its head intermitently in the past six years, but
was never fixed. HIS and HIS_D now have the same radii.
This pull request cause widespread integration test trajectory changes.
All unit tests pass.