Adopted clustering of protein chains for two structures
Changed the criteria to differentiate between helical and cyclic
symmetry. For example, 3J4F has both C2 and helical symmetry. Since the
helical RMSD is lower than the cylic RMSD, now helical symmetry is
assigned in this case.

A new parameter: helixRmsdThreshold was added to QuatSymmetryParameters
that can be used to adjust the preference of helical vs cyclic RMSD.

This update also fixes and an array of of bounds exception in helical
symmetry detection.
Merge branch 'master' of https://github.com/pwrose/symmetry
adding more details for how to load PDP domains
local cleanup
 increasing version nr