made secondary structure calculation work with store/proxy classes
made secondary structure calculation work with store/proxy classes

- cg support pending (depends on helixorient)

arose/ngl,arose/ngl,arose/ngl,fredludlow/ngl,j0kaso/ngl,j0kaso/ngl,j0kaso/ngl,fredludlow/ngl,fredludlow/ngl,arose/ngl,fredludlow/ngl