rewrote all polyconf functions to use updated atom names

[recombinatrix]

Overhaul of PolyConf code to update nomenclature to align with the manuscript.

I have changed the atom names in all my methods to align with the names I used in the manuscript.

atom names in extend changed from P1, P2, Q1, Q2 to Q, P, S, R, as the old scheme became unreadable when you needed to add monomer subscripts
atom names for linearization to changed from R, S to V1 V2, as R and S are now part of the core mapping
atom names for everything that interacted with dihedrals and dist() changed from a1 a2 to J K, to align with dihedral notation conventions that are older than I am.
_rotate() changed to rotate() as this function will (on rare occasions) be directly called by users

all references to dummy atom names changed to dummies in PolyConf.Polymer and PolyConf.PDB

Polyconf examples were completely overhauled