Rework atom specification nomenclature for PolyConf

[recombinatrix]

Users are reporting difficulty assigning PQRS atoms in extend, and JK atoms in gen_pairlist. It might be worth reworking how these inputs are given. One idea is to ask the user to specify the two bonds that will be colinear, rather than the two atompairs that are used in the mapping. Then the user would specify something like existing_mapping_bond={'P':'CA','Q':'C'},incoming_mapping_bond={'P':'CX','Q':'CY'}, or even existing_mapping_bond=('CA','C'),incoming_mapping_bond=('CX','CY'),only with keyword names that aren't terrible.

Maybe PQ and PQprime, or something in that vein?

Need to build this in in a way to not invalidate previous scripts.

[recombinatrix]

It might be nice if we can define monomers in a way that would detect when the user has mixed up the relative orientation of the two bonds (P1 mapped to Q2, Q1 mapped to P2). Hard to define consistently, as I want to let the user decide which atoms are dummies in any particular use case.

Could be addressed as part of the move to graph representation in the core datastructure.