reworked atom names to align with manuscript#61
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recombinatrix merged 3 commits intomainfrom Feb 17, 2025
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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, Q2toQ, P, S, Rrespectively, as the old scheme became unreadable when you needed to add monomer subscriptsatom names for linearization to changed from
R, StoV1, V2, asRandSare now part of the core mappingatom names for everything that interacted with dihedrals and
dist()changed froma1 a2toJ K, to align with dihedral notation conventions that are older than I am._rotate()changed torotate()as this function will (on rare occasions) be directly called by usersall references to dummy atom names changed to dummies in
PolyConf.PolymerandPolyConf.PDBtests updated to align with new nomenclature
Polyconf examples were completely overhauled