Filter bridge-extension dihedrals#10
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The
_remove_residual_ghost_dihedralsfunction previously handled two patterns of spurious ghost/physical dihedral coupling (cross-bridge and ghost-middle), but missed a third: dihedrals of the formreal–ghost–ghost–ghost, where a real bridge atom sits at one terminal and the remaining three atoms lie inside a ghost group. This pattern arises when the ghost group contains a ring, most critically cyclopropyl, where the ring topology creates multiple dihedral paths from the bridge into the ring interior (bridge–CP1–CP2–X) with large force constants (~4.6 kcal/mol). Left in place, these terms constrain the ghost ring's orientation relative to the real scaffold even at λ=0, introducing spurious torsional coupling.. A newbridge_extensioncase removes all such dihedrals; the intended anchor dihedrals (real–real–ghost–ghost) are unaffected. The fix also removes analogous depth-extension terms in linear ghost chains, which were previously left in by omission but are equally unphysical and have no role in the Boresch factorisation.