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Commit bbfe676
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* Add linear spacer modification for ring-breaking ghost bridges.
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* Remove cross-bond angles spanning ring-making/breaking bonds in the state where the bond is absent.
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* Fixed missing removal of bridge-extension dihedrals (`real–ghost–ghost–ghost`) that arise when a ghost group contains a ring, e.g. cyclopropyl, where the ring topology creates spurious torsional coupling between the real scaffold and the ghost ring interior.
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* Auto-zero anchor dihedrals when the immediate ghost atom lies on a ring within the ghost subgraph. The ring topology already constrains the ghost orientation relative to the bridge, making the anchor redundant.
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[2025.2.0](https://github.com/openbiosim/loch/compare/2025.1.0...2025.2.0) - Mar 2026
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[2025.2.0](https://github.com/openbiosim/ghostly/compare/2025.1.0...2025.2.0) - Mar 2026
* Ensure that there are independent, per-state, physical neighbours. This removes the spurious cross-state ghost filter that resulted in a downgrading of junction types when multiple junctions were present in the molecule.
@@ -23,7 +28,7 @@ Changelog
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* Fixed angle removal logic for ring and sp2 bridge atoms: when stiffening is skipped (``stiffen_ring_bridges=False`` or ``stiffen_sp2_bridges=False``), all ghost-containing angles are now preserved at their original force field values rather than removing the intraghost angles (dual junctions) or the sacrificial physical-bridge-ghost angle (triple junctions).
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* Changed the default for ``--optimise-angles`` to ``False``. Angle optimisation is conformer-dependent: different input geometries can yield different equilibrium angles for the same perturbation, adding variability to the resulting force field. The original force field theta0 is sufficient given the small ``k_soft`` value. Optimisation can still be enabled explicitly to follow Boresch et al. (JCTC 2021) strictly.
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[2025.1.0](https://github.com/OpenBioSim/loch/releases/tag/2025.1.0) - Nov 2025
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[2025.1.0](https://github.com/OpenBioSim/ghostly/releases/tag/2025.1.0) - Nov 2025
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