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CHANGELOG.md

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Changelog
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=========
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[2026.1.0](https://github.com/openbiosim/loch/compare/2025.2.0...2026.1.0) - ********
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* Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.
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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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* 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.
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* Added a fallback for failed angle optimisation to ensure that the original equilibrium value is preserved when convergence fails.
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* Added new ``--stiffen-ring-bridges`` option to control whether angle stiffening is applied to ring bridge atoms. (Default: False)
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* Added ``--stiffen-sp2-bridges`` to control whether angle stiffening is applied to SP2 bridge atoms. (Default: False)
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* Added ``--soften-anchors`` option to scale the force constants of surviving mixed ghost/physical dihedrals. (Default: 1.0, i.e. no softening)
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* Added rotamer anchor detection and options to stiffen the force constant using ``--stiffen-rotamers`` and ``--k-rotamer``. (Default: False, 50 kcal/mol)
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* Added scoring functionality to try to avoid anchoring through transmuting or bridge atoms where possible.
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* Handle edge cases for ring-breaking perturbations.
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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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* Initial public release.

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