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Changelog

2026.2.0 - ********

  • Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.
  • Revert auto-zeroing of anchor dihedrals for ring-constrained immediate ghosts: a singly-attached ring still has one unconstrained rotational degree of freedom about the bridge-ghost bond, so removing the anchor reintroduces flapping risk.

2026.1.0 - Jun 2026

  • Add linear spacer modification for ring-breaking ghost bridges.
  • 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.
  • 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.

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.
  • Added a fallback for failed angle optimisation to ensure that the original equilibrium value is preserved when convergence fails.
  • Added new --stiffen-ring-bridges option to control whether angle stiffening is applied to ring bridge atoms. (Default: False)
  • Added --stiffen-sp2-bridges to control whether angle stiffening is applied to SP2 bridge atoms. (Default: False)
  • Added --soften-anchors option to scale the force constants of surviving mixed ghost/physical dihedrals. (Default: 1.0, i.e. no softening)
  • Added rotamer anchor detection and options to stiffen the force constant using --stiffen-rotamers and --k-rotamer. (Default: False, 50 kcal/mol)
  • Added scoring functionality to try to avoid anchoring through transmuting or bridge atoms where possible.
  • Handle edge cases for ring-breaking perturbations.
  • 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).
  • 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.

2025.1.0 - Nov 2025

  • Initial public release.