Skip to content

CHANGELOG.md

Latest commit

 

History

History
39 lines (29 loc) · 3.99 KB

CHANGELOG.md

File metadata and controls

39 lines (29 loc) · 3.99 KB
Raw

Changelog

2026.3.0 - XXXX

  • Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.
  • Stiffen the intraghost angle to 180 degrees for dual junctions with two ghost branches instead of removing it. With both ghosts confined to the normal of the physical plane, removal left the same-side arrangement degenerate at the end state, giving large free energy errors for e.g. methoxy and hydroxyl perturbations when the input geometry had both ghosts on the same side #17.

2026.2.0 - Sep 2026

  • 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.