Fix issue #22

CHANGELOG.md

@@ -10,6 +10,13 @@ Changelog
 * Added ``--single-well-anchors`` and ``--k-single-well`` to replace surviving anchor dihedrals with a single-well cosine potential whose minimum is the geometry of the end state where the ghost is physical. Multi-well anchors, e.g. the n=2 term of a dummy hydrogen on a carbonyl oxygen, can trap ghosts in an alternative well at intermediate lambda, giving hysteresis between independently equilibrated windows. Anchors with zero force constants or an ill-defined reference dihedral are left unchanged. (Default: False, 5 kcal/mol) [#19](https://github.com/OpenBioSim/ghostly/pull/19).
 * Record the options used for each modification in a ``ghostly_options`` property on each modified molecule, and raise an error when modifying a system that has already been modified, unless ``--force`` is used. Forced modifications are applied on top of the existing ones [#20](https://github.com/OpenBioSim/ghostly/pull/20).
 * Added support for Python 3.13 and 3.14, and dropped support for Python 3.10 and 3.11.
+* Fixed bridge atoms being typed by RDKit on end states with ghost atoms attached, where bond orders often couldn't be inferred, leaving every heavy atom typed as sp3 with no aromaticity. Bridge typing no longer uses RDKit. The chirality check used by ``--linearise-ring-break`` now converts the ghost-free end state, and skips linearisation with a warning if bond orders can't be inferred [#23](https://github.com/OpenBioSim/ghostly/pull/23).
+* Decide triple junction planarity from the energy needed to flatten the angle terms between the physical neighbours of the bridge, rather than its RDKit hybridisation. Junctions with a missing angle term are treated as non-planar [#23](https://github.com/OpenBioSim/ghostly/pull/23).
+* Decide whether a bridge is in a ring, for stiffening and keeping impropers, from the physical atoms of the end state, so rings closed only by ghost atoms don't count [#23](https://github.com/OpenBioSim/ghostly/pull/23).
+* Keep improper dihedrals that hold a single ghost in the plane of a ring bridge, since nothing else stops the ghost crossing the plane when the angles aren't stiffened, and remove the ``--stiffen-ring-bridges`` option [#23](https://github.com/OpenBioSim/ghostly/pull/23).
+* Always stiffen ghost angles at bridges that aren't in a ring, and remove the ``--stiffen-sp2-bridges`` option. Without impropers, the angle terms of an sp2 bridge don't hold a ghost in the plane, so skipping stiffening let it cross freely. At linear bridges, angles through poorly-scoring physical neighbours are stiffened too, since the ghost angles can only all be satisfied at 90 degrees [#23](https://github.com/OpenBioSim/ghostly/pull/23).
+* Detect rotatable bridge bonds from the angle terms of the bridge, rather than its RDKit hybridisation, so that rotamer detection is consistent with junction planarity [#23](https://github.com/OpenBioSim/ghostly/pull/23).
+* Remove dihedrals and impropers involving ghost atoms that pass through an angle that is linear at the end state, e.g. anchor dihedrals at a terminal junction whose physical neighbour is a nitrile carbon. These terms are undefined for collinear atoms, where their forces diverge [#23](https://github.com/OpenBioSim/ghostly/pull/23).
 
 [2026.2.0](https://github.com/openbiosim/ghostly/compare/2026.1.0...2026.2.0) - Sep 2026
 ----------------------------------------------------------------------------------------

README.md

@@ -28,20 +28,24 @@ handle the diversity of perturbations encountered in practice:
 
 - **Anchor selection scoring:** physical anchor atoms are scored to avoid
   transmuting or bridge atoms, preventing geometrically inconsistent constraints.
-- **Ring and sp2 bridge handling:** angle stiffening is skipped by default for
-  ring and sp2 bridges, where local geometry already constrains the ghost and
-  90° stiffening would introduce significant strain. It can be re-enabled via
-  `--stiffen-ring-bridges` and `--stiffen-sp2-bridges`.
+- **Ring bridge handling:** ring bridges are not stiffened. Instead, their
+  improper dihedrals with a single ghost are kept, holding the ghost in the
+  plane of the ring, where the rigid ring keeps the coupling acceptable. All
+  other bridges are stiffened.
+- **Junction planarity:** whether a triple junction, or a bridge for rotamer
+  detection, is planar is decided from the energy needed to flatten the angle
+  terms between its neighbours.
 - **Residual term cleanup:** a post-processing pass removes mixed improper
-  dihedrals and cross-bridge dihedrals missed by the per-bridge junction
-  handlers, as well as angles where a ghost atom is the central atom and both
-  terminal atoms are physical.
+  dihedrals (other than those at ring bridges) and cross-bridge dihedrals
+  missed by the per-bridge junction handlers, as well as angles where a ghost
+  atom is the central atom and both terminal atoms are physical.
 - **Mixed dihedral softening:** surviving mixed ghost/physical dihedrals can
   be softened via `--soften-anchors` to allow ghost groups to reorient and
   avoid steric clashes at small λ.
-- **Rotamer stiffening:** `--stiffen-rotamers` replaces rotatable sp3 anchor
-  dihedrals with a stiff single-well cosine to control ghost orientation
-  through flexible bonds.
+- **Rotamer stiffening:** `--stiffen-rotamers` replaces anchor dihedrals
+  across rotatable bonds, i.e. those not in a ring whose bridge atom is neither
+  planar nor linear, with a stiff single-well cosine to control ghost
+  orientation through flexible bonds.
 - **Ring-breaking perturbations:** adjacent bridges with independent ghost
   groups retain each other as physical neighbours; angles with a ghost central
   atom spanning two physical neighbours are replaced by a linear spacer

src/ghostly/_cli.py

@@ -182,7 +182,7 @@ def run():
         help="""
              Whether to replace rotamer anchor dihedrals with a stiff
              single-well cosine potential. When a bridge-physical bond is
-             rotatable (not in a ring, sp3 bridge), surviving anchor
+             rotatable (not in a ring, non-planar bridge), surviving anchor
              dihedrals can allow rotameric transitions of ghost atoms at
              intermediate lambda.
              """,
@@ -202,34 +202,6 @@ def run():
         required=False,
     )
 
-    parser.add_argument(
-        "--stiffen-ring-bridges",
-        action="store_true",
-        help="""
-             Apply 90 degree angle stiffening when the bridge atom is in a
-             ring. By default this is skipped since the ring geometry already
-             constrains the ghost position and stiffening introduces strain.
-             A warning is logged when this is enabled and a ring bridge is
-             detected.
-             """,
-        default=False,
-        required=False,
-    )
-
-    parser.add_argument(
-        "--stiffen-sp2-bridges",
-        action="store_true",
-        help="""
-             Apply 90 degree angle stiffening when the bridge atom is sp2 and
-             not in a ring. By default this is skipped since sp2 hybridisation
-             already constrains the ghost to the molecular plane and stiffening
-             introduces ~30 degrees of strain. A warning is logged when this
-             is enabled and an sp2 bridge is detected.
-             """,
-        default=False,
-        required=False,
-    )
-
     parser.add_argument(
         "--linearise-ring-break",
         action=argparse.BooleanOptionalAction,
@@ -434,8 +406,6 @@ def run():
             k_single_well=k_single_well.value(),
             stiffen_rotamers=args.stiffen_rotamers,
             k_rotamer=k_rotamer.value(),
-            stiffen_ring_bridges=args.stiffen_ring_bridges,
-            stiffen_sp2_bridges=args.stiffen_sp2_bridges,
             linearise_ring_break=args.linearise_ring_break,
             force=args.force,
         )