From fd50a8f8e08d3aa13fb718dd7b6c8761719b2679 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 17 May 2026 22:17:55 -0700
Subject: [PATCH 1/2] Fix aromatic ring detection not accounting for
 hybridization

---
 CHANGELOG.md                                  |  1 +
 .../structure/structure/unit/rings.ts         | 33 ++++++++++++++++++-
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6ca223246..e9bde57dc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix memory leak in `State.dispose()` not invoking transformer `dispose` callbacks for live cells
 - Fix bugs in ModelServer surroundingLigands endpoint, resulting in omitWater not honored
 - Fix `Volume` and `Isosurface` getBoundingSphere ignoring instances
+- Fix aromatic ring detection not accounting for hybridization
 
 ## [v5.9.0] - 2026-05-03
 - Fix edge case when `PluginSpec.animations` is empty
diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index 21f095fa5..3549906e5 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -95,10 +95,22 @@ namespace UnitRing {
         Elements.SN, Elements.SB,
         Elements.BI
     ] as ElementSymbol[]);
+    /**
+     * Elements that are sp3 (and therefore non-aromatic) when degree >= 4 with no pi bonds.
+     * Excludes O (never realistically reaches degree 4) and N (quaternary N can be aromatic,
+     * but is guarded by the hasPiBond check below).
+     */
+    const Sp3RingCheckElements = new Set([
+        Elements.B, Elements.C, Elements.N,
+        Elements.SI, Elements.P, Elements.S,
+        Elements.GE, Elements.AS,
+        Elements.SN, Elements.SB,
+        Elements.BI
+    ] as ElementSymbol[]);
     const AromaticRingPlanarityThreshold = 0.05;
 
     export function isAromatic(unit: Unit.Atomic, ring: UnitRing): boolean {
-        const { elements, bonds: { b, offset, edgeProps: { flags } } } = unit;
+        const { elements, bonds: { b, offset, edgeProps: { flags, order } } } = unit;
         const { type_symbol, label_comp_id } = unit.model.atomicHierarchy.atoms;
 
         // ignore Proline (can be flat because of bad geometry)
@@ -120,6 +132,25 @@ namespace UnitRing {
                 }
             }
         }
+
+        for (let i = 0, il = ring.length; i < il; ++i) {
+            const aI = ring[i];
+            const elem = type_symbol.value(elements[aI]);
+            if (!Sp3RingCheckElements.has(elem)) continue;
+
+            let degree = 0;
+            let hasPiBond = false;
+            for (let j = offset[aI], jl = offset[aI + 1]; j < jl; ++j) {
+                degree += 1;
+                const f = flags[j];
+                const o = order[j];
+                if (BondType.is(BondType.Flag.Aromatic, f) || o === 2 || o === 3) {
+                    hasPiBond = true;
+                }
+            }
+            if (degree >= 4 && !hasPiBond) return false;
+        }
+
         if (aromaticBondCount === 2 * ring.length) return true;
         if (!hasAromaticRingElement) return false;
         if (ring.length < 5) return false;

From bcd304d058b7ebc1ef4f8222d1c498d71e77d2c4 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 17 May 2026 22:19:04 -0700
Subject: [PATCH 2/2] header

---
 src/mol-model/structure/structure/unit/rings.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mol-model/structure/structure/unit/rings.ts b/src/mol-model/structure/structure/unit/rings.ts
index 3549906e5..40f323515 100644
--- a/src/mol-model/structure/structure/unit/rings.ts
+++ b/src/mol-model/structure/structure/unit/rings.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>