From 98eaefa8014e175682f687426cce366680db4da4 Mon Sep 17 00:00:00 2001
From: dajiaohuang <mikewushuwen@outlook.com>
Date: Wed, 21 Oct 2026 08:00:03 +0800
Subject: [PATCH] fix: reset picking shapes before frame rebuilds

---
 src/GLModel.ts                        |  4 +++
 src/intersectionShapes.d.ts           |  7 +++++
 src/intersectionShapes.js             | 10 +++++++
 tests/jest/intersectionShapes.test.js | 42 +++++++++++++++++++++++++++
 4 files changed, 63 insertions(+)
 create mode 100644 src/intersectionShapes.d.ts
 create mode 100644 src/intersectionShapes.js
 create mode 100644 tests/jest/intersectionShapes.test.js

diff --git a/src/GLModel.ts b/src/GLModel.ts
index 2a5d244e..311ed9b5 100644
--- a/src/GLModel.ts
+++ b/src/GLModel.ts
@@ -20,6 +20,7 @@ import { ArrowSpec } from "GLShape";
 import { ParserOptionsSpec } from "./parsers/ParserOptionsSpec";
 import { LabelSpec } from "Label";
 import { assignBonds } from "./parsers/utils/assignBonds";
+import { resetIntersectionShapes } from "./intersectionShapes";
 
 /**
  * GLModel represents a group of related atoms
@@ -1666,6 +1667,9 @@ export class GLModel {
         for (let ai = 0; ai < atoms.length; ai++) this._coordIndex.set(atoms[ai], ai);
         this._coordAtomCount = atoms.length;
 
+        // Picking shapes are stored on atoms, so clear stale frame geometry before rebuilding.
+        resetIntersectionShapes(atoms);
+
         var ret = new Object3D();
         var cartoonAtoms = [];
         var lineGeometries: Record<number, Geometry> = {};
diff --git a/src/intersectionShapes.d.ts b/src/intersectionShapes.d.ts
new file mode 100644
index 00000000..76ceb8ed
--- /dev/null
+++ b/src/intersectionShapes.d.ts
@@ -0,0 +1,7 @@
+interface InteractiveAtom {
+    clickable?: boolean;
+    hoverable?: boolean;
+    intersectionShape?: any;
+}
+
+export function resetIntersectionShapes(atoms: InteractiveAtom[]): void;
diff --git a/src/intersectionShapes.js b/src/intersectionShapes.js
new file mode 100644
index 00000000..127147f7
--- /dev/null
+++ b/src/intersectionShapes.js
@@ -0,0 +1,10 @@
+function resetIntersectionShapes(atoms) {
+    for (var i = 0; i < atoms.length; i++) {
+        var atom = atoms[i];
+        if (atom && (atom.clickable || atom.hoverable)) {
+            atom.intersectionShape = { sphere: [], cylinder: [], line: [], triangle: [] };
+        }
+    }
+}
+
+module.exports = { resetIntersectionShapes: resetIntersectionShapes };
diff --git a/tests/jest/intersectionShapes.test.js b/tests/jest/intersectionShapes.test.js
new file mode 100644
index 00000000..ff689628
--- /dev/null
+++ b/tests/jest/intersectionShapes.test.js
@@ -0,0 +1,42 @@
+const { resetIntersectionShapes } = require("../../src/intersectionShapes");
+
+function oldShapes() {
+    return { sphere: ["stale"], cylinder: ["stale"], line: ["stale"], triangle: ["stale"] };
+}
+
+describe("picking-shape rebuilds", () => {
+    test("keeps clickable and hoverable frame shapes bounded on revisits", () => {
+        const frames = [
+            [
+                { clickable: true, intersectionShape: oldShapes() },
+                { hoverable: true, intersectionShape: oldShapes() },
+                { intersectionShape: { sphere: ["unchanged"] } },
+            ],
+            [{ clickable: true, intersectionShape: oldShapes() }],
+        ];
+        const noninteractiveShapes = frames[0][2].intersectionShape;
+
+        for (let rebuild = 0; rebuild < 200; rebuild++) {
+            const frame = frames[rebuild % frames.length];
+            resetIntersectionShapes(frame);
+            for (const atom of frame) {
+                if (atom.clickable || atom.hoverable) {
+                    atom.intersectionShape.sphere.push(rebuild);
+                    atom.intersectionShape.cylinder.push(rebuild);
+                }
+            }
+        }
+
+        for (const frame of frames) {
+            for (const atom of frame) {
+                if (atom.clickable || atom.hoverable) {
+                    expect(atom.intersectionShape.sphere).toHaveLength(1);
+                    expect(atom.intersectionShape.cylinder).toHaveLength(1);
+                    expect(atom.intersectionShape.line).toHaveLength(0);
+                    expect(atom.intersectionShape.triangle).toHaveLength(0);
+                }
+            }
+        }
+        expect(frames[0][2].intersectionShape).toBe(noninteractiveShapes);
+    });
+});