fix bounding sphere calculations

CHANGELOG.md

@@ -19,6 +19,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add `MultiSampleParams.reduceFlicker` (to be able to switch it off)
 - Add `alphaThickness` parameter to adjust alpha of spheres for radius
 - Add `blockIndex` parameter to TrajectoryFromMmCif
+- Fix bounding sphere calculation for "element-like" visuals
 
 ## [v3.39.0] - 2023-09-02
 

src/mol-repr/structure/visual/element-point.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -71,7 +72,7 @@ export function createElementPoint(ctx: VisualContext, unit: Unit, structure: St
     // re-use boundingSphere if it has not changed much
     let boundingSphere: Sphere3D;
     Vec3.scale(center, center, 1 / count);
-    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
         boundingSphere = oldBoundingSphere;
     } else {
         boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);

src/mol-repr/structure/visual/util/element.ts

@@ -101,7 +101,7 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
     // re-use boundingSphere if it has not changed much
     let boundingSphere: Sphere3D;
     Vec3.scale(center, center, 1 / count);
-    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
         boundingSphere = oldBoundingSphere;
     } else {
         boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * sizeFactor + 0.05);
@@ -167,7 +167,7 @@ export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, stru
     // re-use boundingSphere if it has not changed much
     let boundingSphere: Sphere3D;
     Vec3.scale(center, center, 1 / count);
-    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
         boundingSphere = oldBoundingSphere;
     } else {
         boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * sizeFactor + 0.05);

src/mol-repr/structure/visual/util/link.ts

@@ -4,6 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Zhenyu Zhang <jump2cn@gmail.com>
  * @author Gianluca Tomasello <giagitom@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { Vec3 } from '../../../../mol-math/linear-algebra';
@@ -247,7 +248,7 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
 
     // re-use boundingSphere if it has not changed much
     Vec3.scale(center, center, 1 / count);
-    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
         return { mesh: m, boundingSphere: oldBoundingSphere };
     } else {
         return { mesh: m };
@@ -356,7 +357,7 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
 
     // re-use boundingSphere if it has not changed much
     Vec3.scale(center, center, 1 / count);
-    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
         return { cylinders: c, boundingSphere: oldBoundingSphere };
     } else {
         return { cylinders: c };
@@ -466,7 +467,7 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
 
     // re-use boundingSphere if it has not changed much
     Vec3.scale(center, center, 1 / count);
-    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) {
         return { lines: l, boundingSphere: oldBoundingSphere };
     } else {
         return { lines: l };