fix bounding box bug

src/mol-math/geometry/lookup3d/grid.ts

@@ -168,7 +168,7 @@ function _build(state: BuildState): Grid3D {
 
 function build(data: PositionData, boundary: Boundary, cellSizeOrCount?: Vec3 | number) {
     // need to expand the grid bounds to avoid rounding errors
-    const expandedBox = Box3D.expand(Box3D.empty(), boundary.box, Vec3.create(0.5, 0.5, 0.5));
+    const expandedBox = Box3D.expand(Box3D(), boundary.box, Vec3.create(0.5, 0.5, 0.5));
     const { indices } = data;
 
     const S = Box3D.size(Vec3.zero(), expandedBox);

src/mol-math/geometry/primitives/box3d.ts

@@ -13,12 +13,12 @@ import { Sphere3D } from './sphere3d';
 interface Box3D { min: Vec3, max: Vec3 }
 
 function Box3D() {
-    return Box3D.empty();
+    return Box3D.zero();
 }
 
 namespace Box3D {
     export function create(min: Vec3, max: Vec3): Box3D { return { min, max }; }
-    export function empty(): Box3D { return { min: Vec3(), max: Vec3() }; }
+    export function zero(): Box3D { return { min: Vec3(), max: Vec3() }; }
 
     export function copy(out: Box3D, a: Box3D): Box3D {
         Vec3.copy(out.min, a.min);
@@ -27,7 +27,7 @@ namespace Box3D {
     }
 
     export function clone(a: Box3D): Box3D {
-        return copy(empty(), a);
+        return copy(zero(), a);
     }
 
     /** Get box from sphere, uses extrema if available */
@@ -77,6 +77,7 @@ namespace Box3D {
         return tmpSizeV[0] * tmpSizeV[1] * tmpSizeV[2];
     }
 
+    /** Sets min to Number.MAX_VALUE and max to -Number.MAX_VALUE */
     export function setEmpty(box: Box3D): Box3D {
         Vec3.set(box.min, Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE);
         Vec3.set(box.max, -Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE);

src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts

@@ -71,7 +71,7 @@ export namespace VolumeStreaming {
 
         // fake the info
         const info = entryData || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: Volume.IsoValue.relative(0) };
-        const box = (structure && structure.boundary.box) || Box3D.empty();
+        const box = (structure && structure.boundary.box) || Box3D();
 
         return {
             view: PD.MappedStatic(defaultView || (info.kind === 'em' ? 'cell' : 'selection-box'), {
@@ -304,13 +304,13 @@ export namespace VolumeStreaming {
 
         private getBoxFromLoci(loci: StructureElement.Loci | EmptyLoci): Box3D {
             if (Loci.isEmpty(loci)) {
-                return Box3D.empty();
+                return Box3D();
             }
 
             const parent = this.plugin.helpers.substructureParent.get(loci.structure, true);
-            if (!parent) return Box3D.empty();
+            if (!parent) return Box3D();
             const root = this.getStructureRoot();
-            if (!root || root.obj?.data !== parent.obj?.data) return Box3D.empty();
+            if (!root || root.obj?.data !== parent.obj?.data) return Box3D();
 
             const extendedLoci = StructureElement.Loci.extendToWholeResidues(loci);
             const box = StructureElement.Loci.getBoundary(extendedLoci).box;
@@ -341,14 +341,14 @@ export namespace VolumeStreaming {
         private updateSelectionBox(loci: StructureElement.Loci | EmptyLoci) {
             if (Loci.areEqual(this.lastLoci, loci)) {
                 this.lastLoci = EmptyLoci;
-                this.updateSelectionBoxParams(Box3D.empty());
+                this.updateSelectionBoxParams(Box3D());
                 return;
             }
 
             this.lastLoci = loci;
 
             if (isEmptyLoci(loci)) {
-                this.updateSelectionBoxParams(Box3D.empty());
+                this.updateSelectionBoxParams(Box3D());
                 return;
             }
 
@@ -373,7 +373,7 @@ export namespace VolumeStreaming {
                     break;
                 case 'selection-box': {
                     if (switchedToSelection) {
-                        box = this.getBoxFromLoci(this.lastLoci) || Box3D.empty();
+                        box = this.getBoxFromLoci(this.lastLoci) || Box3D();
                     } else {
                         box = Box3D.create(Vec3.clone(params.entry.params.view.params.bottomLeft), Vec3.clone(params.entry.params.view.params.topRight));
                     }

src/mol-repr/volume/direct-volume.ts

@@ -25,7 +25,7 @@ import { eachVolumeLoci } from './util';
 import { encodeFloatRGBtoArray } from '../../mol-util/float-packing';
 
 function getBoundingBox(gridDimension: Vec3, transform: Mat4) {
-    const bbox = Box3D.empty();
+    const bbox = Box3D.setEmpty(Box3D());
     Box3D.add(bbox, gridDimension);
     Box3D.transform(bbox, bbox, transform);
     return bbox;