molstar 3.3.0 → 3.5.0

package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -142,20 +142,30 @@ function createInterUnitBondCylinderImpostors(ctx, structure, theme, props, cyli
     if (!structure.interUnitBonds.edgeCount)
         return Cylinders.createEmpty(cylinders);
     var builderProps = getInterUnitBondCylinderBuilderProps(structure, theme, props);
-    var m = createLinkCylinderImpostors(ctx, builderProps, props, cylinders);
-    var child = structure.child;
-    var sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
-    return m;
+    var _a = createLinkCylinderImpostors(ctx, builderProps, props, cylinders), c = _a.cylinders, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        c.setBoundingSphere(boundingSphere);
+    }
+    else if (c.cylinderCount > 0) {
+        var child = structure.child;
+        var sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
+        c.setBoundingSphere(sphere);
+    }
+    return c;
 }
 function createInterUnitBondCylinderMesh(ctx, structure, theme, props, mesh) {
     if (!structure.interUnitBonds.edgeCount)
         return Mesh.createEmpty(mesh);
     var builderProps = getInterUnitBondCylinderBuilderProps(structure, theme, props);
-    var m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
-    var child = structure.child;
-    var sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
+    var _a = createLinkCylinderMesh(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var child = structure.child;
+        var sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
     return m;
 }
 export var InterUnitBondCylinderParams = __assign(__assign(__assign(__assign({}, ComplexMeshParams), ComplexCylindersParams), BondCylinderParams), { sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: PD.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: PD.Boolean(true), includeParent: PD.Boolean(false) });

package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/bond-inter-unit-line.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -96,10 +96,15 @@ function createInterUnitBondLines(ctx, structure, theme, props, lines) {
         },
         ignore: makeInterBondIgnoreTest(structure, props)
     };
-    var l = createLinkLines(ctx, builderProps, props, lines);
-    var child = structure.child;
-    var sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * props.sizeFactor);
-    l.setBoundingSphere(sphere);
+    var _a = createLinkLines(ctx, builderProps, props, lines), l = _a.lines, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        l.setBoundingSphere(boundingSphere);
+    }
+    else if (l.lineCount > 0) {
+        var child = structure.child;
+        var sphere = Sphere3D.expand(Sphere3D(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * sizeFactor);
+        l.setBoundingSphere(sphere);
+    }
     return l;
 }
 export var InterUnitBondLineParams = __assign(__assign(__assign({}, ComplexLinesParams), BondLineParams), { includeParent: PD.Boolean(false) });

package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js

@@ -162,9 +162,14 @@ function createIntraUnitBondCylinderImpostors(ctx, unit, structure, theme, props
     if (child && !childUnit)
         return Cylinders.createEmpty(cylinders);
     var builderProps = getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props);
-    var c = createLinkCylinderImpostors(ctx, builderProps, props, cylinders);
-    var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
-    c.setBoundingSphere(sphere);
+    var _a = createLinkCylinderImpostors(ctx, builderProps, props, cylinders), c = _a.cylinders, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        c.setBoundingSphere(boundingSphere);
+    }
+    else if (c.cylinderCount > 0) {
+        var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
+        c.setBoundingSphere(sphere);
+    }
     return c;
 }
 function createIntraUnitBondCylinderMesh(ctx, unit, structure, theme, props, mesh) {
@@ -177,9 +182,14 @@ function createIntraUnitBondCylinderMesh(ctx, unit, structure, theme, props, mes
     if (child && !childUnit)
         return Mesh.createEmpty(mesh);
     var builderProps = getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props);
-    var m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
-    var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
+    var _a = createLinkCylinderMesh(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * props.sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
     return m;
 }
 export var IntraUnitBondCylinderParams = __assign(__assign(__assign(__assign({}, UnitsMeshParams), UnitsCylindersParams), BondCylinderParams), { sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: PD.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: PD.Boolean(true), includeParent: PD.Boolean(false) });

package/lib/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -122,9 +122,14 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
         },
         ignore: makeIntraBondIgnoreTest(structure, unit, props)
     };
-    var l = createLinkLines(ctx, builderProps, props, lines);
-    var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
-    l.setBoundingSphere(sphere);
+    var _b = createLinkLines(ctx, builderProps, props, lines), l = _b.lines, boundingSphere = _b.boundingSphere;
+    if (boundingSphere) {
+        l.setBoundingSphere(boundingSphere);
+    }
+    else if (l.lineCount > 0) {
+        var sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
+        l.setBoundingSphere(sphere);
+    }
     return l;
 }
 export var IntraUnitBondLineParams = __assign(__assign(__assign({}, UnitsLinesParams), BondLineParams), { includeParent: PD.Boolean(false) });

package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js

@@ -14,6 +14,7 @@ import { UnitsMeshParams } from '../units-visual';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { LocationIterator } from '../../../mol-geo/util/location-iterator';
 import { getAltResidueLociFromId } from './util/common';
+import { Sphere3D } from '../../../mol-math/geometry';
 function createCarbohydrateLinkCylinderMesh(ctx, structure, theme, props, mesh) {
     var _a = structure.carbohydrates, links = _a.links, elements = _a.elements;
     var linkSizeFactor = props.linkSizeFactor;
@@ -34,7 +35,15 @@ function createCarbohydrateLinkCylinderMesh(ctx, structure, theme, props, mesh)
             return theme.size.size(location) * linkSizeFactor;
         },
     };
-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    var _b = createLinkCylinderMesh(ctx, builderProps, props, mesh), m = _b.mesh, boundingSphere = _b.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * linkSizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 export var CarbohydrateLinkParams = __assign(__assign(__assign({}, UnitsMeshParams), LinkCylinderParams), { linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }) });
 export function CarbohydrateLinkVisual(materialId) {

package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js

@@ -15,6 +15,7 @@ import { OrderedSet, Interval } from '../../../mol-data/int';
 import { EmptyLoci } from '../../../mol-model/loci';
 import { getElementIdx, MetalsSet } from '../../../mol-model/structure/structure/unit/bonds/common';
 import { getAltResidueLociFromId, getAltResidueLoci } from './util/common';
+import { Sphere3D } from '../../../mol-math/geometry';
 function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props, mesh) {
     var _a = structure.carbohydrates, terminalLinks = _a.terminalLinks, elements = _a.elements;
     var terminalLinkSizeFactor = props.terminalLinkSizeFactor;
@@ -53,7 +54,15 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props
             return MetalsSet.has(beI) ? 1 /* Dashed */ : 0 /* Solid */;
         }
     };
-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    var _b = createLinkCylinderMesh(ctx, builderProps, props, mesh), m = _b.mesh, boundingSphere = _b.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * terminalLinkSizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
 export var CarbohydrateTerminalLinkParams = __assign(__assign(__assign({}, UnitsMeshParams), LinkCylinderParams), { terminalLinkSizeFactor: PD.Numeric(0.2, { min: 0, max: 3, step: 0.01 }) });
 export function CarbohydrateTerminalLinkVisual(materialId) {

package/lib/mol-repr/structure/visual/element-point.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/element-point.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,6 +11,8 @@ import { PointsBuilder } from '../../../mol-geo/geometry/points/points-builder';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { ElementIterator, getElementLoci, eachElement, makeElementIgnoreTest } from './util/element';
 import { Sphere3D } from '../../../mol-math/geometry';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+var v3add = Vec3.add;
 export var ElementPointParams = __assign(__assign({}, UnitsPointsParams), { pointSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), traceOnly: PD.Boolean(false) });
 // TODO size
 export function createElementPoint(ctx, unit, structure, theme, props, points) {
@@ -24,23 +26,40 @@ export function createElementPoint(ctx, unit, structure, theme, props, points) {
     var p = Vec3();
     var pos = unit.conformation.invariantPosition;
     var ignore = makeElementIgnoreTest(structure, unit, props);
+    var center = Vec3();
+    var count = 0;
     if (ignore) {
         for (var i = 0; i < n; ++i) {
             if (ignore(elements[i]))
                 continue;
             pos(elements[i], p);
+            v3add(center, center, p);
+            count += 1;
             builder.add(p[0], p[1], p[2], i);
         }
     }
     else {
         for (var i = 0; i < n; ++i) {
             pos(elements[i], p);
+            v3add(center, center, p);
+            count += 1;
             builder.add(p[0], p[1], p[2], i);
         }
     }
+    var oldBoundingSphere = points ? Sphere3D.clone(points.boundingSphere) : undefined;
     var pt = builder.getPoints();
-    var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
-    pt.setBoundingSphere(sphere);
+    if (count === 0)
+        return pt;
+    // re-use boundingSphere if it has not changed much
+    var boundingSphere;
+    Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        boundingSphere = oldBoundingSphere;
+    }
+    else {
+        boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    }
+    pt.setBoundingSphere(boundingSphere);
     return pt;
 }
 export function ElementPointVisual(materialId) {

package/lib/mol-repr/structure/visual/gaussian-density-volume.js

@@ -12,7 +12,6 @@ import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 import { eachElement, eachSerialElement, ElementIterator, getElementLoci, getSerialElementLoci } from './util/element';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { UnitsDirectVolumeParams, UnitsDirectVolumeVisual } from '../units-visual';
-import { getStructureExtraRadius, getUnitExtraRadius } from './util/common';
 function createGaussianDensityVolume(ctx, structure, theme, props, directVolume) {
     return __awaiter(this, void 0, void 0, function () {
         var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
@@ -33,7 +32,7 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
                     cellDim = Mat4.getScaling(Vec3(), transform);
                     axisOrder = Vec3.create(0, 1, 2);
                     vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
-                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
             }
@@ -91,7 +90,7 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
                     cellDim = Mat4.getScaling(Vec3(), transform);
                     axisOrder = Vec3.create(0, 1, 2);
                     vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
             }

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,7 +14,7 @@ import { TextureMesh } from '../../../mol-geo/geometry/texture-mesh/texture-mesh
 import { extractIsosurface } from '../../../mol-gl/compute/marching-cubes/isosurface';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { ComplexMeshParams, ComplexMeshVisual, ComplexTextureMeshVisual, ComplexTextureMeshParams } from '../complex-visual';
-import { getUnitExtraRadius, getStructureExtraRadius, getVolumeSliceInfo } from './util/common';
+import { getVolumeSliceInfo } from './util/common';
 import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
 import { applyTextureMeshColorSmoothing } from '../../../mol-geo/geometry/texture-mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
@@ -51,14 +51,14 @@ export function StructureGaussianSurfaceVisual(materialId, structure, props, web
 //
 function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var smoothness, _a, transform, field, idField, radiusFactor, resolution, params, surface, sphere;
+        var smoothness, _a, transform, field, idField, radiusFactor, resolution, maxRadius, params, surface, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: Math.exp(-smoothness) / radiusFactor,
                         scalarField: field,
@@ -71,7 +71,7 @@ function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         Mesh.uniformTriangleGroup(surface);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     return [2 /*return*/, surface];
             }
@@ -128,14 +128,14 @@ export function GaussianSurfaceMeshVisual(materialId) {
 //
 function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var smoothness, _a, transform, field, idField, radiusFactor, resolution, params, surface, sphere;
+        var smoothness, _a, transform, field, idField, radiusFactor, resolution, maxRadius, params, surface, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, computeStructureGaussianDensity(structure, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: Math.exp(-smoothness) / radiusFactor,
                         scalarField: field,
@@ -148,7 +148,7 @@ function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh)
                     Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         Mesh.uniformTriangleGroup(surface);
-                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     return [2 /*return*/, surface];
             }
@@ -225,7 +225,7 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                     axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
-                    boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
                     return [2 /*return*/, surface];
@@ -308,7 +308,7 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                     axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
-                    boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
                     return [2 /*return*/, surface];

package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,17 +11,16 @@ import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/
 import { UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { Sphere3D } from '../../../mol-math/geometry';
-import { getUnitExtraRadius } from './util/common';
 function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
     return __awaiter(this, void 0, void 0, function () {
-        var smoothness, _a, transform, field, idField, params, wireframe, sphere;
+        var smoothness, _a, transform, field, idField, maxRadius, params, wireframe, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: Math.exp(-smoothness),
                         scalarField: field,
@@ -31,7 +30,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
                 case 2:
                     wireframe = _b.sent();
                     Lines.transform(wireframe, transform);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     wireframe.setBoundingSphere(sphere);
                     return [2 /*return*/, wireframe];
             }

package/lib/mol-repr/structure/visual/molecular-surface-mesh.js

@@ -11,7 +11,7 @@ import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { computeUnitMolecularSurface } from './util/molecular-surface';
 import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
-import { CommonSurfaceParams, getUnitExtraRadius } from './util/common';
+import { CommonSurfaceParams } from './util/common';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
@@ -19,12 +19,12 @@ export var MolecularSurfaceMeshParams = __assign(__assign(__assign(__assign({},
 //
 function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var _a, transform, field, idField, resolution, params, surface, iterations, sphere;
+        var _a, transform, field, idField, resolution, maxRadius, params, surface, iterations, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, resolution = _a.resolution;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, resolution = _a.resolution, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: props.probeRadius,
                         scalarField: field,
@@ -40,7 +40,7 @@ function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         Mesh.uniformTriangleGroup(surface);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     surface.meta.resolution = resolution;
                     return [2 /*return*/, surface];

package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,18 +11,18 @@ import { Lines } from '../../../mol-geo/geometry/lines/lines';
 import { computeUnitMolecularSurface } from './util/molecular-surface';
 import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/algorithm';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
-import { CommonSurfaceParams, getUnitExtraRadius } from './util/common';
+import { CommonSurfaceParams } from './util/common';
 import { Sphere3D } from '../../../mol-math/geometry';
 export var MolecularSurfaceWireframeParams = __assign(__assign(__assign(__assign({}, UnitsLinesParams), MolecularSurfaceCalculationParams), CommonSurfaceParams), { sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }) });
 //
 function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lines) {
     return __awaiter(this, void 0, void 0, function () {
-        var _a, transform, field, idField, params, wireframe, sphere;
+        var _a, transform, field, idField, maxRadius, params, wireframe, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: props.probeRadius,
                         scalarField: field,
@@ -32,7 +32,7 @@ function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lin
                 case 2:
                     wireframe = _b.sent();
                     Lines.transform(wireframe, transform);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     wireframe.setBoundingSphere(sphere);
                     return [2 /*return*/, wireframe];
             }

package/lib/mol-repr/structure/visual/util/common.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -85,5 +85,3 @@ export declare function getStructureConformationAndRadius(structure: Structure,
 export declare function isHydrogen(unit: Unit, element: ElementIndex): boolean;
 export declare function isH(atomicNumber: ArrayLike<number>, element: ElementIndex): boolean;
 export declare function isTrace(unit: Unit, element: ElementIndex): boolean;
-export declare function getUnitExtraRadius(unit: Unit): number;
-export declare function getStructureExtraRadius(structure: Structure): number;

package/lib/mol-repr/structure/visual/util/common.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -273,26 +273,3 @@ export function isTrace(unit, element) {
         return true;
     return false;
 }
-export function getUnitExtraRadius(unit) {
-    if (Unit.isAtomic(unit))
-        return 4;
-    var max = 0;
-    var elements = unit.elements;
-    var r = unit.conformation.r;
-    for (var i = 0, _i = elements.length; i < _i; i++) {
-        var _r = r(elements[i]);
-        if (_r > max)
-            max = _r;
-    }
-    return max + 1;
-}
-export function getStructureExtraRadius(structure) {
-    var max = 0;
-    for (var _a = 0, _b = structure.unitSymmetryGroups; _a < _b.length; _a++) {
-        var ug = _b[_a];
-        var r = getUnitExtraRadius(ug.units[0]);
-        if (r > max)
-            max = r;
-    }
-    return max;
-}

package/lib/mol-repr/structure/visual/util/element.js

@@ -17,6 +17,8 @@ import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
 import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-builder';
 import { isTrace, isH } from './common';
 import { Sphere3D } from '../../../../mol-math/geometry';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+var v3add = Vec3.add;
 export function makeElementIgnoreTest(structure, unit, props) {
     var ignoreHydrogens = props.ignoreHydrogens, traceOnly = props.traceOnly;
     var atomicNumber = unit.model.atomicHierarchy.derived.atom.atomicNumber;
@@ -48,20 +50,36 @@ export function createElementSphereMesh(ctx, unit, structure, theme, props, mesh
     var ignore = makeElementIgnoreTest(structure, unit, props);
     var l = StructureElement.Location.create(structure, unit);
     var themeSize = theme.size.size;
+    var center = Vec3();
     var maxSize = 0;
+    var count = 0;
     for (var i = 0; i < elementCount; i++) {
         if (ignore && ignore(elements[i]))
             continue;
         l.element = elements[i];
         pos(elements[i], v);
+        v3add(center, center, v);
+        count += 1;
         builderState.currentGroup = i;
         var size = themeSize(l);
         if (size > maxSize)
             maxSize = size;
         addSphere(builderState, v, size * sizeFactor, detail);
     }
+    var oldBoundingSphere = mesh ? Sphere3D.clone(mesh.boundingSphere) : undefined;
     var m = MeshBuilder.getMesh(builderState);
-    m.setBoundingSphere(Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * sizeFactor + 0.05));
+    if (count === 0)
+        return m;
+    // re-use boundingSphere if it has not changed much
+    var boundingSphere;
+    Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        boundingSphere = oldBoundingSphere;
+    }
+    else {
+        boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * sizeFactor + 0.05);
+    }
+    m.setBoundingSphere(boundingSphere);
     return m;
 }
 export function createElementSphereImpostor(ctx, unit, structure, theme, props, spheres) {
@@ -77,19 +95,35 @@ export function createElementSphereImpostor(ctx, unit, structure, theme, props,
     var ignore = makeElementIgnoreTest(structure, unit, props);
     var l = StructureElement.Location.create(structure, unit);
     var themeSize = theme.size.size;
+    var center = Vec3();
     var maxSize = 0;
+    var count = 0;
     for (var i = 0; i < elementCount; i++) {
         if (ignore === null || ignore === void 0 ? void 0 : ignore(elements[i]))
             continue;
         pos(elements[i], v);
         builder.add(v[0], v[1], v[2], i);
+        v3add(center, center, v);
+        count += 1;
         l.element = elements[i];
         var size = themeSize(l);
         if (size > maxSize)
             maxSize = size;
     }
+    var oldBoundingSphere = spheres ? Sphere3D.clone(spheres.boundingSphere) : undefined;
     var s = builder.getSpheres();
-    s.setBoundingSphere(Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * props.sizeFactor + 0.05));
+    if (count === 0)
+        return s;
+    // re-use boundingSphere if it has not changed much
+    var boundingSphere;
+    Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        boundingSphere = oldBoundingSphere;
+    }
+    else {
+        boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, maxSize * props.sizeFactor + 0.05);
+    }
+    s.setBoundingSphere(boundingSphere);
     return s;
 }
 export function eachElement(loci, structureGroup, apply) {