molstar 3.3.0 → 3.3.1

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) {

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

@@ -9,6 +9,7 @@ import { Mesh } from '../../../../mol-geo/geometry/mesh/mesh';
 import { VisualContext } from '../../../visual';
 import { Lines } from '../../../../mol-geo/geometry/lines/lines';
 import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
+import { Sphere3D } from '../../../../mol-math/geometry/primitives/sphere3d';
 export declare const LinkCylinderParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
@@ -75,14 +76,23 @@ export declare const enum LinkStyle {
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, mesh?: Mesh): Mesh;
+export declare function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, mesh?: Mesh): {
+    mesh: Mesh;
+    boundingSphere?: Sphere3D;
+};
 /**
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, cylinders?: Cylinders): Cylinders;
+export declare function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, cylinders?: Cylinders): {
+    cylinders: Cylinders;
+    boundingSphere?: Sphere3D;
+};
 /**
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkLineProps, lines?: Lines): Lines;
+export declare function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkLineProps, lines?: Lines): {
+    lines: Lines;
+    boundingSphere?: Sphere3D;
+};

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

@@ -13,6 +13,7 @@ import { Lines } from '../../../../mol-geo/geometry/lines/lines';
 import { LinesBuilder } from '../../../../mol-geo/geometry/lines/lines-builder';
 import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
 import { CylindersBuilder } from '../../../../mol-geo/geometry/cylinders/cylinders-builder';
+import { Sphere3D } from '../../../../mol-math/geometry/primitives/sphere3d';
 export var LinkCylinderParams = {
     linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
     linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
@@ -75,13 +76,15 @@ var v3dot = Vec3.dot;
 export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
-        return Mesh.createEmpty(mesh);
+        return { mesh: Mesh.createEmpty(mesh) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, radialSegments = props.radialSegments, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
     var vertexCountEstimate = radialSegments * 2 * linkCount * 2;
     var builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
     var va = Vec3();
     var vb = Vec3();
     var vShift = Vec3();
+    var center = Vec3();
+    var count = 0;
     var cylinderProps = {
         radiusTop: 1,
         radiusBottom: 1,
@@ -94,6 +97,9 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
         if (ignore && ignore(edgeIndex))
             continue;
         position(va, vb, edgeIndex);
+        v3add(center, center, va);
+        v3add(center, center, vb);
+        count += 2;
         v3sub(tmpV12, vb, va);
         var dirFlag = v3dot(tmpV12, up) > 0;
         var linkRadius = radius(edgeIndex);
@@ -181,7 +187,18 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             addCylinder(builderState, va, vb, 0.5, cylinderProps);
         }
     }
-    return MeshBuilder.getMesh(builderState);
+    var oldBoundingSphere = mesh ? Sphere3D.clone(mesh.boundingSphere) : undefined;
+    var m = MeshBuilder.getMesh(builderState);
+    if (count === 0)
+        return { mesh: m };
+    // 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) {
+        return { mesh: m, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { mesh: m };
+    }
 }
 /**
  * Each edge is included twice to allow for coloring/picking
@@ -190,7 +207,7 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
 export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
-        return Cylinders.createEmpty(cylinders);
+        return { cylinders: Cylinders.createEmpty(cylinders) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
     var cylindersCountEstimate = linkCount * 2;
     var builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
@@ -198,6 +215,8 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
     var vb = Vec3();
     var vm = Vec3();
     var vShift = Vec3();
+    var center = Vec3();
+    var count = 0;
     // automatically adjust length for evenly spaced dashed cylinders
     var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
@@ -207,6 +226,9 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
         if (ignore && ignore(edgeIndex))
             continue;
         position(va, vb, edgeIndex);
+        v3add(center, center, va);
+        v3add(center, center, vb);
+        count += 2;
         var linkRadius = radius(edgeIndex);
         var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
@@ -269,7 +291,18 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
             builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], 1, linkCap, linkStub, edgeIndex);
         }
     }
-    return builder.getCylinders();
+    var oldBoundingSphere = cylinders ? Sphere3D.clone(cylinders.boundingSphere) : undefined;
+    var c = builder.getCylinders();
+    if (count === 0)
+        return { cylinders: c };
+    // 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) {
+        return { cylinders: c, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { cylinders: c };
+    }
 }
 /**
  * Each edge is included twice to allow for coloring/picking
@@ -278,7 +311,7 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
 export function createLinkLines(ctx, linkBuilder, props, lines) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, ignore = linkBuilder.ignore;
     if (!linkCount)
-        return Lines.createEmpty(lines);
+        return { lines: Lines.createEmpty(lines) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount;
     var linesCountEstimate = linkCount * 2;
     var builder = LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
@@ -286,6 +319,8 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
     var vb = Vec3();
     var vm = Vec3();
     var vShift = Vec3();
+    var center = Vec3();
+    var count = 0;
     // automatically adjust length for evenly spaced dashed lines
     var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
@@ -297,6 +332,9 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
         if (ignore && ignore(edgeIndex))
             continue;
         position(va, vb, edgeIndex);
+        v3add(center, center, va);
+        v3add(center, center, vb);
+        count += 2;
         var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
         if (linkStyle === 0 /* Solid */) {
             v3scale(vm, v3add(vm, va, vb), 0.5);
@@ -354,5 +392,16 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
             builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], edgeIndex);
         }
     }
-    return builder.getLines();
+    var oldBoundingSphere = lines ? Sphere3D.clone(lines.boundingSphere) : undefined;
+    var l = builder.getLines();
+    if (count === 0)
+        return { lines: l };
+    // 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) {
+        return { lines: l, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { lines: l };
+    }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.3.0",
+  "version": "3.3.1",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {