diff --git a/CHANGELOG.md b/CHANGELOG.md
index 810d7bfd82ec51aac6a61334f67f19657ad8db73..aeac889940b2d93a7bc88ed2732c34840e08f617 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,7 +17,12 @@ Note that since we don't clearly distinguish between a public and private interf
- Update clip `defines` only when changed
- Check for identity in structure/unit areEqual methods
- Avoid cloning of structure representation parameters
+ - Make SymmetryOperator.createMapping monomorphic
+ - Improve bonding-sphere calculation
+ - Defer Scene properties calculation (markerAverage, opacityAverage, hasOpaque)
+ - Improve checks in in UnitsRepresentation setVisualState
- Add StructureElement.Loci.forEachLocation
+- Add RepresentationRegistry.clear and ThemeRegistry.clear
## [v3.28.0] - 2022-12-20
diff --git a/src/mol-gl/renderable/util.ts b/src/mol-gl/renderable/util.ts
index cb54c9a737dd471d6b3cf3e6b3571111618abbf6..c642c6507a62e48bfda5e4d0a3cdc131a5e1ec49 100644
--- a/src/mol-gl/renderable/util.ts
+++ b/src/mol-gl/renderable/util.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -10,6 +10,10 @@ import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
import { TextureFilter } from '../webgl/texture';
import { arrayMinMax } from '../../mol-util/array';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3fromArray = Vec3.fromArray;
+const v3transformMat4Offset = Vec3.transformMat4Offset;
+
export function calculateTextureInfo(n: number, itemSize: number) {
n = Math.max(n, 2); // observed issues with 1 pixel textures
const sqN = Math.sqrt(n);
@@ -137,21 +141,21 @@ export function calculateInvariantBoundingSphere(position: Float32Array, positio
boundaryHelper.reset();
for (let i = 0, _i = positionCount * 3; i < _i; i += step) {
- Vec3.fromArray(v, position, i);
+ v3fromArray(v, position, i);
boundaryHelper.includePosition(v);
}
boundaryHelper.finishedIncludeStep();
for (let i = 0, _i = positionCount * 3; i < _i; i += step) {
- Vec3.fromArray(v, position, i);
+ v3fromArray(v, position, i);
boundaryHelper.radiusPosition(v);
}
const sphere = boundaryHelper.getSphere();
- if (positionCount <= 98) {
+ if (positionCount <= 14) {
const extrema: Vec3[] = [];
for (let i = 0, _i = positionCount * 3; i < _i; i += step) {
- extrema.push(Vec3.fromArray(Vec3(), position, i));
+ extrema.push(v3fromArray(Vec3(), position, i));
}
Sphere3D.setExtrema(sphere, extrema);
}
@@ -174,28 +178,28 @@ export function calculateTransformBoundingSphere(invariantBoundingSphere: Sphere
const { center, radius, extrema } = invariantBoundingSphere;
// only use extrema if there are not too many transforms
- if (extrema && transformCount < 50) {
+ if (extrema && transformCount <= 14) {
for (let i = 0, _i = transformCount; i < _i; ++i) {
for (const e of extrema) {
- Vec3.transformMat4Offset(v, e, transform, 0, 0, i * 16);
+ v3transformMat4Offset(v, e, transform, 0, 0, i * 16);
boundaryHelper.includePosition(v);
}
}
boundaryHelper.finishedIncludeStep();
for (let i = 0, _i = transformCount; i < _i; ++i) {
for (const e of extrema) {
- Vec3.transformMat4Offset(v, e, transform, 0, 0, i * 16);
+ v3transformMat4Offset(v, e, transform, 0, 0, i * 16);
boundaryHelper.radiusPosition(v);
}
}
} else {
for (let i = 0, _i = transformCount; i < _i; ++i) {
- Vec3.transformMat4Offset(v, center, transform, 0, 0, i * 16);
+ v3transformMat4Offset(v, center, transform, 0, 0, i * 16);
boundaryHelper.includePositionRadius(v, radius);
}
boundaryHelper.finishedIncludeStep();
for (let i = 0, _i = transformCount; i < _i; ++i) {
- Vec3.transformMat4Offset(v, center, transform, 0, 0, i * 16);
+ v3transformMat4Offset(v, center, transform, 0, 0, i * 16);
boundaryHelper.radiusPositionRadius(v, radius);
}
}
diff --git a/src/mol-gl/scene.ts b/src/mol-gl/scene.ts
index b8a8252b941c13baff32c3951cd8b1193c1f664f..a8d32ab433578eadd79980ce165fb49dc9864cfe 100644
--- a/src/mol-gl/scene.ts
+++ b/src/mol-gl/scene.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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>
@@ -105,6 +105,10 @@ namespace Scene {
let boundingSphereDirty = true;
let boundingSphereVisibleDirty = true;
+ let markerAverageDirty = true;
+ let opacityAverageDirty = true;
+ let hasOpaqueDirty = true;
+
let markerAverage = 0;
let opacityAverage = 0;
let hasOpaque = false;
@@ -165,9 +169,9 @@ namespace Scene {
}
renderables.sort(renderableSort);
- markerAverage = calculateMarkerAverage();
- opacityAverage = calculateOpacityAverage();
- hasOpaque = calculateHasOpaque();
+ markerAverageDirty = true;
+ opacityAverageDirty = true;
+ hasOpaqueDirty = true;
return true;
}
@@ -189,9 +193,9 @@ namespace Scene {
const newVisibleHash = computeVisibleHash();
if (newVisibleHash !== visibleHash) {
boundingSphereVisibleDirty = true;
- markerAverage = calculateMarkerAverage();
- opacityAverage = calculateOpacityAverage();
- hasOpaque = calculateHasOpaque();
+ markerAverageDirty = true;
+ opacityAverageDirty = true;
+ hasOpaqueDirty = true;
visibleHash = newVisibleHash;
return true;
} else {
@@ -268,9 +272,9 @@ namespace Scene {
} else {
syncVisibility();
}
- markerAverage = calculateMarkerAverage();
- opacityAverage = calculateOpacityAverage();
- hasOpaque = calculateHasOpaque();
+ markerAverageDirty = true;
+ opacityAverageDirty = true;
+ hasOpaqueDirty = true;
},
add: (o: GraphicsRenderObject) => commitQueue.add(o),
remove: (o: GraphicsRenderObject) => commitQueue.remove(o),
@@ -311,12 +315,24 @@ namespace Scene {
return boundingSphereVisible;
},
get markerAverage() {
+ if (markerAverageDirty) {
+ markerAverage = calculateMarkerAverage();
+ markerAverageDirty = false;
+ }
return markerAverage;
},
get opacityAverage() {
+ if (opacityAverageDirty) {
+ opacityAverage = calculateOpacityAverage();
+ opacityAverageDirty = false;
+ }
return opacityAverage;
},
get hasOpaque() {
+ if (hasOpaqueDirty) {
+ hasOpaque = calculateHasOpaque();
+ hasOpaqueDirty = false;
+ }
return hasOpaque;
},
};
diff --git a/src/mol-math/geometry/boundary-helper.ts b/src/mol-math/geometry/boundary-helper.ts
index c49ff1afddb6bd9a9816495bb94a963afc1ae87e..6f91c16ea78f011c7a4b63be520df1fbfc942b6e 100644
--- a/src/mol-math/geometry/boundary-helper.ts
+++ b/src/mol-math/geometry/boundary-helper.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -13,6 +13,7 @@ import { Box3D } from './primitives/box3d';
export class BoundaryHelper {
private dir: Vec3[];
+ private dirLength: number;
private minDist: number[] = [];
private maxDist: number[] = [];
@@ -56,13 +57,13 @@ export class BoundaryHelper {
}
includePosition(p: Vec3) {
- for (let i = 0, il = this.dir.length; i < il; ++i) {
+ for (let i = 0; i < this.dirLength; ++i) {
this.computeExtrema(i, p);
}
}
includePositionRadius(center: Vec3, radius: number) {
- for (let i = 0, il = this.dir.length; i < il; ++i) {
+ for (let i = 0; i < this.dirLength; ++i) {
this.computeSphereExtrema(i, center, radius);
}
}
@@ -101,7 +102,7 @@ export class BoundaryHelper {
}
reset() {
- for (let i = 0, il = this.dir.length; i < il; ++i) {
+ for (let i = 0; i < this.dirLength; ++i) {
this.minDist[i] = Infinity;
this.maxDist[i] = -Infinity;
this.extrema[i * 2] = Vec3();
@@ -112,6 +113,7 @@ export class BoundaryHelper {
constructor(quality: EposQuality) {
this.dir = getEposDir(quality);
+ this.dirLength = this.dir.length;
this.reset();
}
}
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index cbc2a5eda01f3d26d0f059e3e496d6743f8a4de9..279478b5e2f4bcc20aa5a2aeef4d221fbaa3e0af 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -177,11 +177,15 @@ namespace SymmetryOperator {
export interface Coordinates { x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number> }
- export function createMapping<T extends number>(operator: SymmetryOperator, coords: Coordinates, radius?: ((index: T) => number)): ArrayMapping<T> {
- const invariantPosition = SymmetryOperator.createCoordinateMapper(SymmetryOperator.Default, coords);
- const position = operator.isIdentity ? invariantPosition : SymmetryOperator.createCoordinateMapper(operator, coords);
+ function _createMapping<T extends number>(operator: SymmetryOperator, coords: Coordinates, radius: ((index: T) => number)): ArrayMapping<T> {
+ const invariantPosition = createCoordinateMapper(SymmetryOperator.Default, coords);
+ const position = operator.isIdentity ? invariantPosition : createCoordinateMapper(operator, coords);
const { x, y, z } = createProjections(operator, coords);
- return { operator, coordinates: coords, invariantPosition, position, x, y, z, r: radius ? radius : _zeroRadius };
+ return { operator, coordinates: coords, invariantPosition, position, x, y, z, r: radius };
+ }
+
+ export function createMapping<T extends number>(operator: SymmetryOperator, coords: Coordinates, radius: ((index: T) => number) = _zeroRadius) {
+ return _createMapping(operator, coords, radius);
}
export function createCoordinateMapper<T extends number>(t: SymmetryOperator, coords: Coordinates): CoordinateMapper<T> {
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index b6c8fc172ce33c6e4c4fec473c3788d661dbb7f5..6f6d1a814f71bd7dd1f5933d68c521d399c05ab6 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -46,7 +46,7 @@ namespace Unit {
export function create<K extends Kind>(id: number, invariantId: number, chainGroupId: number, traits: Traits, kind: Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set, props?: K extends Kind.Atomic ? AtomicProperties : CoarseProperties): Unit {
switch (kind) {
- case Kind.Atomic: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), props ?? AtomicProperties());
+ case Kind.Atomic: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation), props ?? AtomicProperties());
case Kind.Spheres: return createCoarse(id, invariantId, chainGroupId, traits, model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), props ?? CoarseProperties());
case Kind.Gaussians: return createCoarse(id, invariantId, chainGroupId, traits, model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), props ?? CoarseProperties());
}
diff --git a/src/mol-repr/representation.ts b/src/mol-repr/representation.ts
index ef534488d887eace73375402f9c1dacddfc631fd..4718fc6662f38afc276bd10aecfaaf80c696a2c7 100644
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/representation.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -135,6 +135,12 @@ export class RepresentationRegistry<D, S extends Representation.State> {
getApplicableTypes(data: D) {
return getTypes(this.getApplicableList(data));
}
+
+ clear() {
+ this._list.length = 0;
+ this._map.clear();
+ this._name.clear();
+ }
}
//
diff --git a/src/mol-repr/structure/registry.ts b/src/mol-repr/structure/registry.ts
index 8b5c5a5b5a451894a79339e952ccd3b82ca66945..348b19b5a534eadb0ead6cf2571a909ac8cdaafe 100644
--- a/src/mol-repr/structure/registry.ts
+++ b/src/mol-repr/structure/registry.ts
@@ -41,7 +41,7 @@ export namespace StructureRepresentationRegistry {
'carbohydrate': CarbohydrateRepresentationProvider,
'ellipsoid': EllipsoidRepresentationProvider,
'gaussian-surface': GaussianSurfaceRepresentationProvider,
- 'gaussian-volume': GaussianVolumeRepresentationProvider, // TODO disabled for now, needs more work
+ 'gaussian-volume': GaussianVolumeRepresentationProvider,
'label': LabelRepresentationProvider,
'line': LineRepresentationProvider,
'molecular-surface': MolecularSurfaceRepresentationProvider,
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index b713ede00253e42f34151a19bd149f1157fd7e06..a286188a54102892db8a07baaf137b747c0683ce 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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>
@@ -232,12 +232,16 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
if (substance !== undefined) visual.setSubstance(substance, webgl);
if (clipping !== undefined) visual.setClipping(clipping);
if (themeStrength !== undefined) visual.setThemeStrength(themeStrength);
- if (transform !== undefined) visual.setTransform(transform);
+ if (transform !== undefined) {
+ if (transform !== _state.transform || !Mat4.areEqual(transform, _state.transform, EPSILON)) {
+ visual.setTransform(transform);
+ }
+ }
if (unitTransforms !== undefined) {
if (unitTransforms) {
// console.log(group.hashCode, unitTransforms.getSymmetryGroupTransforms(group))
visual.setTransform(undefined, unitTransforms.getSymmetryGroupTransforms(group));
- } else {
+ } else if (unitTransforms !== _state.unitTransforms) {
visual.setTransform(undefined, null);
}
}
diff --git a/src/mol-theme/theme.ts b/src/mol-theme/theme.ts
index 1ba9a7e3f07c8b37c69963aa047a387bc0099be6..84aac3d8f3a94f8897313ec885c0c9f462140412 100644
--- a/src/mol-theme/theme.ts
+++ b/src/mol-theme/theme.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -156,4 +156,10 @@ export class ThemeRegistry<T extends ColorTheme<any, any> | SizeTheme<any>> {
getApplicableTypes(ctx: ThemeDataContext) {
return getTypes(this.getApplicableList(ctx));
}
+
+ clear() {
+ this._list.length = 0;
+ this._map.clear();
+ this._name.clear();
+ }
}
\ No newline at end of file