molstar 3.0.0-dev.9 → 3.1.0

package/lib/mol-plugin-ui/controls.js

@@ -14,6 +14,7 @@ import { StructureSourceControls } from './structure/source';
 import { VolumeStreamingControls, VolumeSourceControls } from './structure/volume';
 import { PluginConfig } from '../mol-plugin/config';
 import { StructureSuperpositionControls } from './structure/superposition';
+import { StructureQuickStylesControls } from './structure/quick-styles';
 var TrajectoryViewportControls = /** @class */ (function (_super) {
     __extends(TrajectoryViewportControls, _super);
     function TrajectoryViewportControls() {
@@ -290,7 +291,7 @@ var DefaultStructureTools = /** @class */ (function (_super) {
         return _super !== null && _super.apply(this, arguments) || this;
     }
     DefaultStructureTools.prototype.render = function () {
-        return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-section-header' }, { children: [_jsx(Icon, { svg: BuildSvg }, void 0), "Structure Tools"] }), void 0), _jsx(StructureSourceControls, {}, void 0), _jsx(StructureMeasurementsControls, {}, void 0), _jsx(StructureSuperpositionControls, {}, void 0), _jsx(StructureComponentControls, {}, void 0), this.plugin.config.get(PluginConfig.VolumeStreaming.Enabled) && _jsx(VolumeStreamingControls, {}, void 0), _jsx(VolumeSourceControls, {}, void 0), _jsx(CustomStructureControls, {}, void 0)] }, void 0);
+        return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-section-header' }, { children: [_jsx(Icon, { svg: BuildSvg }, void 0), "Structure Tools"] }), void 0), _jsx(StructureSourceControls, {}, void 0), _jsx(StructureMeasurementsControls, {}, void 0), _jsx(StructureSuperpositionControls, {}, void 0), _jsx(StructureQuickStylesControls, {}, void 0), _jsx(StructureComponentControls, {}, void 0), this.plugin.config.get(PluginConfig.VolumeStreaming.Enabled) && _jsx(VolumeStreamingControls, {}, void 0), _jsx(VolumeSourceControls, {}, void 0), _jsx(CustomStructureControls, {}, void 0)] }, void 0);
     };
     return DefaultStructureTools;
 }(PluginUIComponent));

package/lib/mol-plugin-ui/structure/quick-styles.d.ts

@@ -0,0 +1,25 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+/// <reference types="react" />
+import { CollapsableControls, PurePluginUIComponent } from '../base';
+import { MagicWandSvg } from '../controls/icons';
+export declare class StructureQuickStylesControls extends CollapsableControls {
+    defaultState(): {
+        isCollapsed: boolean;
+        header: string;
+        brand: {
+            accent: "gray";
+            svg: typeof MagicWandSvg;
+        };
+    };
+    renderControls(): JSX.Element;
+}
+export declare class QuickStyles extends PurePluginUIComponent {
+    default(): Promise<void>;
+    illustrative(): Promise<void>;
+    stylized(): Promise<void>;
+    render(): JSX.Element;
+}

package/lib/mol-plugin-ui/structure/quick-styles.js

@@ -0,0 +1,128 @@
+import { __assign, __awaiter, __extends, __generator } from "tslib";
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { Color } from '../../mol-util/color';
+import { CollapsableControls, PurePluginUIComponent } from '../base';
+import { Button } from '../controls/common';
+import { MagicWandSvg } from '../controls/icons';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PostprocessingParams } from '../../mol-canvas3d/passes/postprocessing';
+import { PluginConfig } from '../../mol-plugin/config';
+import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
+var StructureQuickStylesControls = /** @class */ (function (_super) {
+    __extends(StructureQuickStylesControls, _super);
+    function StructureQuickStylesControls() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    StructureQuickStylesControls.prototype.defaultState = function () {
+        return {
+            isCollapsed: false,
+            header: 'Quick Styles',
+            brand: { accent: 'gray', svg: MagicWandSvg }
+        };
+    };
+    StructureQuickStylesControls.prototype.renderControls = function () {
+        return _jsx(_Fragment, { children: _jsx(QuickStyles, {}, void 0) }, void 0);
+    };
+    return StructureQuickStylesControls;
+}(CollapsableControls));
+export { StructureQuickStylesControls };
+var QuickStyles = /** @class */ (function (_super) {
+    __extends(QuickStyles, _super);
+    function QuickStyles() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    QuickStyles.prototype.default = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var structures, preset, provider, p;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        structures = this.plugin.managers.structure.hierarchy.selection.structures;
+                        preset = this.plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+                        provider = this.plugin.builders.structure.representation.resolveProvider(preset);
+                        return [4 /*yield*/, this.plugin.managers.structure.component.applyPreset(structures, provider)];
+                    case 1:
+                        _a.sent();
+                        this.plugin.managers.structure.component.setOptions(PD.getDefaultValues(StructureComponentManager.OptionsParams));
+                        if (this.plugin.canvas3d) {
+                            p = PD.getDefaultValues(PostprocessingParams);
+                            this.plugin.canvas3d.setProps({
+                                postprocessing: { outline: p.outline, occlusion: p.occlusion }
+                            });
+                        }
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    QuickStyles.prototype.illustrative = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var structures;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        structures = this.plugin.managers.structure.hierarchy.selection.structures;
+                        return [4 /*yield*/, this.plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations.illustrative)];
+                    case 1:
+                        _a.sent();
+                        if (this.plugin.canvas3d) {
+                            this.plugin.canvas3d.setProps({
+                                postprocessing: {
+                                    outline: {
+                                        name: 'on',
+                                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
+                                    },
+                                    occlusion: {
+                                        name: 'on',
+                                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
+                                    },
+                                }
+                            });
+                        }
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    QuickStyles.prototype.stylized = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var pp;
+            return __generator(this, function (_a) {
+                this.plugin.managers.structure.component.setOptions(__assign(__assign({}, this.plugin.managers.structure.component.state.options), { ignoreLight: true }));
+                if (this.plugin.canvas3d) {
+                    pp = this.plugin.canvas3d.props.postprocessing;
+                    this.plugin.canvas3d.setProps({
+                        postprocessing: {
+                            outline: {
+                                name: 'on',
+                                params: pp.outline.name === 'on'
+                                    ? pp.outline.params
+                                    : { scale: 1, color: Color(0x000000), threshold: 0.33 }
+                            },
+                            occlusion: {
+                                name: 'on',
+                                params: pp.occlusion.name === 'on'
+                                    ? pp.occlusion.params
+                                    : { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
+                            },
+                        }
+                    });
+                }
+                return [2 /*return*/];
+            });
+        });
+    };
+    QuickStyles.prototype.render = function () {
+        var _this = this;
+        return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" }), void 0), _jsx(Button, __assign({ noOverflow: true, title: 'Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.', onClick: function () { return _this.stylized(); }, style: { width: 'auto' } }, { children: "Stylized" }), void 0), _jsx(Button, __assign({ noOverflow: true, title: 'Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.', onClick: function () { return _this.illustrative(); }, style: { width: 'auto' } }, { children: "Illustrative" }), void 0)] }), void 0);
+    };
+    return QuickStyles;
+}(PurePluginUIComponent));
+export { QuickStyles };
+//# sourceMappingURL=quick-styles.js.map

package/lib/mol-plugin-ui/structure/superposition.js

@@ -159,8 +159,8 @@ var SuperpositionControls = /** @class */ (function (_super) {
                         _i++;
                         return [3 /*break*/, 1];
                     case 4:
-                        rmsd /= transforms.length - 1;
-                        this.plugin.log.info("Superposed ".concat(input.length, " structures with avg. RMSD ").concat(rmsd.toFixed(2), "."));
+                        rmsd /= Math.max(transforms.length - 1, 1);
+                        this.plugin.log.info("Superposed ".concat(input.length, " structures with avg. RMSD ").concat(rmsd.toFixed(2), " \u00C5."));
                         return [4 /*yield*/, new Promise(function (res) { return requestAnimationFrame(res); })];
                     case 5:
                         _a.sent();

package/lib/mol-plugin-ui/structure/volume.js

@@ -65,16 +65,16 @@ var VolumeStreamingControls = /** @class */ (function (_super) {
         return !!((_b = (_a = InitVolumeStreaming.definition).isApplicable) === null || _b === void 0 ? void 0 : _b.call(_a, pivot.obj, pivot.transform, this.plugin));
     };
     VolumeStreamingControls.prototype.renderEnable = function () {
-        var _a;
+        var _a, _b;
         var pivot = this.pivot;
         if (!pivot.cell.parent)
             return null;
         var root = StateSelection.findTagInSubtree(pivot.cell.parent.tree, this.pivot.cell.transform.ref, VolumeStreaming.RootTag);
         var rootCell = root && pivot.cell.parent.cells.get(root);
         var simpleApply = rootCell && rootCell.status === 'error'
-            ? { header: 'Error enabling', icon: ErrorSvg, title: rootCell.errorText }
-            : rootCell && ((_a = rootCell.obj) === null || _a === void 0 ? void 0 : _a.data.entries.length) === 0
-                ? { header: 'Error enabling', icon: ErrorSvg, title: 'No entry for streaming found' }
+            ? { header: !!rootCell.errorText && ((_a = rootCell.errorText) === null || _a === void 0 ? void 0 : _a.includes('404')) ? 'No Density Data Available' : 'Error Enabling', icon: ErrorSvg, title: rootCell.errorText }
+            : rootCell && ((_b = rootCell.obj) === null || _b === void 0 ? void 0 : _b.data.entries.length) === 0
+                ? { header: 'Error Enabling', icon: ErrorSvg, title: 'No Entry for Streaming Found' }
                 : { header: 'Enable', icon: CheckSvg, title: 'Enable' };
         return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: InitVolumeStreaming, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: simpleApply }, void 0);
     };

package/lib/mol-plugin-ui/viewport/simple-settings.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>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-plugin-ui/viewport/simple-settings.js

@@ -1,7 +1,7 @@
 import { __assign, __awaiter, __extends, __generator } from "tslib";
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 /**
- * 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>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -44,10 +44,7 @@ var LayoutOptions = {
     'left': 'Left Panel'
 };
 var SimpleSettingsParams = {
-    spin: PD.Group({
-        spin: Canvas3DParams.trackball.params.spin,
-        speed: Canvas3DParams.trackball.params.spinSpeed
-    }, { pivot: 'spin' }),
+    animate: Canvas3DParams.trackball.params.animate,
     camera: Canvas3DParams.camera,
     background: PD.Group({
         color: PD.Color(Color(0xFCFBF9), { label: 'Background', description: 'Custom background color' }),
@@ -97,7 +94,7 @@ var SimpleSettingsMapping = ParamMapping({
         var renderer = canvas.renderer;
         return {
             layout: props.layout,
-            spin: { spin: !!canvas.trackball.spin, speed: canvas.trackball.spinSpeed },
+            animate: canvas.trackball.animate,
             camera: canvas.camera,
             background: {
                 color: renderer.backgroundColor,
@@ -113,8 +110,7 @@ var SimpleSettingsMapping = ParamMapping({
     },
     update: function (s, props) {
         var canvas = props.canvas;
-        canvas.trackball.spin = s.spin.spin;
-        canvas.trackball.spinSpeed = s.spin.speed;
+        canvas.trackball.animate = s.animate;
         canvas.camera = s.camera;
         canvas.transparentBackground = s.background.transparent;
         canvas.renderer.backgroundColor = s.background.color;

package/lib/mol-repr/shape/loci/common.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 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>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-repr/shape/loci/common.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 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>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -9,9 +9,9 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { ColorNames } from '../../../mol-util/color/names';
 import { Text } from '../../../mol-geo/geometry/text/text';
 export var MeasurementRepresentationCommonTextParams = {
-    customText: PD.Text('', { label: 'Text', description: 'Override the label with custom value.' }),
+    customText: PD.Text('', { label: 'Text', description: 'Override the label with custom value.', isEssential: true }),
     textColor: PD.Color(ColorNames.black, { isEssential: true }),
-    textSize: PD.Numeric(0.5, { min: 0.1, max: 5, step: 0.1 }, { isEssential: true }),
+    textSize: PD.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
 };
 export var LociLabelTextParams = __assign(__assign(__assign({}, Text.Params), MeasurementRepresentationCommonTextParams), { borderWidth: PD.Numeric(0.2, { min: 0, max: 0.5, step: 0.01 }) });
 //# sourceMappingURL=common.js.map

package/lib/mol-repr/structure/registry.d.ts

@@ -13,7 +13,7 @@ export declare namespace StructureRepresentationRegistry {
     export const BuiltIn: {
         cartoon: import("./representation").StructureRepresentationProvider<{
             sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
-            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
             bumpFrequency: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             unitKinds: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"spheres" | "gaussians" | "atomic">;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;

package/lib/mol-repr/structure/representation/cartoon.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>
  */
@@ -10,7 +10,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
 export declare const CartoonParams: {
     sizeFactor: PD.Numeric;
-    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
     bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
@@ -48,7 +48,7 @@ export declare const CartoonParams: {
 export declare type CartoonParams = typeof CartoonParams;
 export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure): {
     sizeFactor: PD.Numeric;
-    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
     bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
@@ -87,7 +87,7 @@ export declare type CartoonRepresentation = StructureRepresentation<CartoonParam
 export declare function CartoonRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CartoonParams>): CartoonRepresentation;
 export declare const CartoonRepresentationProvider: StructureRepresentationProvider<{
     sizeFactor: PD.Numeric;
-    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
     bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;

package/lib/mol-repr/structure/representation/cartoon.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>
  */
@@ -24,7 +24,7 @@ var CartoonVisuals = {
     'nucleotide-ring': function (ctx, getParams) { return UnitsRepresentation('Nucleotide ring mesh', ctx, getParams, NucleotideRingVisual); },
     'direction-wedge': function (ctx, getParams) { return UnitsRepresentation('Polymer direction wedge', ctx, getParams, PolymerDirectionVisual); }
 };
-export var CartoonParams = __assign(__assign(__assign(__assign(__assign(__assign({}, PolymerTraceParams), PolymerGapParams), NucleotideBlockParams), NucleotideRingParams), PolymerDirectionParams), { sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], PD.objectToOptions(CartoonVisuals)), bumpFrequency: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory) });
+export var CartoonParams = __assign(__assign(__assign(__assign(__assign(__assign({}, PolymerTraceParams), PolymerGapParams), NucleotideBlockParams), NucleotideRingParams), PolymerDirectionParams), { sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], PD.objectToOptions(CartoonVisuals)), bumpFrequency: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory) });
 export function getCartoonParams(ctx, structure) {
     var params = PD.clone(CartoonParams);
     var hasNucleotides = false;
@@ -37,7 +37,7 @@ export function getCartoonParams(ctx, structure) {
     });
     params.visuals.defaultValue = ['polymer-trace'];
     if (hasNucleotides)
-        params.visuals.defaultValue.push('nucleotide-block');
+        params.visuals.defaultValue.push('nucleotide-ring');
     if (hasGaps)
         params.visuals.defaultValue.push('polymer-gap');
     return params;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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/carbohydrate-link-cylinder.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>
  */
@@ -77,6 +77,7 @@ function getLinkLoci(pickingId, structure, id) {
     }
     return EmptyLoci;
 }
+var __linkIndicesSet = new Set();
 function eachCarbohydrateLink(loci, structure, apply) {
     var changed = false;
     if (!StructureElement.Loci.is(loci))
@@ -87,12 +88,15 @@ function eachCarbohydrateLink(loci, structure, apply) {
     var _loop_1 = function (unit, indices) {
         if (!Unit.isAtomic(unit))
             return "continue";
+        __linkIndicesSet.clear();
         OrderedSet.forEach(indices, function (v) {
-            // TODO avoid duplicate calls to apply
             var linkIndices = getLinkIndices(unit, unit.elements[v]);
             for (var i = 0, il = linkIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(linkIndices[i])))
-                    changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(Interval.ofSingleton(linkIndices[i])))
+                        changed = true;
+                }
             }
         });
     };

package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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/carbohydrate-symbol-mesh.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>
  */
@@ -22,8 +22,8 @@ import { EmptyLoci } from '../../../mol-model/loci';
 import { getAltResidueLociFromId } from './util/common';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
 var t = Mat4.identity();
-var sVec = Vec3.zero();
-var pd = Vec3.zero();
+var sVec = Vec3();
+var pd = Vec3();
 var SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
 var box = Box();
 var perforatedBox = PerforatedBox();
@@ -182,6 +182,7 @@ function getCarbohydrateLoci(pickingId, structure, id) {
     }
     return EmptyLoci;
 }
+var __elementIndicesSet = new Set();
 /** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
 function eachCarbohydrate(loci, structure, apply) {
     var getElementIndices = structure.carbohydrates.getElementIndices;
@@ -193,12 +194,15 @@ function eachCarbohydrate(loci, structure, apply) {
     var _loop_1 = function (unit, indices) {
         if (!Unit.isAtomic(unit))
             return "continue";
+        __elementIndicesSet.clear();
         OrderedSet.forEach(indices, function (v) {
-            // TODO avoid duplicate calls to apply
             var elementIndices = getElementIndices(unit, unit.elements[v]);
             for (var i = 0, il = elementIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(elementIndices[i] * 2)))
-                    changed = true;
+                if (!__elementIndicesSet.has(elementIndices[i])) {
+                    __elementIndicesSet.add(elementIndices[i]);
+                    if (apply(Interval.ofSingleton(elementIndices[i] * 2)))
+                        changed = true;
+                }
             }
         });
     };

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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/carbohydrate-terminal-link-cylinder.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>
  */
@@ -101,6 +101,7 @@ function getTerminalLinkLoci(pickingId, structure, id) {
     }
     return EmptyLoci;
 }
+var __linkIndicesSet = new Set();
 function eachTerminalLink(loci, structure, apply) {
     var changed = false;
     if (!StructureElement.Loci.is(loci))
@@ -111,12 +112,15 @@ function eachTerminalLink(loci, structure, apply) {
     var _loop_1 = function (unit, indices) {
         if (!Unit.isAtomic(unit))
             return "continue";
+        __linkIndicesSet.clear();
         OrderedSet.forEach(indices, function (v) {
-            // TODO avoid duplicate calls to apply
             var linkIndices = getTerminalLinkIndices(unit, unit.elements[v]);
             for (var i = 0, il = linkIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(linkIndices[i])))
-                    changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(Interval.ofSingleton(linkIndices[i])))
+                        changed = true;
+                }
             }
         });
     };

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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-mesh.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
  */
@@ -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, props.probeRadius + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, getUnitExtraRadius(unit));
                     surface.setBoundingSphere(sphere);
                     surface.meta.resolution = resolution;
                     return [2 /*return*/, surface];

package/lib/mol-repr/structure/visual/util/bond.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/util/bond.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>
  */
@@ -206,6 +206,7 @@ export function getInterBondLoci(pickingId, structure, id) {
     }
     return EmptyLoci;
 }
+var __unitMap = new Map();
 export function eachInterBond(loci, structure, apply, isMarking) {
     var changed = false;
     if (Bond.isLoci(loci)) {
@@ -225,17 +226,16 @@ export function eachInterBond(loci, structure, apply, isMarking) {
             return false;
         if (isMarking && loci.elements.length === 1)
             return false; // only a single unit
-        var map_1 = new Map();
         for (var _b = 0, _c = loci.elements; _b < _c.length; _b++) {
             var e = _c[_b];
-            map_1.set(e.unit.id, e.indices);
+            __unitMap.set(e.unit.id, e.indices);
         }
         var _loop_2 = function (e) {
             var unit = e.unit;
             if (!Unit.isAtomic(unit))
                 return "continue";
             structure.interUnitBonds.getConnectedUnits(unit.id).forEach(function (b) {
-                var otherLociIndices = map_1.get(b.unitB);
+                var otherLociIndices = __unitMap.get(b.unitB);
                 if (!isMarking || otherLociIndices) {
                     OrderedSet.forEach(e.indices, function (v) {
                         if (!b.connectedIndices.includes(v))
@@ -255,6 +255,7 @@ export function eachInterBond(loci, structure, apply, isMarking) {
             var e = _e[_d];
             _loop_2(e);
         }
+        __unitMap.clear();
     }
     return changed;
 }

package/lib/mol-repr/visual.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/visual.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>
  */
@@ -49,6 +49,7 @@ var Visual;
         var array = tMarker.ref.value.array;
         var currentStatus = markerStatus.ref.value;
         if (!isEveryLoci(loci)) {
+            // assume that all interval are non-overlapping
             var intervalSize_1 = 0;
             lociApply(loci, function (interval) {
                 intervalSize_1 += Interval.size(interval);

package/lib/mol-state/transform.js

@@ -54,7 +54,12 @@ var Transform;
             if (!!s === !!t)
                 continue;
             changed = true;
-            a[k] = s;
+            if (s !== void 0) {
+                a[k] = s;
+            }
+            else {
+                delete a[k];
+            }
         }
         for (var _b = 0, _c = Object.keys(a); _b < _c.length; _b++) {
             var k = _c[_b];
@@ -62,7 +67,12 @@ var Transform;
             if (!!s === !!t)
                 continue;
             changed = true;
-            a[k] = s;
+            if (s !== void 0) {
+                a[k] = s;
+            }
+            else {
+                delete a[k];
+            }
         }
         return changed;
     }