molstar 3.0.0-dev.9 → 3.1.0

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

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MoreHorizSvg = exports.LinearScaleSvg = exports.LaunchSvg = exports.HomeOutlinedSvg = exports.HelpOutlineSvg = exports.GetAppSvg = exports.FullscreenSvg = exports.FlipToFrontSvg = exports.ExtensionSvg = exports.ErrorSvg = exports.DeleteSvg = exports.DeleteOutlinedSvg = exports.CropOrginalSvg = exports.CropFreeSvg = exports.CropSvg = exports.CopySvg = exports.CodeSvg = exports.CloudUploadSvg = exports.CloseSvg = exports.ClearSvg = exports.CheckSvg = exports.CenterFocusStrongSvg = exports.CancelSvg = exports.CancelOutlinedSvg = exports.CameraSvg = exports.CameraOutlinedSvg = exports.BuildSvg = exports.BuildOutlinedSvg = exports.BrushSvg = exports.BookmarksOutlinedSvg = exports.BlurOnSvg = exports.AutorenewSvg = exports.ArrowUpwardSvg = exports.ArrowRightSvg = exports.ArrowDropDownSvg = exports.ArrowDownwardSvg = exports.AddSvg = exports.AccountTreeOutlinedSvg = exports.PencilRulerSvg = exports.FileOutlineSvg = exports.CursorDefaultOutlineSvg = exports.CubeSendSvg = exports.CubeScanSvg = exports.CubeOutlineSvg = exports.MoleculeSvg = exports.SetSvg = exports.IntersectSvg = exports.SubtractSvg = exports.UnionSvg = exports.Icon = void 0;
-exports.SuperpositionSvg = exports.SuperposeChainsSvg = exports.SuperposeAtomsSvg = exports.SelectionModeSvg = exports.WarningSvg = exports.VisibilityOutlinedSvg = exports.VisibilityOffOutlinedSvg = exports.TuneSvg = exports.SwapHorizSvg = exports.SubscriptionsOutlinedSvg = exports.StopSvg = exports.SkipPreviousSvg = exports.ScatterPlotSvg = exports.SaveOutlinedSvg = exports.RestoreSvg = exports.RemoveSvg = exports.RefreshSvg = exports.PlayArrowSvg = exports.OpenInBrowserSvg = exports.NavigateNextSvg = exports.NavigateBeforeSvg = void 0;
+exports.LinearScaleSvg = exports.LaunchSvg = exports.HomeOutlinedSvg = exports.HelpOutlineSvg = exports.GetAppSvg = exports.FullscreenSvg = exports.FlipToFrontSvg = exports.ExtensionSvg = exports.ErrorSvg = exports.DeleteSvg = exports.DeleteOutlinedSvg = exports.CropOrginalSvg = exports.CropFreeSvg = exports.CropSvg = exports.CopySvg = exports.CodeSvg = exports.CloudUploadSvg = exports.CloseSvg = exports.ClearSvg = exports.CheckSvg = exports.CenterFocusStrongSvg = exports.CancelSvg = exports.CancelOutlinedSvg = exports.CameraSvg = exports.CameraOutlinedSvg = exports.BuildSvg = exports.BuildOutlinedSvg = exports.BrushSvg = exports.BookmarksOutlinedSvg = exports.BlurOnSvg = exports.AutorenewSvg = exports.ArrowUpwardSvg = exports.ArrowRightSvg = exports.ArrowDropDownSvg = exports.ArrowDownwardSvg = exports.AddSvg = exports.AccountTreeOutlinedSvg = exports.MagicWandSvg = exports.PencilRulerSvg = exports.FileOutlineSvg = exports.CursorDefaultOutlineSvg = exports.CubeSendSvg = exports.CubeScanSvg = exports.CubeOutlineSvg = exports.MoleculeSvg = exports.SetSvg = exports.IntersectSvg = exports.SubtractSvg = exports.UnionSvg = exports.Icon = void 0;
+exports.SuperpositionSvg = exports.SuperposeChainsSvg = exports.SuperposeAtomsSvg = exports.SelectionModeSvg = exports.WarningSvg = exports.VisibilityOutlinedSvg = exports.VisibilityOffOutlinedSvg = exports.TuneSvg = exports.SwapHorizSvg = exports.SubscriptionsOutlinedSvg = exports.StopSvg = exports.SkipPreviousSvg = exports.ScatterPlotSvg = exports.SaveOutlinedSvg = exports.RestoreSvg = exports.RemoveSvg = exports.RefreshSvg = exports.PlayArrowSvg = exports.OpenInBrowserSvg = exports.NavigateNextSvg = exports.NavigateBeforeSvg = exports.MoreHorizSvg = void 0;
 var tslib_1 = require("tslib");
 var jsx_runtime_1 = require("react/jsx-runtime");
 function Icon(props) {
@@ -30,10 +30,10 @@ function MoleculeSvg() { return _Molecule; }
 exports.MoleculeSvg = MoleculeSvg;
 // The following icons are adapted from https://materialdesignicons.com/ and
 // licensed with https://github.com/Templarian/MaterialDesign/blob/master/LICENSE
-var _CubeOutline = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: "M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z" }, void 0) }), void 0);
+var _CubeOutline = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: 'M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z' }, void 0) }), void 0);
 function CubeOutlineSvg() { return _CubeOutline; }
 exports.CubeOutlineSvg = CubeOutlineSvg;
-var _CubeScan = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: "M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z" }, void 0) }), void 0);
+var _CubeScan = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: 'M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z' }, void 0) }), void 0);
 function CubeScanSvg() { return _CubeScan; }
 exports.CubeScanSvg = CubeScanSvg;
 var _CubeSend = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: "M16,4L9,8.04V15.96L16,20L23,15.96V8.04M16,6.31L19.8,8.5L16,10.69L12.21,8.5M0,7V9H7V7M11,10.11L15,12.42V17.11L11,14.81M21,10.11V14.81L17,17.11V12.42M2,11V13H7V11M4,15V17H7V15" }, void 0) }), void 0);
@@ -45,9 +45,12 @@ exports.CursorDefaultOutlineSvg = CursorDefaultOutlineSvg;
 var _FileOutline = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { fill: 'currentColor', d: 'M14,2H6A2,2 0 0,0 4,4V20A2,2 0 0,0 6,22H18A2,2 0 0,0 20,20V8L14,2M18,20H6V4H13V9H18V20Z' }, void 0) }), void 0);
 function FileOutlineSvg() { return _FileOutline; }
 exports.FileOutlineSvg = FileOutlineSvg;
-var _PencilRuler = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: "M3 17.25V21H6.75L17.81 9.93L14.06 6.18L3 17.25M22.61 18.36L18.36 22.61L13.16 17.41L14.93 15.64L15.93 16.64L18.4 14.16L19.82 15.58L18.36 17L19.42 18L20.84 16.6L22.61 18.36M6.61 10.83L1.39 5.64L5.64 1.39L7.4 3.16L4.93 5.64L6 6.7L8.46 4.22L9.88 5.64L8.46 7.05L9.46 8.05L6.61 10.83M20.71 7C21.1 6.61 21.1 6 20.71 5.59L18.37 3.29C18 2.9 17.35 2.9 16.96 3.29L15.12 5.12L18.87 8.87L20.71 7Z" }, void 0) }), void 0);
+var _PencilRuler = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px' }, { children: (0, jsx_runtime_1.jsx)("path", { d: 'M3 17.25V21H6.75L17.81 9.93L14.06 6.18L3 17.25M22.61 18.36L18.36 22.61L13.16 17.41L14.93 15.64L15.93 16.64L18.4 14.16L19.82 15.58L18.36 17L19.42 18L20.84 16.6L22.61 18.36M6.61 10.83L1.39 5.64L5.64 1.39L7.4 3.16L4.93 5.64L6 6.7L8.46 4.22L9.88 5.64L8.46 7.05L9.46 8.05L6.61 10.83M20.71 7C21.1 6.61 21.1 6 20.71 5.59L18.37 3.29C18 2.9 17.35 2.9 16.96 3.29L15.12 5.12L18.87 8.87L20.71 7Z' }, void 0) }), void 0);
 function PencilRulerSvg() { return _PencilRuler; }
 exports.PencilRulerSvg = PencilRulerSvg;
+var _MagicWand = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24' }, { children: (0, jsx_runtime_1.jsx)("path", { fill: 'currentColor', d: 'M7.5,5.6L5,7L6.4,4.5L5,2L7.5,3.4L10,2L8.6,4.5L10,7L7.5,5.6M19.5,15.4L22,14L20.6,16.5L22,19L19.5,17.6L17,19L18.4,16.5L17,14L19.5,15.4M22,2L20.6,4.5L22,7L19.5,5.6L17,7L18.4,4.5L17,2L19.5,3.4L22,2M13.34,12.78L15.78,10.34L13.66,8.22L11.22,10.66L13.34,12.78M14.37,7.29L16.71,9.63C17.1,10 17.1,10.65 16.71,11.04L5.04,22.71C4.65,23.1 4,23.1 3.63,22.71L1.29,20.37C0.9,20 0.9,19.35 1.29,18.96L12.96,7.29C13.35,6.9 14,6.9 14.37,7.29Z' }, void 0) }), void 0);
+function MagicWandSvg() { return _MagicWand; }
+exports.MagicWandSvg = MagicWandSvg;
 // The following icons are adapted from https://material-ui.com/components/material-icons/ and
 // licensed with https://github.com/mui-org/material-ui/blob/master/LICENSE
 var _AccountTreeOutlined = (0, jsx_runtime_1.jsx)("svg", (0, tslib_1.__assign)({ width: '24px', height: '24px', viewBox: '0 0 24 24' }, { children: (0, jsx_runtime_1.jsx)("path", { d: 'M22 11V3h-7v3H9V3H2v8h7V8h2v10h4v3h7v-8h-7v3h-2V8h2v3h7zM7 9H4V5h3v4zm10 6h3v4h-3v-4zm0-10h3v4h-3V5z' }, void 0) }), void 0);

package/lib/commonjs/mol-plugin-ui/controls.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -17,6 +17,7 @@ var source_1 = require("./structure/source");
 var volume_1 = require("./structure/volume");
 var config_1 = require("../mol-plugin/config");
 var superposition_1 = require("./structure/superposition");
+var quick_styles_1 = require("./structure/quick-styles");
 var TrajectoryViewportControls = /** @class */ (function (_super) {
     (0, tslib_1.__extends)(TrajectoryViewportControls, _super);
     function TrajectoryViewportControls() {
@@ -293,7 +294,7 @@ var DefaultStructureTools = /** @class */ (function (_super) {
         return _super !== null && _super.apply(this, arguments) || this;
     }
     DefaultStructureTools.prototype.render = function () {
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-section-header' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.BuildSvg }, void 0), "Structure Tools"] }), void 0), (0, jsx_runtime_1.jsx)(source_1.StructureSourceControls, {}, void 0), (0, jsx_runtime_1.jsx)(measurements_1.StructureMeasurementsControls, {}, void 0), (0, jsx_runtime_1.jsx)(superposition_1.StructureSuperpositionControls, {}, void 0), (0, jsx_runtime_1.jsx)(components_1.StructureComponentControls, {}, void 0), this.plugin.config.get(config_1.PluginConfig.VolumeStreaming.Enabled) && (0, jsx_runtime_1.jsx)(volume_1.VolumeStreamingControls, {}, void 0), (0, jsx_runtime_1.jsx)(volume_1.VolumeSourceControls, {}, void 0), (0, jsx_runtime_1.jsx)(CustomStructureControls, {}, void 0)] }, void 0);
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-section-header' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.BuildSvg }, void 0), "Structure Tools"] }), void 0), (0, jsx_runtime_1.jsx)(source_1.StructureSourceControls, {}, void 0), (0, jsx_runtime_1.jsx)(measurements_1.StructureMeasurementsControls, {}, void 0), (0, jsx_runtime_1.jsx)(superposition_1.StructureSuperpositionControls, {}, void 0), (0, jsx_runtime_1.jsx)(quick_styles_1.StructureQuickStylesControls, {}, void 0), (0, jsx_runtime_1.jsx)(components_1.StructureComponentControls, {}, void 0), this.plugin.config.get(config_1.PluginConfig.VolumeStreaming.Enabled) && (0, jsx_runtime_1.jsx)(volume_1.VolumeStreamingControls, {}, void 0), (0, jsx_runtime_1.jsx)(volume_1.VolumeSourceControls, {}, void 0), (0, jsx_runtime_1.jsx)(CustomStructureControls, {}, void 0)] }, void 0);
     };
     return DefaultStructureTools;
 }(base_1.PluginUIComponent));

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

@@ -0,0 +1,131 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.QuickStyles = exports.StructureQuickStylesControls = void 0;
+var tslib_1 = require("tslib");
+var jsx_runtime_1 = require("react/jsx-runtime");
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+var representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
+var color_1 = require("../../mol-util/color");
+var base_1 = require("../base");
+var common_1 = require("../controls/common");
+var icons_1 = require("../controls/icons");
+var param_definition_1 = require("../../mol-util/param-definition");
+var postprocessing_1 = require("../../mol-canvas3d/passes/postprocessing");
+var config_1 = require("../../mol-plugin/config");
+var component_1 = require("../../mol-plugin-state/manager/structure/component");
+var StructureQuickStylesControls = /** @class */ (function (_super) {
+    (0, tslib_1.__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: icons_1.MagicWandSvg }
+        };
+    };
+    StructureQuickStylesControls.prototype.renderControls = function () {
+        return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(QuickStyles, {}, void 0) }, void 0);
+    };
+    return StructureQuickStylesControls;
+}(base_1.CollapsableControls));
+exports.StructureQuickStylesControls = StructureQuickStylesControls;
+var QuickStyles = /** @class */ (function (_super) {
+    (0, tslib_1.__extends)(QuickStyles, _super);
+    function QuickStyles() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    QuickStyles.prototype.default = function () {
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var structures, preset, provider, p;
+            return (0, tslib_1.__generator)(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        structures = this.plugin.managers.structure.hierarchy.selection.structures;
+                        preset = this.plugin.config.get(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.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(param_definition_1.ParamDefinition.getDefaultValues(component_1.StructureComponentManager.OptionsParams));
+                        if (this.plugin.canvas3d) {
+                            p = param_definition_1.ParamDefinition.getDefaultValues(postprocessing_1.PostprocessingParams);
+                            this.plugin.canvas3d.setProps({
+                                postprocessing: { outline: p.outline, occlusion: p.occlusion }
+                            });
+                        }
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    QuickStyles.prototype.illustrative = function () {
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var structures;
+            return (0, tslib_1.__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, representation_preset_1.PresetStructureRepresentations.illustrative)];
+                    case 1:
+                        _a.sent();
+                        if (this.plugin.canvas3d) {
+                            this.plugin.canvas3d.setProps({
+                                postprocessing: {
+                                    outline: {
+                                        name: 'on',
+                                        params: { scale: 1, color: (0, color_1.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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var pp;
+            return (0, tslib_1.__generator)(this, function (_a) {
+                this.plugin.managers.structure.component.setOptions((0, tslib_1.__assign)((0, tslib_1.__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: (0, color_1.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 (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__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), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__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), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__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;
+}(base_1.PurePluginUIComponent));
+exports.QuickStyles = QuickStyles;
+//# sourceMappingURL=quick-styles.js.map

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

@@ -162,8 +162,8 @@ 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/commonjs/mol-plugin-ui/structure/volume.js

@@ -68,16 +68,16 @@ var VolumeStreamingControls = /** @class */ (function (_super) {
         return !!((_b = (_a = transformers_1.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 = mol_state_1.StateSelection.findTagInSubtree(pivot.cell.parent.tree, this.pivot.cell.transform.ref, behavior_1.VolumeStreaming.RootTag);
         var rootCell = root && pivot.cell.parent.cells.get(root);
         var simpleApply = rootCell && rootCell.status === 'error'
-            ? { header: 'Error enabling', icon: icons_1.ErrorSvg, title: rootCell.errorText }
-            : rootCell && ((_a = rootCell.obj) === null || _a === void 0 ? void 0 : _a.data.entries.length) === 0
-                ? { header: 'Error enabling', icon: icons_1.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: icons_1.ErrorSvg, title: rootCell.errorText }
+            : rootCell && ((_b = rootCell.obj) === null || _b === void 0 ? void 0 : _b.data.entries.length) === 0
+                ? { header: 'Error Enabling', icon: icons_1.ErrorSvg, title: 'No Entry for Streaming Found' }
                 : { header: 'Enable', icon: icons_1.CheckSvg, title: 'Enable' };
         return (0, jsx_runtime_1.jsx)(apply_action_1.ApplyActionControl, { state: pivot.cell.parent, action: transformers_1.InitVolumeStreaming, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: simpleApply }, void 0);
     };

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

@@ -4,7 +4,7 @@ exports.SimpleSettingsControl = void 0;
 var tslib_1 = require("tslib");
 var jsx_runtime_1 = require("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>
@@ -47,10 +47,7 @@ var LayoutOptions = {
     'left': 'Left Panel'
 };
 var SimpleSettingsParams = {
-    spin: param_definition_1.ParamDefinition.Group({
-        spin: canvas3d_1.Canvas3DParams.trackball.params.spin,
-        speed: canvas3d_1.Canvas3DParams.trackball.params.spinSpeed
-    }, { pivot: 'spin' }),
+    animate: canvas3d_1.Canvas3DParams.trackball.params.animate,
     camera: canvas3d_1.Canvas3DParams.camera,
     background: param_definition_1.ParamDefinition.Group({
         color: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xFCFBF9), { label: 'Background', description: 'Custom background color' }),
@@ -100,7 +97,7 @@ var SimpleSettingsMapping = (0, param_mapping_1.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,
@@ -116,8 +113,7 @@ var SimpleSettingsMapping = (0, param_mapping_1.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/commonjs/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/commonjs/mol-repr/shape/loci/common.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -12,9 +12,9 @@ var param_definition_1 = require("../../../mol-util/param-definition");
 var names_1 = require("../../../mol-util/color/names");
 var text_1 = require("../../../mol-geo/geometry/text/text");
 exports.MeasurementRepresentationCommonTextParams = {
-    customText: param_definition_1.ParamDefinition.Text('', { label: 'Text', description: 'Override the label with custom value.' }),
+    customText: param_definition_1.ParamDefinition.Text('', { label: 'Text', description: 'Override the label with custom value.', isEssential: true }),
     textColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black, { isEssential: true }),
-    textSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.1, max: 5, step: 0.1 }, { isEssential: true }),
+    textSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
 };
 exports.LociLabelTextParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, text_1.Text.Params), exports.MeasurementRepresentationCommonTextParams), { borderWidth: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 0.5, step: 0.01 }) });
 //# sourceMappingURL=common.js.map

package/lib/commonjs/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/commonjs/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/commonjs/mol-repr/structure/representation/cartoon.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -27,7 +27,7 @@ var CartoonVisuals = {
     'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
     'direction-wedge': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer direction wedge', ctx, getParams, polymer_direction_wedge_1.PolymerDirectionVisual); }
 };
-exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
+exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getCartoonParams(ctx, structure) {
     var params = param_definition_1.ParamDefinition.clone(exports.CartoonParams);
     var hasNucleotides = false;
@@ -40,7 +40,7 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -81,6 +81,7 @@ function getLinkLoci(pickingId, structure, id) {
     }
     return loci_1.EmptyLoci;
 }
+var __linkIndicesSet = new Set();
 function eachCarbohydrateLink(loci, structure, apply) {
     var changed = false;
     if (!structure_1.StructureElement.Loci.is(loci))
@@ -91,12 +92,15 @@ function eachCarbohydrateLink(loci, structure, apply) {
     var _loop_1 = function (unit, indices) {
         if (!structure_1.Unit.isAtomic(unit))
             return "continue";
+        __linkIndicesSet.clear();
         int_1.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(int_1.Interval.ofSingleton(linkIndices[i])))
-                    changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(int_1.Interval.ofSingleton(linkIndices[i])))
+                        changed = true;
+                }
             }
         });
     };

package/lib/commonjs/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/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -25,8 +25,8 @@ var loci_1 = require("../../../mol-model/loci");
 var common_1 = require("./util/common");
 var base_1 = require("../../../mol-geo/geometry/base");
 var t = linear_algebra_1.Mat4.identity();
-var sVec = linear_algebra_1.Vec3.zero();
-var pd = linear_algebra_1.Vec3.zero();
+var sVec = (0, linear_algebra_1.Vec3)();
+var pd = (0, linear_algebra_1.Vec3)();
 var SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
 var box = (0, box_1.Box)();
 var perforatedBox = (0, box_1.PerforatedBox)();
@@ -186,6 +186,7 @@ function getCarbohydrateLoci(pickingId, structure, id) {
     }
     return loci_1.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;
@@ -197,12 +198,15 @@ function eachCarbohydrate(loci, structure, apply) {
     var _loop_1 = function (unit, indices) {
         if (!structure_1.Unit.isAtomic(unit))
             return "continue";
+        __elementIndicesSet.clear();
         int_1.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(int_1.Interval.ofSingleton(elementIndices[i] * 2)))
-                    changed = true;
+                if (!__elementIndicesSet.has(elementIndices[i])) {
+                    __elementIndicesSet.add(elementIndices[i]);
+                    if (apply(int_1.Interval.ofSingleton(elementIndices[i] * 2)))
+                        changed = true;
+                }
             }
         });
     };

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -105,6 +105,7 @@ function getTerminalLinkLoci(pickingId, structure, id) {
     }
     return loci_1.EmptyLoci;
 }
+var __linkIndicesSet = new Set();
 function eachTerminalLink(loci, structure, apply) {
     var changed = false;
     if (!structure_1.StructureElement.Loci.is(loci))
@@ -115,12 +116,15 @@ function eachTerminalLink(loci, structure, apply) {
     var _loop_1 = function (unit, indices) {
         if (!structure_1.Unit.isAtomic(unit))
             return "continue";
+        __linkIndicesSet.clear();
         int_1.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(int_1.Interval.ofSingleton(linkIndices[i])))
-                    changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(int_1.Interval.ofSingleton(linkIndices[i])))
+                        changed = true;
+                }
             }
         });
     };

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -43,7 +43,7 @@ function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     mesh_1.Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         mesh_1.Mesh.uniformTriangleGroup(surface);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.probeRadius + (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, (0, common_1.getUnitExtraRadius)(unit));
                     surface.setBoundingSphere(sphere);
                     surface.meta.resolution = resolution;
                     return [2 /*return*/, surface];

package/lib/commonjs/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>
  */