molstar 2.3.9 → 3.0.0-dev.10

package/lib/commonjs/mol-plugin/behavior/dynamic/representation.d.ts

@@ -12,7 +12,7 @@ export declare const HighlightLoci: import("../../../mol-state/transformer").Sta
         hoverHighlightOnly: Binding;
         hoverHighlightOnlyExtend: Binding;
     }>;
-    ignore: PD.Value<("empty-loci" | "cell-loci" | "every-loci" | "isosurface-loci" | "element-loci" | "structure-loci" | "bond-loci" | "data-loci" | "shape-loci" | "group-loci" | "volume-loci")[]>;
+    ignore: PD.Value<("element-loci" | "structure-loci" | "bond-loci" | "volume-loci" | "isosurface-loci" | "cell-loci" | "every-loci" | "empty-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
     preferAtoms: PD.BooleanParam;
     mark: PD.BooleanParam;
 }>>;
@@ -25,7 +25,7 @@ export declare const SelectLoci: import("../../../mol-state/transformer").StateT
         clickDeselect: Binding;
         clickDeselectAllOnEmpty: Binding;
     }>;
-    ignore: PD.Value<("empty-loci" | "cell-loci" | "every-loci" | "isosurface-loci" | "element-loci" | "structure-loci" | "bond-loci" | "data-loci" | "shape-loci" | "group-loci" | "volume-loci")[]>;
+    ignore: PD.Value<("element-loci" | "structure-loci" | "bond-loci" | "volume-loci" | "isosurface-loci" | "cell-loci" | "every-loci" | "empty-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
     preferAtoms: PD.BooleanParam;
     mark: PD.BooleanParam;
 }>>;

package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js

@@ -56,12 +56,11 @@ exports.HighlightLoci = behavior_1.PluginBehavior.create({
         class_1.prototype.register = function () {
             var _this = this;
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, function (_a) {
-                var _b;
                 var current = _a.current, buttons = _a.buttons, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0) {
+                if (_this.params.ignore.includes(loci.kind)) {
                     _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: loci_1.EmptyLoci });
                     return;
                 }
@@ -159,16 +158,15 @@ exports.SelectLoci = behavior_1.PluginBehavior.create({
                 return l - k;
             });
             this.subscribeObservable(this.ctx.behaviors.interaction.click, function (_a) {
-                var _b;
                 var current = _a.current, button = _a.button, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy || !_this.ctx.selectionMode)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0)
+                if (_this.params.ignore.includes(loci.kind))
                     return;
                 // only trigger the 1st action that matches
                 for (var _i = 0, actions_1 = actions; _i < actions_1.length; _i++) {
-                    var _c = actions_1[_i], binding = _c[0], action = _c[1], condition = _c[2];
+                    var _b = actions_1[_i], binding = _b[0], action = _b[1], condition = _b[2];
                     if (binding_1.Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
                         action({ repr: current.repr, loci: loci });
                         break;
@@ -192,7 +190,7 @@ exports.SelectLoci = behavior_1.PluginBehavior.create({
                         structure_1.Structure.areEquivalent(structure, oldStructure) &&
                         structure_1.Structure.areHierarchiesEqual(structure, oldStructure))
                         return;
-                    var reprs = _this.ctx.state.data.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D, ref));
+                    var reprs = _this.ctx.state.data.select(mol_state_1.StateSelection.children(ref).ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D));
                     for (var _i = 0, reprs_1 = reprs; _i < reprs_1.length; _i++) {
                         var repr = reprs_1[_i];
                         _this.applySelectMark(repr.transform.ref, true);

package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -7,6 +7,7 @@
 import { PluginBehavior } from '../../../behavior';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginContext } from '../../../context';
+import { Clip } from '../../../../mol-util/clip';
 declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     expandRadius: PD.Numeric;
     targetParams: PD.Group<PD.Normalize<{
@@ -18,9 +19,24 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     nciParams: PD.Group<PD.Normalize<{
         [x: string]: any;
     }>>;
-    components: PD.MultiSelect<"target" | "interactions" | "surroundings">;
+    components: PD.MultiSelect<"target" | "surroundings" | "interactions">;
     excludeTargetFromSurroundings: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 declare type StructureFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof StructureFocusRepresentationParams>>;
 export declare enum StructureFocusRepresentationTags {

package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js

@@ -19,6 +19,8 @@ var mol_state_1 = require("../../../../mol-state");
 var size_1 = require("../../../../mol-theme/size");
 var param_definition_1 = require("../../../../mol-util/param-definition");
 var commands_1 = require("../../../commands");
+var material_1 = require("../../../../mol-util/material");
+var clip_1 = require("../../../../mol-util/clip");
 var StructureFocusRepresentationParams = function (plugin) {
     var reprParams = transforms_1.StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
     return {
@@ -41,7 +43,9 @@ var StructureFocusRepresentationParams = function (plugin) {
         }),
         components: param_definition_1.ParamDefinition.MultiSelect(FocusComponents, param_definition_1.ParamDefinition.arrayToOptions(FocusComponents)),
         excludeTargetFromSurroundings: param_definition_1.ParamDefinition.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
-        ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false)
+        ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false),
+        material: material_1.Material.getParam(),
+        clip: param_definition_1.ParamDefinition.Group(clip_1.Clip.Params),
     };
 };
 var FocusComponents = ['target', 'surroundings', 'interactions'];
@@ -69,7 +73,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
     StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
         return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.params.targetParams), { type: {
                 name: reprParams.type.name,
-                params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens })
+                params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip })
             } });
     };
     StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {

package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts

@@ -55,7 +55,7 @@ export declare namespace VolumeStreaming {
                 isSelection: boolean;
                 bottomLeft: Vec3;
                 topRight: Vec3;
-            }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+            }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
                 bottomLeft: Vec3;
                 topRight: Vec3;
             }>, "box"> | PD.NamedParams<PD.Normalize<{
@@ -87,7 +87,7 @@ export declare namespace VolumeStreaming {
             isSelection: boolean;
             bottomLeft: Vec3;
             topRight: Vec3;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
             bottomLeft: Vec3;
             topRight: Vec3;
         }>, "box"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts

@@ -29,9 +29,9 @@ declare const CreateVolumeStreamingInfo: StateTransformer<SO.Molecule.Structure,
     serverUrl: string;
     entries: PD.Normalize<PD.Values<{
         dataId: PD.Text<string>;
-        source: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "x-ray"> | PD.NamedParams<PD.Normalize<{
+        source: PD.Mapped<PD.NamedParams<PD.Normalize<{
             isoValue: any;
-        }>, "em">>;
+        }>, "em"> | PD.NamedParams<PD.Normalize<unknown>, "x-ray">>;
     }>>[];
 }>>;
 export { CreateVolumeStreamingBehavior };
@@ -44,7 +44,7 @@ declare const CreateVolumeStreamingBehavior: StateTransformer<VolumeServerInfo,
             isSelection: any;
             bottomLeft: any;
             topRight: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
             bottomLeft: any;
             topRight: any;
         }>, "box"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-plugin/commands.d.ts

@@ -50,6 +50,7 @@ export declare const PluginCommands: {
                     durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
                     data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
+                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -66,6 +67,7 @@ export declare const PluginCommands: {
                     durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
                     data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
+                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -96,6 +98,7 @@ export declare const PluginCommands: {
                     durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
                     data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
+                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -116,6 +119,7 @@ export declare const PluginCommands: {
                     durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
                     data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
+                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
                     canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -228,6 +232,7 @@ export declare const PluginCommands: {
                     outline: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         scale: any;
                         threshold: any;
+                        color: any;
                     }>, "on">;
                     antialiasing: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         edgeThreshold: any;
@@ -259,25 +264,26 @@ export declare const PluginCommands: {
                     selectStrength: number;
                     markerPriority: number;
                     xrayEdgeFalloff: number;
-                    style: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        lightIntensity: any;
-                        ambientIntensity: any;
-                        metalness: any;
-                        roughness: any;
-                        reflectivity: any;
-                    }>, "custom"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "matte"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "flat"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "glossy"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "metallic"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "plastic">;
-                    clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        variant: any;
-                        objects: any;
-                    }>;
+                    light: import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                        inclination: number;
+                        azimuth: number;
+                        color: import("../mol-util/color").Color;
+                        intensity: number;
+                    }>[];
+                    ambientColor: import("../mol-util/color").Color;
+                    ambientIntensity: number;
                 }>>;
                 trackball: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                     noScroll: boolean;
                     rotateSpeed: number;
                     zoomSpeed: number;
                     panSpeed: number;
-                    spin: boolean;
-                    spinSpeed: number;
+                    animate: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                        speed: any;
+                    }>, "spin"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                        speed: any;
+                        angle: any;
+                    }>, "rock">;
                     staticMoving: boolean;
                     dynamicDampingFactor: number;
                     minDistance: number;
@@ -324,7 +330,11 @@ export declare const PluginCommands: {
                         flipSided: any;
                         flatShaded: any;
                         xrayShaded: any;
+                        bumpFrequency: any;
+                        bumpAmplitude: any;
                         quality: any;
+                        material: any;
+                        clip: any;
                     }>, "on">;
                 }>>;
             }>> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void);

package/lib/commonjs/mol-plugin/config.d.ts

@@ -47,7 +47,7 @@ export declare const PluginConfig: {
         ShowAnimation: PluginConfigItem<boolean>;
     };
     Download: {
-        DefaultPdbProvider: PluginConfigItem<"rcsb" | "pdbe">;
+        DefaultPdbProvider: PluginConfigItem<"rcsb" | "pdbe" | "pdbj">;
         DefaultEmdbProvider: PluginConfigItem<EmdbDownloadProvider>;
     };
     Structure: {
@@ -58,6 +58,7 @@ export declare const PluginConfig: {
             highSymmetryUnitCount: number;
             fiberResidueCount: number;
         }>;
+        DefaultRepresentationPreset: PluginConfigItem<string>;
         DefaultRepresentationPresetParams: PluginConfigItem<StructureRepresentationPresetProvider.CommonParams>;
     };
 };

package/lib/commonjs/mol-plugin/config.js

@@ -8,6 +8,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PluginConfigManager = exports.PluginConfig = exports.PluginConfigItem = void 0;
 var structure_1 = require("../mol-model/structure");
+var features_1 = require("./features");
 var PluginConfigItem = /** @class */ (function () {
     function PluginConfigItem(key, defaultValue) {
         this.key = key;
@@ -19,22 +20,6 @@ var PluginConfigItem = /** @class */ (function () {
 }());
 exports.PluginConfigItem = PluginConfigItem;
 function item(key, defaultValue) { return new PluginConfigItem(key, defaultValue); }
-function preferWebGl1() {
-    if (typeof navigator === 'undefined' || typeof window === 'undefined')
-        return false;
-    // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1 (but is working in Safari tech preview)
-    // prefer webgl 1 based on the userAgent substring
-    if (navigator.userAgent.indexOf('Version/15.1 Safari') > 0) {
-        return true;
-    }
-    // Check for iOS device which enabled WebGL2 recently but it doesn't seem
-    // to be full up to speed yet.
-    // adapted from https://stackoverflow.com/questions/9038625/detect-if-device-is-ios
-    var isIOS = /iPad|iPhone|iPod/.test(navigator.userAgent);
-    var isAppleDevice = navigator.userAgent.includes('Macintosh');
-    var isTouchScreen = navigator.maxTouchPoints >= 4; // true for iOS 13 (and hopefully beyond)
-    return !window.MSStream && (isIOS || (isAppleDevice && isTouchScreen));
-}
 exports.PluginConfig = {
     item: item,
     General: {
@@ -44,10 +29,10 @@ exports.PluginConfig = {
         PixelScale: item('plugin-config.pixel-scale', 1),
         PickScale: item('plugin-config.pick-scale', 0.25),
         PickPadding: item('plugin-config.pick-padding', 3),
-        EnableWboit: item('plugin-config.enable-wboit', true),
+        EnableWboit: item('plugin-config.enable-wboit', features_1.PluginFeatureDetection.wboit),
         // as of Oct 1 2021, WebGL 2 doesn't work on iOS 15.
         // TODO: check back in a few weeks to see if it was fixed
-        PreferWebGl1: item('plugin-config.prefer-webgl1', preferWebGl1()),
+        PreferWebGl1: item('plugin-config.prefer-webgl1', features_1.PluginFeatureDetection.preferWebGl1),
     },
     State: {
         DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),
@@ -75,6 +60,7 @@ exports.PluginConfig = {
     },
     Structure: {
         SizeThresholds: item('structure.size-thresholds', structure_1.Structure.DefaultSizeThresholds),
+        DefaultRepresentationPreset: item('structure.default-representation-preset', 'auto'),
         DefaultRepresentationPresetParams: item('structure.default-representation-preset-params', {})
     }
 };

package/lib/commonjs/mol-plugin/features.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+export declare const PluginFeatureDetection: {
+    readonly preferWebGl1: boolean;
+    readonly wboit: boolean;
+};

package/lib/commonjs/mol-plugin/features.js

@@ -0,0 +1,38 @@
+"use strict";
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PluginFeatureDetection = void 0;
+exports.PluginFeatureDetection = {
+    get preferWebGl1() {
+        if (typeof navigator === 'undefined' || typeof window === 'undefined')
+            return false;
+        // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1, 15.2. It is working in Safari 15.4 tech preview, so disabling all versions before that.
+        // prefer webgl 1 based on the userAgent substring
+        var unpportedSafariVersions = [
+            'Version/15.1 Safari',
+            'Version/15.2 Safari',
+            'Version/15.3 Safari'
+        ];
+        if (unpportedSafariVersions.some(function (v) { return navigator.userAgent.indexOf(v) > 0; })) {
+            return true;
+        }
+        // Check for iOS device which enabled WebGL2 recently but it doesn't seem
+        // to be full up to speed yet.
+        // adapted from https://stackoverflow.com/questions/9038625/detect-if-device-is-ios
+        var isIOS = /iPad|iPhone|iPod/.test(navigator.userAgent);
+        var isAppleDevice = navigator.userAgent.includes('Macintosh');
+        var isTouchScreen = navigator.maxTouchPoints >= 4; // true for iOS 13 (and hopefully beyond)
+        return !window.MSStream && (isIOS || (isAppleDevice && isTouchScreen));
+    },
+    get wboit() {
+        if (typeof navigator === 'undefined' || typeof window === 'undefined')
+            return true;
+        // disable Wboit in Safari 15
+        return !/Version\/15.\d Safari/.test(navigator.userAgent);
+    }
+};
+//# sourceMappingURL=features.js.map

package/lib/commonjs/mol-plugin/layout.d.ts

@@ -12,10 +12,10 @@ export declare const PluginLayoutStateParams: {
     isExpanded: PD.BooleanParam;
     showControls: PD.BooleanParam;
     regionState: PD.Group<PD.Normalize<{
-        left: "full" | "collapsed" | "hidden";
-        top: "full" | "hidden";
-        right: "full" | "hidden";
-        bottom: "full" | "hidden";
+        left: "hidden" | "full" | "collapsed";
+        top: "hidden" | "full";
+        right: "hidden" | "full";
+        bottom: "hidden" | "full";
     }>>;
     controlsDisplay: PD.Value<PluginLayoutControlsDisplay>;
 };

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

package/lib/commonjs/mol-plugin/spec.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -19,6 +19,7 @@ var transforms_1 = require("../mol-plugin-state/transforms");
 var transformers_1 = require("../mol-plugin/behavior/dynamic/volume-streaming/transformers");
 var state_interpolation_1 = require("../mol-plugin-state/animation/built-in/state-interpolation");
 var spin_structure_1 = require("../mol-plugin-state/animation/built-in/spin-structure");
+var camera_rock_1 = require("../mol-plugin-state/animation/built-in/camera-rock");
 var PluginSpec;
 (function (PluginSpec) {
     function Action(action, params) {
@@ -70,6 +71,8 @@ var DefaultPluginSpec = function () { return ({
         PluginSpec.Action(transforms_1.StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
         PluginSpec.Action(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
         PluginSpec.Action(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
+        PluginSpec.Action(transforms_1.StateTransforms.Representation.ClippingStructureRepresentation3DFromScript),
+        PluginSpec.Action(transforms_1.StateTransforms.Representation.SubstanceStructureRepresentation3DFromScript),
         PluginSpec.Action(volume_1.AssignColorVolume),
         PluginSpec.Action(transforms_1.StateTransforms.Volume.VolumeFromCcp4),
         PluginSpec.Action(transforms_1.StateTransforms.Volume.VolumeFromDsn6),
@@ -96,6 +99,7 @@ var DefaultPluginSpec = function () { return ({
     animations: [
         model_index_1.AnimateModelIndex,
         camera_spin_1.AnimateCameraSpin,
+        camera_rock_1.AnimateCameraRock,
         state_snapshots_1.AnimateStateSnapshots,
         assembly_unwind_1.AnimateAssemblyUnwind,
         spin_structure_1.AnimateStructureSpin,

package/lib/commonjs/mol-plugin/state.d.ts

@@ -13,6 +13,7 @@ import { InteractivityManager } from '../mol-plugin-state/manager/interactivity'
 import { StructureFocusSnapshot } from '../mol-plugin-state/manager/structure/focus';
 import { PluginContext } from './context';
 import { PluginComponent } from '../mol-plugin-state/component';
+import { StructureComponentManager } from '../mol-plugin-state/manager/structure/component';
 export { PluginState };
 declare class PluginState extends PluginComponent {
     private plugin;
@@ -50,6 +51,7 @@ declare class PluginState extends PluginComponent {
         durationInMs: PD.Numeric;
         data: PD.BooleanParam;
         behavior: PD.BooleanParam;
+        componentManager: PD.BooleanParam;
         animation: PD.BooleanParam;
         startAnimation: PD.BooleanParam;
         canvas3d: PD.BooleanParam;
@@ -63,6 +65,7 @@ declare class PluginState extends PluginComponent {
         durationInMs: PD.Numeric;
         data: PD.BooleanParam;
         behavior: PD.BooleanParam;
+        componentManager: PD.BooleanParam;
         animation: PD.BooleanParam;
         startAnimation: PD.BooleanParam;
         canvas3d: PD.BooleanParam;
@@ -85,6 +88,7 @@ declare namespace PluginState {
         durationInMs: PD.Numeric;
         data: PD.BooleanParam;
         behavior: PD.BooleanParam;
+        componentManager: PD.BooleanParam;
         animation: PD.BooleanParam;
         startAnimation: PD.BooleanParam;
         canvas3d: PD.BooleanParam;
@@ -99,6 +103,7 @@ declare namespace PluginState {
         durationInMs: PD.Numeric;
         data: PD.BooleanParam;
         behavior: PD.BooleanParam;
+        componentManager: PD.BooleanParam;
         animation: PD.BooleanParam;
         startAnimation: PD.BooleanParam;
         canvas3d: PD.BooleanParam;
@@ -126,6 +131,9 @@ declare namespace PluginState {
             props?: InteractivityManager.Props;
         };
         structureFocus?: StructureFocusSnapshot;
+        structureComponentManager?: {
+            options?: StructureComponentManager.Options;
+        };
         durationInMs?: number;
     }
     type SnapshotType = 'json' | 'molj' | 'zip' | 'molx';

package/lib/commonjs/mol-plugin/state.js

@@ -65,37 +65,46 @@ var PluginState = /** @class */ (function (_super) {
             canvas3d: p.canvas3d ? { props: (_b = this.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.props } : void 0,
             interactivity: p.interactivity ? { props: this.plugin.managers.interactivity.props } : void 0,
             structureFocus: this.plugin.managers.structure.focus.getSnapshot(),
+            structureComponentManager: p.componentManager ? {
+                options: this.plugin.managers.structure.component.state.options
+            } : void 0,
             durationInMs: p === null || p === void 0 ? void 0 : p.durationInMs
         };
     };
     PluginState.prototype.setSnapshot = function (snapshot) {
-        var _a;
+        var _a, _b, _c;
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
             var settings;
-            return (0, tslib_1.__generator)(this, function (_b) {
-                switch (_b.label) {
+            return (0, tslib_1.__generator)(this, function (_d) {
+                switch (_d.label) {
                     case 0: return [4 /*yield*/, this.animation.stop()];
                     case 1:
-                        _b.sent();
-                        if (!snapshot.behaviour) return [3 /*break*/, 3];
-                        return [4 /*yield*/, this.plugin.runTask(this.behaviors.setSnapshot(snapshot.behaviour))];
+                        _d.sent();
+                        if (!((_a = snapshot.structureComponentManager) === null || _a === void 0 ? void 0 : _a.options)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, this.plugin.managers.structure.component.setOptions((_b = snapshot.structureComponentManager) === null || _b === void 0 ? void 0 : _b.options)];
                     case 2:
-                        _b.sent();
-                        _b.label = 3;
+                        _d.sent();
+                        _d.label = 3;
                     case 3:
-                        if (!snapshot.data) return [3 /*break*/, 5];
-                        return [4 /*yield*/, this.plugin.runTask(this.data.setSnapshot(snapshot.data))];
+                        if (!snapshot.behaviour) return [3 /*break*/, 5];
+                        return [4 /*yield*/, this.plugin.runTask(this.behaviors.setSnapshot(snapshot.behaviour))];
                     case 4:
-                        _b.sent();
-                        _b.label = 5;
+                        _d.sent();
+                        _d.label = 5;
                     case 5:
-                        if (!((_a = snapshot.canvas3d) === null || _a === void 0 ? void 0 : _a.props)) return [3 /*break*/, 7];
-                        settings = param_definition_1.ParamDefinition.normalizeParams(canvas3d_1.Canvas3DParams, snapshot.canvas3d.props, 'children');
-                        return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: settings })];
+                        if (!snapshot.data) return [3 /*break*/, 7];
+                        return [4 /*yield*/, this.plugin.runTask(this.data.setSnapshot(snapshot.data))];
                     case 6:
-                        _b.sent();
-                        _b.label = 7;
+                        _d.sent();
+                        _d.label = 7;
                     case 7:
+                        if (!((_c = snapshot.canvas3d) === null || _c === void 0 ? void 0 : _c.props)) return [3 /*break*/, 9];
+                        settings = param_definition_1.ParamDefinition.normalizeParams(canvas3d_1.Canvas3DParams, snapshot.canvas3d.props, 'children');
+                        return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: settings })];
+                    case 8:
+                        _d.sent();
+                        _d.label = 9;
+                    case 9:
                         if (snapshot.interactivity) {
                             if (snapshot.interactivity.props)
                                 this.plugin.managers.interactivity.setProps(snapshot.interactivity.props);
@@ -156,6 +165,7 @@ exports.PluginState = PluginState;
         durationInMs: param_definition_1.ParamDefinition.Numeric(1500, { min: 100, max: 15000, step: 100 }, { label: 'Duration in ms' }),
         data: param_definition_1.ParamDefinition.Boolean(true),
         behavior: param_definition_1.ParamDefinition.Boolean(false),
+        componentManager: param_definition_1.ParamDefinition.Boolean(true),
         animation: param_definition_1.ParamDefinition.Boolean(true),
         startAnimation: param_definition_1.ParamDefinition.Boolean(false),
         canvas3d: param_definition_1.ParamDefinition.Boolean(true),