molstar 2.3.9 → 3.0.0-dev.10

package/lib/apps/viewer/app.js

@@ -0,0 +1,515 @@
+/**
+ * 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>
+ */
+import { __assign, __awaiter, __generator, __spreadArray } from "tslib";
+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { CellPack } from '../../extensions/cellpack';
+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { GeometryExport } from '../../extensions/geo-export';
+import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
+import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
+import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
+import { createPluginUI } from '../../mol-plugin-ui';
+import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { StateObjectRef } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+var CustomFormats = [
+    ['g3d', G3dProvider]
+];
+var Extensions = {
+    'cellpack': PluginSpec.Behavior(CellPack),
+    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
+    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
+    'g3d': PluginSpec.Behavior(G3DFormat),
+    'mp4-export': PluginSpec.Behavior(Mp4Export),
+    'geo-export': PluginSpec.Behavior(GeometryExport),
+    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+};
+var DefaultViewerOptions = {
+    customFormats: CustomFormats,
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive',
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
+    collapseRightPanel: false,
+    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: PluginConfig.General.PixelScale.defaultValue,
+    pickScale: PluginConfig.General.PickScale.defaultValue,
+    pickPadding: PluginConfig.General.PickPadding.defaultValue,
+    enableWboit: PluginConfig.General.EnableWboit.defaultValue,
+    preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+};
+var Viewer = /** @class */ (function () {
+    function Viewer(plugin) {
+        this.plugin = plugin;
+    }
+    Viewer.create = function (elementOrId, options) {
+        var _a;
+        if (options === void 0) { options = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var o, defaultSpec, spec, element, plugin;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        o = __assign(__assign({}, DefaultViewerOptions), options);
+                        defaultSpec = DefaultPluginUISpec();
+                        spec = {
+                            actions: defaultSpec.actions,
+                            behaviors: __spreadArray(__spreadArray([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
+                            animations: __spreadArray([], defaultSpec.animations || [], true),
+                            customParamEditors: defaultSpec.customParamEditors,
+                            customFormats: o === null || o === void 0 ? void 0 : o.customFormats,
+                            layout: {
+                                initial: {
+                                    isExpanded: o.layoutIsExpanded,
+                                    showControls: o.layoutShowControls,
+                                    controlsDisplay: o.layoutControlsDisplay,
+                                    regionState: {
+                                        bottom: 'full',
+                                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                                        right: o.collapseRightPanel ? 'hidden' : 'full',
+                                        top: 'full',
+                                    }
+                                },
+                            },
+                            components: __assign(__assign({}, defaultSpec.components), { controls: __assign(__assign({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none' }),
+                            config: [
+                                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                                [PluginConfig.General.PixelScale, o.pixelScale],
+                                [PluginConfig.General.PickScale, o.pickScale],
+                                [PluginConfig.General.PickPadding, o.pickPadding],
+                                [PluginConfig.General.EnableWboit, o.enableWboit],
+                                [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+                                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
+                                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                                [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
+                            ]
+                        };
+                        element = typeof elementOrId === 'string'
+                            ? document.getElementById(elementOrId)
+                            : elementOrId;
+                        if (!element)
+                            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
+                        return [4 /*yield*/, createPluginUI(element, spec, {
+                                onBeforeUIRender: function (plugin) {
+                                    // the preset needs to be added before the UI renders otherwise
+                                    // "Download Structure" wont be able to pick it up
+                                    plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
+                                }
+                            })];
+                    case 1:
+                        plugin = _b.sent();
+                        return [2 /*return*/, new Viewer(plugin)];
+                }
+            });
+        });
+    };
+    Viewer.prototype.setRemoteSnapshot = function (id) {
+        var url = "".concat(this.plugin.config.get(PluginConfig.State.CurrentServer), "/get/").concat(id);
+        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url: url });
+    };
+    Viewer.prototype.loadSnapshotFromUrl = function (url, type) {
+        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url: url, type: type });
+    };
+    Viewer.prototype.loadStructureFromUrl = function (url, format, isBinary, options) {
+        if (format === void 0) { format = 'mmcif'; }
+        if (isBinary === void 0) { isBinary = false; }
+        var params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'url',
+                params: {
+                    url: Asset.Url(url),
+                    format: format,
+                    isBinary: isBinary,
+                    options: __assign(__assign({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadAllModelsOrAssemblyFromUrl = function (url, format, isBinary, options) {
+        if (format === void 0) { format = 'mmcif'; }
+        if (isBinary === void 0) { isBinary = false; }
+        return __awaiter(this, void 0, void 0, function () {
+            var plugin, data, trajectory;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        plugin = this.plugin;
+                        return [4 /*yield*/, plugin.builders.data.download({ url: url, isBinary: isBinary }, { state: { isGhost: true } })];
+                    case 1:
+                        data = _a.sent();
+                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, format)];
+                    case 2:
+                        trajectory = _a.sent();
+                        return [4 /*yield*/, this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options === null || options === void 0 ? void 0 : options.representationParams })];
+                    case 3:
+                        _a.sent();
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    Viewer.prototype.loadStructureFromData = function (data, format, options) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _data, trajectory;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.plugin.builders.data.rawData({ data: data, label: options === null || options === void 0 ? void 0 : options.dataLabel })];
+                    case 1:
+                        _data = _a.sent();
+                        return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(_data, format)];
+                    case 2:
+                        trajectory = _a.sent();
+                        return [4 /*yield*/, this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default')];
+                    case 3:
+                        _a.sent();
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    Viewer.prototype.loadPdb = function (pdb, options) {
+        var params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        var provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb',
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue
+                        }
+                    },
+                    options: __assign(__assign({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadPdbDev = function (pdbDev) {
+        var params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev',
+                params: {
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadEmdb = function (emdb, options) {
+        var _a;
+        var provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds',
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: (_a = options === null || options === void 0 ? void 0 : options.detail) !== null && _a !== void 0 ? _a : 3,
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadAlphaFoldDb = function (afdb) {
+        var params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'alphafolddb',
+                params: {
+                    id: afdb,
+                    options: __assign(__assign({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadModelArchive = function (id) {
+        var params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'modelarchive',
+                params: {
+                    id: id,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    };
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    Viewer.prototype.loadVolumeFromUrl = function (_a, isovalues, options) {
+        var url = _a.url, format = _a.format, isBinary = _a.isBinary;
+        return __awaiter(this, void 0, void 0, function () {
+            var plugin, update;
+            var _this = this;
+            return __generator(this, function (_b) {
+                plugin = this.plugin;
+                if (!plugin.dataFormats.get(format)) {
+                    throw new Error("Unknown density format: ".concat(format));
+                }
+                if (options === null || options === void 0 ? void 0 : options.isLazy) {
+                    update = this.plugin.build();
+                    update.toRoot().apply(StateTransforms.Data.LazyVolume, {
+                        url: url,
+                        format: format,
+                        entryId: options === null || options === void 0 ? void 0 : options.entryId,
+                        isBinary: isBinary,
+                        isovalues: isovalues.map(function (v) { return (__assign({ alpha: 1, volumeIndex: 0 }, v)); })
+                    });
+                    return [2 /*return*/, update.commit()];
+                }
+                return [2 /*return*/, plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
+                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso;
+                        var _a, _b, _c, _d;
+                        return __generator(this, function (_e) {
+                            switch (_e.label) {
+                                case 0: return [4 /*yield*/, plugin.builders.data.download({ url: url, isBinary: isBinary }, { state: { isGhost: true } })];
+                                case 1:
+                                    data = _e.sent();
+                                    return [4 /*yield*/, plugin.dataFormats.get(format).parse(plugin, data, { entryId: options === null || options === void 0 ? void 0 : options.entryId })];
+                                case 2:
+                                    parsed = _e.sent();
+                                    firstVolume = (parsed.volume || parsed.volumes[0]);
+                                    if (!(firstVolume === null || firstVolume === void 0 ? void 0 : firstVolume.isOk))
+                                        throw new Error('Failed to parse any volume.');
+                                    repr = plugin.build();
+                                    for (_i = 0, isovalues_1 = isovalues; _i < isovalues_1.length; _i++) {
+                                        iso = isovalues_1[_i];
+                                        repr
+                                            .to((_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume)
+                                            .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data, {
+                                            type: 'isosurface',
+                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                                            color: 'uniform',
+                                            colorParams: { value: iso.color }
+                                        }));
+                                    }
+                                    return [4 /*yield*/, repr.commit()];
+                                case 3:
+                                    _e.sent();
+                                    return [2 /*return*/];
+                            }
+                        });
+                    }); })];
+            });
+        });
+    };
+    /**
+     * @example
+     *  viewer.loadTrajectory({
+     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+     *      preset: 'all-models' // or 'default'
+     *  });
+     */
+    Viewer.prototype.loadTrajectory = function (params) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function () {
+            var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
+            return __generator(this, function (_f) {
+                switch (_f.label) {
+                    case 0:
+                        plugin = this.plugin;
+                        if (!(params.model.kind === 'model-data' || params.model.kind === 'model-url')) return [3 /*break*/, 7];
+                        if (!(params.model.kind === 'model-data')) return [3 /*break*/, 2];
+                        return [4 /*yield*/, plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })];
+                    case 1:
+                        _c = _f.sent();
+                        return [3 /*break*/, 4];
+                    case 2: return [4 /*yield*/, plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel })];
+                    case 3:
+                        _c = _f.sent();
+                        _f.label = 4;
+                    case 4:
+                        data = _c;
+                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif')];
+                    case 5:
+                        trajectory_1 = _f.sent();
+                        return [4 /*yield*/, plugin.builders.structure.createModel(trajectory_1)];
+                    case 6:
+                        model = _f.sent();
+                        return [3 /*break*/, 13];
+                    case 7:
+                        if (!(params.model.kind === 'topology-data')) return [3 /*break*/, 9];
+                        return [4 /*yield*/, plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })];
+                    case 8:
+                        _d = _f.sent();
+                        return [3 /*break*/, 11];
+                    case 9: return [4 /*yield*/, plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel })];
+                    case 10:
+                        _d = _f.sent();
+                        _f.label = 11;
+                    case 11:
+                        data = _d;
+                        provider = plugin.dataFormats.get(params.model.format);
+                        return [4 /*yield*/, provider.parse(plugin, data)];
+                    case 12:
+                        model = _f.sent();
+                        _f.label = 13;
+                    case 13:
+                        if (!(params.coordinates.kind === 'coordinates-data')) return [3 /*break*/, 15];
+                        return [4 /*yield*/, plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })];
+                    case 14:
+                        _e = _f.sent();
+                        return [3 /*break*/, 17];
+                    case 15: return [4 /*yield*/, plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel })];
+                    case 16:
+                        _e = _f.sent();
+                        _f.label = 17;
+                    case 17:
+                        data = _e;
+                        provider = plugin.dataFormats.get(params.coordinates.format);
+                        return [4 /*yield*/, provider.parse(plugin, data)];
+                    case 18:
+                        coords = _f.sent();
+                        return [4 /*yield*/, plugin.build().toRoot()
+                                .apply(TrajectoryFromModelAndCoordinates, {
+                                modelRef: model.ref,
+                                coordinatesRef: coords.ref
+                            }, { dependsOn: [model.ref, coords.ref] })
+                                .commit()];
+                    case 19:
+                        trajectory = _f.sent();
+                        return [4 /*yield*/, plugin.builders.structure.hierarchy.applyPreset(trajectory, (_b = params.preset) !== null && _b !== void 0 ? _b : 'default')];
+                    case 20:
+                        preset = _f.sent();
+                        return [2 /*return*/, { model: model, coords: coords, preset: preset }];
+                }
+            });
+        });
+    };
+    Viewer.prototype.handleResize = function () {
+        this.plugin.layout.events.updated.next(void 0);
+    };
+    return Viewer;
+}());
+export { Viewer };
+export var ViewerAutoPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-viewer-auto',
+    display: {
+        name: 'Automatic (w/ Annotation)', group: 'Annotation',
+        description: 'Show standard automatic representation but colored by quality assessment (if available in the model).'
+    },
+    isApplicable: function (a) {
+        return (!!a.data.models.some(function (m) { return QualityAssessment.isApplicable(m, 'pLDDT'); }) ||
+            !!a.data.models.some(function (m) { return QualityAssessment.isApplicable(m, 'qmean'); }));
+    },
+    params: function () { return StructureRepresentationPresetProvider.CommonParams; },
+    apply: function (ref, params, plugin) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function () {
+            var structureCell, structure;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+                        structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
+                        if (!structureCell || !structure)
+                            return [2 /*return*/, {}];
+                        if (!!!structure.models.some(function (m) { return QualityAssessment.isApplicable(m, 'pLDDT'); })) return [3 /*break*/, 2];
+                        return [4 /*yield*/, QualityAssessmentPLDDTPreset.apply(ref, params, plugin)];
+                    case 1: return [2 /*return*/, _b.sent()];
+                    case 2:
+                        if (!!!structure.models.some(function (m) { return QualityAssessment.isApplicable(m, 'qmean'); })) return [3 /*break*/, 4];
+                        return [4 /*yield*/, QualityAssessmentQmeanPreset.apply(ref, params, plugin)];
+                    case 3: return [2 /*return*/, _b.sent()];
+                    case 4: return [4 /*yield*/, PresetStructureRepresentations.auto.apply(ref, params, plugin)];
+                    case 5: return [2 /*return*/, _b.sent()];
+                }
+            });
+        });
+    }
+});
+//# sourceMappingURL=app.js.map

package/lib/apps/viewer/embedded.html

@@ -20,7 +20,7 @@
         <div id="app"></div>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
-            var viewer = new molstar.Viewer('app', {
+            molstar.Viewer.create('app', {
                 layoutIsExpanded: true,
                 layoutShowControls: false,
                 layoutShowRemoteState: false,
@@ -34,11 +34,11 @@
 
                 pdbProvider: 'rcsb',
                 emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
             });
-            viewer.loadPdb('7bv2');
-            viewer.loadEmdb('EMD-30210', { detail: 6 });            
-
-            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>
 </html>