molstar 3.0.0-dev.6 → 3.0.0

package/lib/commonjs/apps/viewer/index.js

@@ -1,523 +1,15 @@
 "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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ViewerAutoPreset = exports.Viewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
 var tslib_1 = require("tslib");
-var behavior_1 = require("../../extensions/anvil/behavior");
-var cellpack_1 = require("../../extensions/cellpack");
-var dnatco_1 = require("../../extensions/dnatco");
-var format_1 = require("../../extensions/g3d/format");
-var geo_export_1 = require("../../extensions/geo-export");
-var behavior_2 = require("../../extensions/model-archive/quality-assessment/behavior");
-var behavior_3 = require("../../extensions/model-archive/quality-assessment/behavior");
-var prop_1 = require("../../extensions/model-archive/quality-assessment/prop");
-var mp4_export_1 = require("../../extensions/mp4-export");
-var pdbe_1 = require("../../extensions/pdbe");
-var rcsb_1 = require("../../extensions/rcsb");
-var structure_1 = require("../../mol-plugin-state/actions/structure");
-var volume_1 = require("../../mol-plugin-state/actions/volume");
-var representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
-var volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
-var transforms_1 = require("../../mol-plugin-state/transforms");
-var model_1 = require("../../mol-plugin-state/transforms/model");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
-var spec_1 = require("../../mol-plugin-ui/spec");
-var commands_1 = require("../../mol-plugin/commands");
-var config_1 = require("../../mol-plugin/config");
-var spec_2 = require("../../mol-plugin/spec");
-var mol_state_1 = require("../../mol-state");
-var assets_1 = require("../../mol-util/assets");
-require("../../mol-util/polyfill");
-var type_helpers_1 = require("../../mol-util/type-helpers");
 require("./embedded.html");
 require("./favicon.ico");
 require("./index.html");
 require('mol-plugin-ui/skin/light.scss');
-var version_1 = require("../../mol-plugin/version");
-Object.defineProperty(exports, "version", { enumerable: true, get: function () { return version_1.PLUGIN_VERSION; } });
-var debug_1 = require("../../mol-util/debug");
-Object.defineProperty(exports, "setDebugMode", { enumerable: true, get: function () { return debug_1.setDebugMode; } });
-Object.defineProperty(exports, "setProductionMode", { enumerable: true, get: function () { return debug_1.setProductionMode; } });
-var CustomFormats = [
-    ['g3d', format_1.G3dProvider]
-];
-var Extensions = {
-    'cellpack': spec_2.PluginSpec.Behavior(cellpack_1.CellPack),
-    'dnatco-confal-pyramids': spec_2.PluginSpec.Behavior(dnatco_1.DnatcoConfalPyramids),
-    'pdbe-structure-quality-report': spec_2.PluginSpec.Behavior(pdbe_1.PDBeStructureQualityReport),
-    'rcsb-assembly-symmetry': spec_2.PluginSpec.Behavior(rcsb_1.RCSBAssemblySymmetry),
-    'rcsb-validation-report': spec_2.PluginSpec.Behavior(rcsb_1.RCSBValidationReport),
-    'anvil-membrane-orientation': spec_2.PluginSpec.Behavior(behavior_1.ANVILMembraneOrientation),
-    'g3d': spec_2.PluginSpec.Behavior(format_1.G3DFormat),
-    'mp4-export': spec_2.PluginSpec.Behavior(mp4_export_1.Mp4Export),
-    'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport),
-    'ma-quality-assessment': spec_2.PluginSpec.Behavior(behavior_2.MAQualityAssessment),
-};
-var DefaultViewerOptions = {
-    customFormats: CustomFormats,
-    extensions: (0, type_helpers_1.ObjectKeys)(Extensions),
-    layoutIsExpanded: true,
-    layoutShowControls: true,
-    layoutShowRemoteState: true,
-    layoutControlsDisplay: 'reactive',
-    layoutShowSequence: true,
-    layoutShowLog: true,
-    layoutShowLeftPanel: true,
-    collapseLeftPanel: false,
-    collapseRightPanel: false,
-    disableAntialiasing: config_1.PluginConfig.General.DisableAntialiasing.defaultValue,
-    pixelScale: config_1.PluginConfig.General.PixelScale.defaultValue,
-    pickScale: config_1.PluginConfig.General.PickScale.defaultValue,
-    pickPadding: config_1.PluginConfig.General.PickPadding.defaultValue,
-    enableWboit: config_1.PluginConfig.General.EnableWboit.defaultValue,
-    viewportShowExpand: config_1.PluginConfig.Viewport.ShowExpand.defaultValue,
-    viewportShowControls: config_1.PluginConfig.Viewport.ShowControls.defaultValue,
-    viewportShowSettings: config_1.PluginConfig.Viewport.ShowSettings.defaultValue,
-    viewportShowSelectionMode: config_1.PluginConfig.Viewport.ShowSelectionMode.defaultValue,
-    viewportShowAnimation: config_1.PluginConfig.Viewport.ShowAnimation.defaultValue,
-    pluginStateServer: config_1.PluginConfig.State.DefaultServer.defaultValue,
-    volumeStreamingServer: config_1.PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
-    volumeStreamingDisabled: !config_1.PluginConfig.VolumeStreaming.Enabled.defaultValue,
-    pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
-    emdbProvider: config_1.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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var o, defaultSpec, spec, element, plugin;
-            return (0, tslib_1.__generator)(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), options);
-                        defaultSpec = (0, spec_1.DefaultPluginUISpec)();
-                        spec = {
-                            actions: defaultSpec.actions,
-                            behaviors: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
-                            animations: (0, tslib_1.__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: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__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: [
-                                [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
-                                [config_1.PluginConfig.General.PixelScale, o.pixelScale],
-                                [config_1.PluginConfig.General.PickScale, o.pickScale],
-                                [config_1.PluginConfig.General.PickPadding, o.pickPadding],
-                                [config_1.PluginConfig.General.EnableWboit, o.enableWboit],
-                                [config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
-                                [config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
-                                [config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
-                                [config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
-                                [config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
-                                [config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
-                                [config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
-                                [config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
-                                [config_1.PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
-                                [config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                                [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
-                                [config_1.PluginConfig.Structure.DefaultRepresentationPreset, exports.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*/, (0, mol_plugin_ui_1.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(exports.ViewerAutoPreset);
-                                }
-                            })];
-                    case 1:
-                        plugin = _b.sent();
-                        return [2 /*return*/, new Viewer(plugin)];
-                }
-            });
-        });
-    };
-    Viewer.prototype.setRemoteSnapshot = function (id) {
-        var url = "".concat(this.plugin.config.get(config_1.PluginConfig.State.CurrentServer), "/get/").concat(id);
-        return commands_1.PluginCommands.State.Snapshots.Fetch(this.plugin, { url: url });
-    };
-    Viewer.prototype.loadSnapshotFromUrl = function (url, type) {
-        return commands_1.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 = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
-            source: {
-                name: 'url',
-                params: {
-                    url: assets_1.Asset.Url(url),
-                    format: format,
-                    isBinary: isBinary,
-                    options: (0, tslib_1.__assign)((0, tslib_1.__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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var plugin, data, trajectory;
-            return (0, tslib_1.__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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var _data, trajectory;
-            return (0, tslib_1.__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 = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
-        var provider = this.plugin.config.get(config_1.PluginConfig.Download.DefaultPdbProvider);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
-            source: {
-                name: 'pdb',
-                params: {
-                    provider: {
-                        id: pdb,
-                        server: {
-                            name: provider,
-                            params: structure_1.PdbDownloadProvider[provider].defaultValue
-                        }
-                    },
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
-                }
-            }
-        }));
-    };
-    Viewer.prototype.loadPdbDev = function (pdbDev) {
-        var params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.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(config_1.PluginConfig.Download.DefaultEmdbProvider);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(volume_1.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 = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
-            source: {
-                name: 'alphafolddb',
-                params: {
-                    id: afdb,
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
-                }
-            }
-        }));
-    };
-    Viewer.prototype.loadModelArchive = function (id) {
-        var params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var plugin, update;
-            var _this = this;
-            return (0, tslib_1.__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(transforms_1.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 ((0, tslib_1.__assign)({ alpha: 1, volumeIndex: 0 }, v)); })
-                    });
-                    return [2 /*return*/, update.commit()];
-                }
-                return [2 /*return*/, plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso;
-                        var _a, _b, _c, _d;
-                        return (0, tslib_1.__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(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
-            return (0, tslib_1.__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(model_1.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;
-}());
-exports.Viewer = Viewer;
-exports.ViewerAutoPreset = (0, representation_preset_1.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 prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); }) ||
-            !!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); }));
-    },
-    params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
-    apply: function (ref, params, plugin) {
-        var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var structureCell, structure;
-            return (0, tslib_1.__generator)(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        structureCell = mol_state_1.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 prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); })) return [3 /*break*/, 2];
-                        return [4 /*yield*/, behavior_3.QualityAssessmentPLDDTPreset.apply(ref, params, plugin)];
-                    case 1: return [2 /*return*/, _b.sent()];
-                    case 2:
-                        if (!!!structure.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); })) return [3 /*break*/, 4];
-                        return [4 /*yield*/, behavior_3.QualityAssessmentQmeanPreset.apply(ref, params, plugin)];
-                    case 3: return [2 /*return*/, _b.sent()];
-                    case 4: return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, params, plugin)];
-                    case 5: return [2 /*return*/, _b.sent()];
-                }
-            });
-        });
-    }
-});
+(0, tslib_1.__exportStar)(require("./app"), exports);
 //# sourceMappingURL=index.js.map

package/lib/commonjs/examples/alpha-orbitals/index.js

@@ -24,7 +24,7 @@ require('mol-plugin-ui/skin/light.scss');
 var AlphaOrbitalsExample = /** @class */ (function () {
     function AlphaOrbitalsExample() {
         this.params = new rxjs_1.BehaviorSubject({});
-        this.state = new rxjs_1.BehaviorSubject({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
+        this.state = new rxjs_1.BehaviorSubject({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: true });
         this.selectors = void 0;
         this.basis = void 0;
         this.currentParams = (0, tslib_1.__assign)({}, this.state.value);

package/lib/commonjs/examples/basic-wrapper/index.js

@@ -244,13 +244,17 @@ var BasicWrapper = /** @class */ (function () {
     BasicWrapper.prototype.toggleSpin = function () {
         if (!this.plugin.canvas3d)
             return;
+        var trackball = this.plugin.canvas3d.props.trackball;
         commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, {
-            settings: function (props) {
-                props.trackball.spin = !props.trackball.spin;
+            settings: {
+                trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } } })
             }
         });
-        if (!this.plugin.canvas3d.props.trackball.spin)
+        if (this.plugin.canvas3d.props.trackball.animate.name !== 'spin') {
             commands_1.PluginCommands.Camera.Reset(this.plugin, {});
+        }
     };
     BasicWrapper.prototype.animateModelIndexTargetFps = function () {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);

package/lib/commonjs/examples/proteopedia-wrapper/index.js

@@ -479,7 +479,13 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         if (!this.plugin.canvas3d)
             return;
         var trackball = this.plugin.canvas3d.props.trackball;
-        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { spin: !trackball.spin }) } });
+        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: {
+                trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } } })
+            }
+        });
     };
     MolStarProteopediaWrapper.prototype.animateModelIndexTargetFps = function () {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -32,6 +32,10 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     sectorOpacity: number;
     doubleSided: boolean;
     flipSided: boolean;