molstar 3.3.1 → 3.6.0

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

@@ -1,12 +1,12 @@
 "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.AddTrajectory = exports.EnableStructureCustomProps = exports.EnableModelCustomProps = exports.UpdateTrajectory = exports.DownloadStructure = exports.PdbDownloadProvider = void 0;
+exports.LoadTrajectory = exports.AddTrajectory = exports.EnableStructureCustomProps = exports.EnableModelCustomProps = exports.UpdateTrajectory = exports.DownloadStructure = exports.PdbDownloadProvider = void 0;
 var tslib_1 = require("tslib");
 var mol_state_1 = require("../../mol-state");
 var mol_task_1 = require("../../mol-task");
@@ -21,6 +21,8 @@ var assets_1 = require("../../mol-util/assets");
 var config_1 = require("../../mol-plugin/config");
 var file_info_1 = require("../../mol-util/file-info");
 var type_helpers_1 = require("../../mol-util/type-helpers");
+var topology_1 = require("../formats/topology");
+var coordinates_1 = require("../formats/coordinates");
 var DownloadModelRepresentationOptions = function (plugin) {
     var representationDefault = plugin.config.get(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.PresetStructureRepresentations.auto.id;
     return param_definition_1.ParamDefinition.Group({
@@ -88,9 +90,9 @@ var DownloadStructure = mol_state_1.StateAction.build({
     }
 })(function (_a, plugin) {
     var params = _a.params, state = _a.state;
-    return mol_task_1.Task.create('Download Structure', function (ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    return mol_task_1.Task.create('Download Structure', function (ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var src, downloadParams, asTrajectory, format, _a, representationPreset, showUnitcell, structure;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     plugin.behaviors.layout.leftPanelTabName.next('data');
@@ -138,9 +140,9 @@ var DownloadStructure = mol_state_1.StateAction.build({
                     asTrajectory = !!src.params.options.asTrajectory;
                     format = 'pdb';
                     return [3 /*break*/, 15];
-                case 8: return [4 /*yield*/, getDownloadParams(src.params.id, function (id) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+                case 8: return [4 /*yield*/, getDownloadParams(src.params.id, function (id) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
                         var url, info;
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                        return tslib_1.__generator(this, function (_a) {
                             switch (_a.label) {
                                 case 0:
                                     url = "https://www.alphafold.ebi.ac.uk/api/prediction/".concat(id.toUpperCase());
@@ -170,15 +172,17 @@ var DownloadStructure = mol_state_1.StateAction.build({
                     asTrajectory = !!src.params.options.asTrajectory;
                     format = 'mol';
                     return [3 /*break*/, 15];
-                case 14: throw new Error("".concat(src.name, " not supported."));
+                case 14:
+                    (0, type_helpers_1.assertUnreachable)(src);
+                    _b.label = 15;
                 case 15:
                     representationPreset = params.source.params.options.representation || plugin.config.get(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.PresetStructureRepresentations.auto.id;
                     showUnitcell = representationPreset !== representation_preset_1.PresetStructureRepresentations.empty.id;
                     structure = src.params.options.type.name === 'auto' ? void 0 : src.params.options.type;
-                    return [4 /*yield*/, state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+                    return [4 /*yield*/, state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
                             var blob, trajectory, _i, downloadParams_1, download, data, provider, trajectory;
                             var _a;
-                            return (0, tslib_1.__generator)(this, function (_b) {
+                            return tslib_1.__generator(this, function (_b) {
                                 switch (_b.label) {
                                     case 0:
                                         if (!(downloadParams.length > 0 && asTrajectory)) return [3 /*break*/, 4];
@@ -242,10 +246,10 @@ var DownloadStructure = mol_state_1.StateAction.build({
 });
 exports.DownloadStructure = DownloadStructure;
 function getDownloadParams(src, url, label, isBinary) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ids, ret, _i, ids_1, id, _a, _b, _c, _d;
         var _e;
-        return (0, tslib_1.__generator)(this, function (_f) {
+        return tslib_1.__generator(this, function (_f) {
             switch (_f.label) {
                 case 0:
                     ids = src.split(/[,\s]/).map(function (id) { return id.trim(); }).filter(function (id) { return !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)); });
@@ -271,8 +275,8 @@ function getDownloadParams(src, url, label, isBinary) {
     });
 }
 function getPdbeDownloadParams(src) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             if (src.name !== 'pdb' || src.params.provider.server.name !== 'pdbe')
                 throw new Error('expected pdbe');
             return [2 /*return*/, src.params.provider.server.params.variant === 'updated'
@@ -284,8 +288,8 @@ function getPdbeDownloadParams(src) {
     });
 }
 function getPdbjDownloadParams(src) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             if (src.name !== 'pdb' || src.params.provider.server.name !== 'pdbj')
                 throw new Error('expected pdbj');
             return [2 /*return*/, getDownloadParams(src.params.provider.id, function (id) { return "https://data.pdbjbk1.pdbj.org/pub/pdb/data/structures/divided/mmCIF/".concat(id.toLowerCase().substring(1, 3), "/").concat(id.toLowerCase(), ".cif"); }, function (id) { return "PDBj: ".concat(id, " (cif)"); }, false)];
@@ -293,8 +297,8 @@ function getPdbjDownloadParams(src) {
     });
 }
 function getRcsbDownloadParams(src) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             if (src.name !== 'pdb' || src.params.provider.server.name !== 'rcsb')
                 throw new Error('expected rcsb');
             return [2 /*return*/, src.params.provider.server.params.encoding === 'cif'
@@ -370,7 +374,7 @@ exports.AddTrajectory = mol_state_1.StateAction.build({
     from: objects_1.PluginStateObject.Root,
     params: function (a, ctx) {
         var state = ctx.state.data;
-        var models = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Model); }), true), state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Topology); }), true);
+        var models = tslib_1.__spreadArray(tslib_1.__spreadArray([], state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Model); }), true), state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Topology); }), true);
         var modelOptions = models.map(function (t) { return [t.transform.ref, t.obj.label]; });
         var coords = state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Coordinates); });
         var coordOptions = coords.map(function (c) { return [c.transform.ref, c.obj.label]; });
@@ -382,9 +386,9 @@ exports.AddTrajectory = mol_state_1.StateAction.build({
 })(function (_a, ctx) {
     var params = _a.params, state = _a.state;
     return mol_task_1.Task.create('Add Trajectory', function (taskCtx) {
-        return state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+        return state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
             var dependsOn, model, structure;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         dependsOn = [params.model, params.coordinates];
@@ -409,3 +413,169 @@ exports.AddTrajectory = mol_state_1.StateAction.build({
         }); }).runInContext(taskCtx);
     });
 });
+exports.LoadTrajectory = mol_state_1.StateAction.build({
+    display: { name: 'Load Trajectory', description: 'Load trajectory of model/topology and coordinates from URL or file.' },
+    from: objects_1.PluginStateObject.Root,
+    params: function (a, ctx) {
+        var options = ctx.dataFormats.options;
+        var modelOptions = options.filter(function (o) { return o[2] === trajectory_1.TrajectoryFormatCategory || o[2] === topology_1.TopologyFormatCategory; });
+        var coordinatesOptions = options.filter(function (o) { return o[2] === coordinates_1.CoordinatesFormatCategory; });
+        var modelExts = [];
+        var coordinatesExts = [];
+        for (var _i = 0, _a = ctx.dataFormats.list; _i < _a.length; _i++) {
+            var provider = _a[_i].provider;
+            if (provider.category === trajectory_1.TrajectoryFormatCategory || provider.category === topology_1.TopologyFormatCategory) {
+                if (provider.binaryExtensions)
+                    modelExts.push.apply(modelExts, provider.binaryExtensions);
+                if (provider.stringExtensions)
+                    modelExts.push.apply(modelExts, provider.stringExtensions);
+            }
+            else if (provider.category === coordinates_1.CoordinatesFormatCategory) {
+                if (provider.binaryExtensions)
+                    coordinatesExts.push.apply(coordinatesExts, provider.binaryExtensions);
+                if (provider.stringExtensions)
+                    coordinatesExts.push.apply(coordinatesExts, provider.stringExtensions);
+            }
+        }
+        return {
+            source: param_definition_1.ParamDefinition.MappedStatic('file', {
+                url: param_definition_1.ParamDefinition.Group({
+                    model: param_definition_1.ParamDefinition.Group({
+                        url: param_definition_1.ParamDefinition.Url(''),
+                        format: param_definition_1.ParamDefinition.Select(modelOptions[0][0], modelOptions),
+                        isBinary: param_definition_1.ParamDefinition.Boolean(false),
+                    }, { isExpanded: true }),
+                    coordinates: param_definition_1.ParamDefinition.Group({
+                        url: param_definition_1.ParamDefinition.Url(''),
+                        format: param_definition_1.ParamDefinition.Select(coordinatesOptions[0][0], coordinatesOptions),
+                    }, { isExpanded: true })
+                }, { isFlat: true }),
+                file: param_definition_1.ParamDefinition.Group({
+                    model: param_definition_1.ParamDefinition.File({ accept: modelExts.map(function (e) { return ".".concat(e); }).join(','), label: 'Model' }),
+                    coordinates: param_definition_1.ParamDefinition.File({ accept: coordinatesExts.map(function (e) { return ".".concat(e); }).join(','), label: 'Coordinates' }),
+                }, { isFlat: true }),
+            }, { options: [['url', 'URL'], ['file', 'File']] })
+        };
+    }
+})(function (_a, ctx) {
+    var params = _a.params, state = _a.state;
+    return mol_task_1.Task.create('Load Trajectory', function (taskCtx) {
+        return state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+            var s, processUrl, processFile, modelParsed, _a, model, coordinates, _b, dependsOn, traj, structure, e_1;
+            return tslib_1.__generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        s = params.source;
+                        if (s.name === 'file' && (s.params.model === null || s.params.coordinates === null)) {
+                            ctx.log.error('No file(s) selected');
+                            return [2 /*return*/];
+                        }
+                        if (s.name === 'url' && (!s.params.model || !s.params.coordinates)) {
+                            ctx.log.error('No URL(s) given');
+                            return [2 /*return*/];
+                        }
+                        processUrl = function (url, format, isBinary) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+                            var data, provider;
+                            return tslib_1.__generator(this, function (_a) {
+                                switch (_a.label) {
+                                    case 0: return [4 /*yield*/, ctx.builders.data.download({ url: url, isBinary: isBinary })];
+                                    case 1:
+                                        data = _a.sent();
+                                        provider = ctx.dataFormats.get(format);
+                                        if (!provider) {
+                                            ctx.log.warn("LoadTrajectory: could not find data provider for '".concat(format, "'"));
+                                            return [2 /*return*/];
+                                        }
+                                        return [2 /*return*/, provider.parse(ctx, data)];
+                                }
+                            });
+                        }); };
+                        processFile = function (file) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+                            var info, isBinary, data, provider;
+                            var _a;
+                            return tslib_1.__generator(this, function (_b) {
+                                switch (_b.label) {
+                                    case 0:
+                                        if (!file)
+                                            throw new Error('No file selected');
+                                        info = (0, file_info_1.getFileInfo)(file.file);
+                                        isBinary = ctx.dataFormats.binaryExtensions.has(info.ext);
+                                        return [4 /*yield*/, ctx.builders.data.readFile({ file: file, isBinary: isBinary })];
+                                    case 1:
+                                        data = (_b.sent()).data;
+                                        provider = ctx.dataFormats.auto(info, (_a = data.cell) === null || _a === void 0 ? void 0 : _a.obj);
+                                        if (!!provider) return [3 /*break*/, 3];
+                                        ctx.log.warn("LoadTrajectory: could not find data provider for '".concat(info.ext, "'"));
+                                        return [4 /*yield*/, ctx.state.data.build().delete(data).commit()];
+                                    case 2:
+                                        _b.sent();
+                                        return [2 /*return*/];
+                                    case 3: return [2 /*return*/, provider.parse(ctx, data)];
+                                }
+                            });
+                        }); };
+                        _c.label = 1;
+                    case 1:
+                        _c.trys.push([1, 16, , 17]);
+                        if (!(s.name === 'url')) return [3 /*break*/, 3];
+                        return [4 /*yield*/, processUrl(s.params.model.url, s.params.model.format, s.params.model.isBinary)];
+                    case 2:
+                        _a = _c.sent();
+                        return [3 /*break*/, 5];
+                    case 3: return [4 /*yield*/, processFile(s.params.model)];
+                    case 4:
+                        _a = _c.sent();
+                        _c.label = 5;
+                    case 5:
+                        modelParsed = _a;
+                        model = void 0;
+                        if (!('trajectory' in modelParsed)) return [3 /*break*/, 7];
+                        return [4 /*yield*/, state.build().to(modelParsed.trajectory)
+                                .apply(model_1.ModelFromTrajectory, { modelIndex: 0 })
+                                .commit()];
+                    case 6:
+                        model = _c.sent();
+                        return [3 /*break*/, 8];
+                    case 7:
+                        model = modelParsed.topology;
+                        _c.label = 8;
+                    case 8:
+                        if (!(s.name === 'url')) return [3 /*break*/, 10];
+                        return [4 /*yield*/, processUrl(s.params.coordinates.url, s.params.coordinates.format, true)];
+                    case 9:
+                        _b = _c.sent();
+                        return [3 /*break*/, 12];
+                    case 10: return [4 /*yield*/, processFile(s.params.coordinates)];
+                    case 11:
+                        _b = _c.sent();
+                        _c.label = 12;
+                    case 12:
+                        coordinates = _b;
+                        dependsOn = [model.ref, coordinates.ref];
+                        traj = state.build().toRoot()
+                            .apply(model_1.TrajectoryFromModelAndCoordinates, {
+                            modelRef: model.ref,
+                            coordinatesRef: coordinates.ref
+                        }, { dependsOn: dependsOn })
+                            .apply(transforms_1.StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
+                        return [4 /*yield*/, state.updateTree(traj).runInContext(taskCtx)];
+                    case 13:
+                        _c.sent();
+                        return [4 /*yield*/, ctx.builders.structure.createStructure(traj.selector)];
+                    case 14:
+                        structure = _c.sent();
+                        return [4 /*yield*/, ctx.builders.structure.representation.applyPreset(structure, 'auto')];
+                    case 15:
+                        _c.sent();
+                        return [3 /*break*/, 17];
+                    case 16:
+                        e_1 = _c.sent();
+                        console.error(e_1);
+                        ctx.log.error("Error loading trajectory");
+                        return [3 /*break*/, 17];
+                    case 17: return [2 /*return*/];
+                }
+            });
+        }); }).runInContext(taskCtx);
+    });
+});

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

@@ -15,6 +15,7 @@ var param_definition_1 = require("../../mol-util/param-definition");
 var objects_1 = require("../objects");
 var assets_1 = require("../../mol-util/assets");
 var transforms_1 = require("../transforms");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 var DownloadDensity = mol_state_1.StateAction.build({
     from: objects_1.PluginStateObject.Root,
     display: { name: 'Download Density', description: 'Load a density from the provided source and create its default visual.' },
@@ -60,10 +61,10 @@ var DownloadDensity = mol_state_1.StateAction.build({
     }
 })(function (_a, plugin) {
     var params = _a.params;
-    return mol_task_1.Task.create('Download Density', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    return mol_task_1.Task.create('Download Density', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var src, downloadParams, provider, data, entryId, volumes;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     src = params.source;
@@ -108,7 +109,7 @@ var DownloadDensity = mol_state_1.StateAction.build({
                                 label: "RCSB PDB X-ray Density Server: ".concat(src.params.provider.id)
                             };
                             break;
-                        default: throw new Error("".concat(src.name, " not supported."));
+                        default: (0, type_helpers_1.assertUnreachable)(src);
                     }
                     return [4 /*yield*/, plugin.builders.data.download(downloadParams)];
                 case 1:
@@ -130,7 +131,7 @@ var DownloadDensity = mol_state_1.StateAction.build({
                             entryId = src.params.provider.id;
                             provider = plugin.dataFormats.get('dscif');
                             break;
-                        default: throw new Error("".concat(src.name, " not supported."));
+                        default: (0, type_helpers_1.assertUnreachable)(src);
                     }
                     if (!provider) {
                         plugin.log.warn('DownloadDensity: Format provider not found.');

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

@@ -7,9 +7,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.StateActions = void 0;
 var tslib_1 = require("tslib");
-var Structure = (0, tslib_1.__importStar)(require("./actions/structure"));
-var Volume = (0, tslib_1.__importStar)(require("./actions/volume"));
-var DataFormat = (0, tslib_1.__importStar)(require("./actions/file"));
+var Structure = tslib_1.__importStar(require("./actions/structure"));
+var Volume = tslib_1.__importStar(require("./actions/volume"));
+var DataFormat = tslib_1.__importStar(require("./actions/file"));
 exports.StateActions = {
     Structure: Structure,
     Volume: Volume,

package/lib/commonjs/mol-plugin-state/animation/built-in/assembly-unwind.js

@@ -76,9 +76,9 @@ exports.AnimateAssemblyUnwind = model_1.PluginStateAnimation.create({
         return update.commit();
     },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, root, anims, update, d, newTime, finished, _i, anims_1, m;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         state = ctx.plugin.state.data;

package/lib/commonjs/mol-plugin-state/animation/built-in/camera-rock.js

@@ -31,9 +31,9 @@ exports.AnimateCameraRock = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var snapshot, phase, angle, position;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 if (t.current === 0) {
                     return [2 /*return*/, { kind: 'next', state: animState }];
                 }
@@ -50,7 +50,7 @@ exports.AnimateCameraRock = model_1.PluginStateAnimation.create({
                 quat_1.Quat.setAxisAngle(_rot, _axis, angle);
                 vec3_1.Vec3.transformQuat(_dir, _dir, _rot);
                 position = vec3_1.Vec3.add((0, vec3_1.Vec3)(), snapshot.target, _dir);
-                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, snapshot), { position: position }), durationMs: 0 });
+                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: tslib_1.__assign(tslib_1.__assign({}, snapshot), { position: position }), durationMs: 0 });
                 if (phase >= 0.99999) {
                     return [2 /*return*/, { kind: 'finished' }];
                 }

package/lib/commonjs/mol-plugin-state/animation/built-in/camera-spin.js

@@ -30,9 +30,9 @@ exports.AnimateCameraSpin = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var snapshot, phase, angle, position;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 if (t.current === 0) {
                     return [2 /*return*/, { kind: 'next', state: animState }];
                 }
@@ -49,7 +49,7 @@ exports.AnimateCameraSpin = model_1.PluginStateAnimation.create({
                 quat_1.Quat.setAxisAngle(_rot, _axis, angle);
                 vec3_1.Vec3.transformQuat(_dir, _dir, _rot);
                 position = vec3_1.Vec3.add((0, vec3_1.Vec3)(), snapshot.target, _dir);
-                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, snapshot), { position: position }), durationMs: 0 });
+                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: tslib_1.__assign(tslib_1.__assign({}, snapshot), { position: position }), durationMs: 0 });
                 if (phase >= 0.99999) {
                     return [2 /*return*/, { kind: 'finished' }];
                 }

package/lib/commonjs/mol-plugin-state/animation/built-in/explode-units.js

@@ -21,9 +21,9 @@ exports.AnimateUnitsExplode = model_1.PluginStateAnimation.create({
     }); },
     initialState: function () { return ({ t: 0 }); },
     setup: function (_, __, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, reprs, update, changed, _i, reprs_1, r, explodes;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 state = plugin.state.data;
                 reprs = state.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D));
                 update = state.build();
@@ -57,9 +57,9 @@ exports.AnimateUnitsExplode = model_1.PluginStateAnimation.create({
         return update.commit();
     },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, anims, update, d, newTime, _i, anims_1, m;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         state = ctx.plugin.state.data;

package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.js

@@ -69,9 +69,9 @@ exports.AnimateModelIndex = model_1.PluginStateAnimation.create({
     },
     initialState: function () { return ({}); },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, models, update, params, palindromeDirections, isEnd, allSingles, _loop_1, _i, models_3, m;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         // limit fps

package/lib/commonjs/mol-plugin-state/animation/built-in/spin-structure.js

@@ -23,9 +23,9 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
     initialState: function () { return ({ t: 0 }); },
     getDuration: function (p) { return ({ kind: 'fixed', durationMs: p.durationInMs }); },
     setup: function (_, __, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, reprs, update, changed, _i, reprs_1, r, spins;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 state = plugin.state.data;
                 reprs = state.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D));
                 update = state.build();
@@ -60,9 +60,9 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, anims, update, d, newTime, _i, anims_1, m;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         state = ctx.plugin.state.data;
@@ -75,7 +75,7 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
                         newTime = (animState.t + d) % 1;
                         for (_i = 0, anims_1 = anims; _i < anims_1.length; _i++) {
                             m = anims_1[_i];
-                            update.to(m).update((0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = m.params) === null || _a === void 0 ? void 0 : _a.values), { t: newTime }));
+                            update.to(m).update(tslib_1.__assign(tslib_1.__assign({}, (_a = m.params) === null || _a === void 0 ? void 0 : _a.values), { t: newTime }));
                         }
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(ctx.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
                     case 1:

package/lib/commonjs/mol-plugin-state/animation/built-in/state-interpolation.js

@@ -23,9 +23,9 @@ exports.AnimateStateInterpolation = model_1.PluginStateAnimation.create({
     },
     initialState: function () { return ({}); },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var snapshots, currentT, srcIndex, tarIndex, _src, _tar, src, tar, state, update, _i, src_1, s, _a, tar_1, t_1, e, f, oldState, newState;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         snapshots = ctx.plugin.managers.snapshot.state.entries;

package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js

@@ -11,8 +11,8 @@ var model_1 = require("../model");
 function setPartialSnapshot(plugin, entry, first) {
     var _a;
     if (first === void 0) { first = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_b) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     if (!entry.snapshot.data) return [3 /*break*/, 2];
@@ -68,9 +68,9 @@ exports.AnimateStateSnapshots = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var ctime, i, _i, _b, s;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 if (t.current >= animState.totalDuration) {
                     return [2 /*return*/, { kind: 'finished' }];
                 }
@@ -89,7 +89,7 @@ exports.AnimateStateSnapshots = model_1.PluginStateAnimation.create({
                     return [2 /*return*/, { kind: 'skip' }];
                 }
                 setPartialSnapshot(ctx.plugin, animState.snapshots[i]);
-                return [2 /*return*/, { kind: 'next', state: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, animState), { currentIndex: i }) }];
+                return [2 /*return*/, { kind: 'next', state: tslib_1.__assign(tslib_1.__assign({}, animState), { currentIndex: i }) }];
             });
         });
     }

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

@@ -34,9 +34,9 @@ var DataBuilder = /** @class */ (function () {
     };
     DataBuilder.prototype.readFile = function (params, options) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var data, fileInfo;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, this.dataState.build().toRoot().apply(data_1.ReadFile, params, options).commit({ revertOnError: true })];
                     case 1: