molstar 3.3.1 → 3.6.0

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

@@ -63,9 +63,9 @@ var PluginCommandManager = /** @class */ (function () {
         this.subs.clear();
     };
     PluginCommandManager.prototype.resolve = function (instance) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var actions, _i, actions_1, a, e_1;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         actions = this.subs.get(instance.cmd.id);

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

@@ -331,6 +331,7 @@ export declare const PluginCommands: {
                         flipSided: any;
                         flatShaded: any;
                         xrayShaded: any;
+                        allowTransparentBackfaces: any;
                         bumpFrequency: any;
                         bumpAmplitude: any;
                         quality: any;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -143,6 +143,7 @@ export declare class PluginContext {
     readonly customModelProperties: CustomProperty.Registry<Model>;
     readonly customStructureProperties: CustomProperty.Registry<Structure>;
     readonly customStructureControls: Map<string, new () => any>;
+    readonly customImportControls: Map<string, new () => any>;
     readonly genericRepresentationControls: Map<string, (selection: StructureHierarchyManager['selection']) => [StructureHierarchyRef[], string]>;
     /**
      * Used to store application specific custom state which is then available

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,7 +8,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PluginContext = void 0;
 var tslib_1 = require("tslib");
-var immer_1 = (0, tslib_1.__importStar)(require("immer"));
+var immer_1 = tslib_1.__importStar(require("immer"));
 var immutable_1 = require("immutable");
 var rxjs_1 = require("rxjs");
 var operators_1 = require("rxjs/operators");
@@ -159,6 +159,7 @@ var PluginContext = /** @class */ (function () {
         this.customModelProperties = new custom_property_1.CustomProperty.Registry();
         this.customStructureProperties = new custom_property_1.CustomProperty.Registry();
         this.customStructureControls = new Map();
+        this.customImportControls = new Map();
         this.genericRepresentationControls = new Map();
         /**
          * Used to store application specific custom state which is then available
@@ -294,8 +295,8 @@ var PluginContext = /** @class */ (function () {
         this.state.dispose();
         this.managers.task.dispose();
         this.helpers.substructureParent.dispose();
-        (0, object_1.objectForEach)(this.managers, function (m) { var _a, _b; return (_b = (_a = m) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a); });
-        (0, object_1.objectForEach)(this.managers.structure, function (m) { var _a, _b; return (_b = (_a = m) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a); });
+        (0, object_1.objectForEach)(this.managers, function (m) { var _a; return (_a = m === null || m === void 0 ? void 0 : m.dispose) === null || _a === void 0 ? void 0 : _a.call(m); });
+        (0, object_1.objectForEach)(this.managers.structure, function (m) { var _a; return (_a = m === null || m === void 0 ? void 0 : m.dispose) === null || _a === void 0 ? void 0 : _a.call(m); });
         this.disposed = true;
     };
     PluginContext.prototype.initBehaviorEvents = function () {
@@ -346,9 +347,9 @@ var PluginContext = /** @class */ (function () {
         this.subs.push((0, rxjs_1.merge)(this.state.data.events.log, this.state.behaviors.events.log).subscribe(function (e) { return _this.events.log.next(e); }));
     };
     PluginContext.prototype.initBehaviors = function () {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var tree, _i, _a, cat, _b, _c, b, cat, _d, _e, b, cat;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
                         tree = this.state.behaviors.build();
@@ -408,9 +409,9 @@ var PluginContext = /** @class */ (function () {
         }
     };
     PluginContext.prototype.init = function () {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         this.subs.push(this.events.log.subscribe(function (e) { return _this.log.entries = _this.log.entries.push(e); }));

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

@@ -32,9 +32,9 @@ exports.PluginLayoutStateParams = {
     controlsDisplay: param_definition_1.ParamDefinition.Value('outside', { isHidden: true })
 };
 var PluginLayout = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(PluginLayout, _super);
+    tslib_1.__extends(PluginLayout, _super);
     function PluginLayout(context) {
-        var _this = _super.call(this, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.PluginLayoutStateParams)), (context.spec.layout && context.spec.layout.initial))) || this;
+        var _this = _super.call(this, tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.PluginLayoutStateParams)), (context.spec.layout && context.spec.layout.initial))) || this;
         _this.context = context;
         _this.events = {
             updated: _this.ev()

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

@@ -36,10 +36,10 @@ exports.PluginSpec = PluginSpec;
 var DefaultPluginSpec = function () { return ({
     actions: [
         PluginSpec.Action(actions_1.StateActions.Structure.DownloadStructure),
-        PluginSpec.Action(actions_1.StateActions.Structure.AddTrajectory),
         PluginSpec.Action(actions_1.StateActions.Volume.DownloadDensity),
         PluginSpec.Action(actions_1.StateActions.DataFormat.DownloadFile),
         PluginSpec.Action(actions_1.StateActions.DataFormat.OpenFiles),
+        PluginSpec.Action(actions_1.StateActions.Structure.LoadTrajectory),
         PluginSpec.Action(actions_1.StateActions.Structure.EnableModelCustomProps),
         PluginSpec.Action(actions_1.StateActions.Structure.EnableStructureCustomProps),
         // Volume streaming

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

@@ -19,7 +19,7 @@ var rxjs_1 = require("rxjs");
 var component_1 = require("../mol-plugin-state/component");
 var config_1 = require("./config");
 var PluginState = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(PluginState, _super);
+    tslib_1.__extends(PluginState, _super);
     function PluginState(plugin) {
         var _this = _super.call(this) || this;
         _this.plugin = plugin;
@@ -39,7 +39,7 @@ var PluginState = /** @class */ (function (_super) {
         };
         _this.snapshotParams = _this.ev.behavior(PluginState.DefaultSnapshotParams);
         _this.setSnapshotParams = function (params) {
-            _this.snapshotParams.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, PluginState.DefaultSnapshotParams), params));
+            _this.snapshotParams.next(tslib_1.__assign(tslib_1.__assign({}, PluginState.DefaultSnapshotParams), params));
         };
         return _this;
     }
@@ -50,7 +50,7 @@ var PluginState = /** @class */ (function (_super) {
     });
     PluginState.prototype.getSnapshot = function (params) {
         var _a, _b;
-        var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.snapshotParams.value), params);
+        var p = tslib_1.__assign(tslib_1.__assign({}, this.snapshotParams.value), params);
         return {
             id: mol_util_1.UUID.create22(),
             data: p.data ? this.data.getSnapshot() : void 0,
@@ -73,9 +73,9 @@ var PluginState = /** @class */ (function (_super) {
     };
     PluginState.prototype.setSnapshot = function (snapshot) {
         var _a, _b, _c;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var settings;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0: return [4 /*yield*/, this.animation.stop()];
                     case 1:

package/lib/commonjs/mol-plugin/util/task-manager.js

@@ -55,9 +55,9 @@ var TaskManager = /** @class */ (function () {
         };
     };
     TaskManager.prototype.run = function (task, params) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var id, ctx, ret;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         id = this.id++;
@@ -113,9 +113,9 @@ exports.TaskManager = TaskManager;
     }
     function testTask(N) {
         var _this = this;
-        return mol_task_1.Task.create('Test', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Test', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var i;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         i = 0;

package/lib/commonjs/mol-plugin/util/toast.js

@@ -13,7 +13,7 @@ var component_1 = require("../../mol-plugin-state/component");
 var immutable_1 = require("immutable");
 var commands_1 = require("../commands");
 var PluginToastManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(PluginToastManager, _super);
+    tslib_1.__extends(PluginToastManager, _super);
     function PluginToastManager(plugin) {
         var _this = _super.call(this, { entries: (0, immutable_1.OrderedMap)() }) || this;
         _this.events = {

package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts

@@ -37,6 +37,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
+            allowTransparentBackfaces: boolean;
             bumpFrequency: number;
             bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
@@ -69,6 +70,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 flipSided: boolean;
                 flatShaded: boolean;
                 xrayShaded: boolean;
+                allowTransparentBackfaces: boolean;
                 bumpFrequency: number;
                 bumpAmplitude: number;
                 quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
@@ -109,6 +111,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
+            allowTransparentBackfaces: boolean;
             bumpFrequency: number;
             bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/commonjs/mol-plugin/util/viewport-screenshot.js

@@ -20,7 +20,7 @@ var download_1 = require("../../mol-util/download");
 var param_definition_1 = require("../../mol-util/param-definition");
 var set_1 = require("../../mol-util/set");
 var ViewportScreenshotHelper = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(ViewportScreenshotHelper, _super);
+    tslib_1.__extends(ViewportScreenshotHelper, _super);
     function ViewportScreenshotHelper(plugin) {
         var _this = _super.call(this) || this;
         _this.plugin = plugin;
@@ -135,10 +135,10 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
                 mode: mutlisample ? 'on' : 'off',
                 sampleLevel: colorBufferFloat && textureFloat ? 4 : 2
             },
-            postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
-                    ? { name: 'on', params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
+            postprocessing: tslib_1.__assign(tslib_1.__assign({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
+                    ? { name: 'on', params: tslib_1.__assign(tslib_1.__assign({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
                     : aoProps }),
-            marking: (0, tslib_1.__assign)({}, c.props.marking)
+            marking: tslib_1.__assign({}, c.props.marking)
         });
     };
     Object.defineProperty(ViewportScreenshotHelper.prototype, "previewPass", {
@@ -157,10 +157,10 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
                     cameraHelper: { axes: this.values.axes },
                     transparentBackground: this.values.transparent,
                     // TODO: optimize because this creates a copy of a large object!
-                    postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
-                            ? { name: 'on', params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
+                    postprocessing: tslib_1.__assign(tslib_1.__assign({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
+                            ? { name: 'on', params: tslib_1.__assign(tslib_1.__assign({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
                             : aoProps }),
-                    marking: (0, tslib_1.__assign)({}, c.props.marking)
+                    marking: tslib_1.__assign({}, c.props.marking)
                 });
                 return this._imagePass;
             }
@@ -182,11 +182,11 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
     };
     ViewportScreenshotHelper.prototype.toggleAutocrop = function () {
         if (this.cropParams.auto) {
-            this.behaviors.cropParams.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.cropParams), { auto: false }));
+            this.behaviors.cropParams.next(tslib_1.__assign(tslib_1.__assign({}, this.cropParams), { auto: false }));
             this.resetCrop();
         }
         else {
-            this.behaviors.cropParams.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.cropParams), { auto: true }));
+            this.behaviors.cropParams.next(tslib_1.__assign(tslib_1.__assign({}, this.cropParams), { auto: true }));
         }
     };
     Object.defineProperty(ViewportScreenshotHelper.prototype, "isFullFrame", {
@@ -304,9 +304,9 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
         return { width: width, height: height, viewport: viewport };
     };
     ViewportScreenshotHelper.prototype.draw = function (ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var _a, width, height, viewport, imageData, canvas, canvasCtx;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         _a = this.getSizeAndViewport(), width = _a.width, height = _a.height, viewport = _a.viewport;
@@ -338,9 +338,9 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
             this.plugin.log.error('clipboard.write not supported!');
             return;
         }
-        return mol_task_1.Task.create('Copy Image', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Copy Image', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var blob, item;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, this.draw(ctx)];
                     case 1:
@@ -363,8 +363,8 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
     };
     ViewportScreenshotHelper.prototype.getImageDataUri = function () {
         var _this = this;
-        return this.plugin.runTask(mol_task_1.Task.create('Generate Image', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        return this.plugin.runTask(mol_task_1.Task.create('Generate Image', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, this.draw(ctx)];
                     case 1:
@@ -385,9 +385,9 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
     };
     ViewportScreenshotHelper.prototype.downloadTask = function (filename) {
         var _this = this;
-        return mol_task_1.Task.create('Download Image', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Download Image', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var blob;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, this.draw(ctx)];
                     case 1:

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,6 +14,41 @@ var file_info_1 = require("../../mol-util/file-info");
 var param_definition_1 = require("../../mol-util/param-definition");
 var zip_1 = require("../../mol-util/zip/zip");
 var objects_1 = require("../objects");
+function processFile(file, plugin, format, visuals) {
+    var _a, _b;
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var info, isBinary, data, provider, parsed;
+        return tslib_1.__generator(this, function (_c) {
+            switch (_c.label) {
+                case 0:
+                    info = (0, file_info_1.getFileInfo)(file.file);
+                    isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
+                    return [4 /*yield*/, plugin.builders.data.readFile({ file: file, isBinary: isBinary })];
+                case 1:
+                    data = (_c.sent()).data;
+                    provider = format === 'auto'
+                        ? plugin.dataFormats.auto(info, (_a = data.cell) === null || _a === void 0 ? void 0 : _a.obj)
+                        : plugin.dataFormats.get(format);
+                    if (!!provider) return [3 /*break*/, 3];
+                    plugin.log.warn("OpenFiles: could not find data provider for '".concat(info.ext, "'"));
+                    return [4 /*yield*/, plugin.state.data.build().delete(data).commit()];
+                case 2:
+                    _c.sent();
+                    return [2 /*return*/];
+                case 3: return [4 /*yield*/, provider.parse(plugin, data)];
+                case 4:
+                    parsed = _c.sent();
+                    if (!visuals) return [3 /*break*/, 6];
+                    return [4 /*yield*/, ((_b = provider.visuals) === null || _b === void 0 ? void 0 : _b.call(provider, plugin, parsed))];
+                case 5:
+                    _c.sent();
+                    _c.label = 6;
+                case 6: return [2 /*return*/];
+            }
+        });
+    });
+}
+;
 exports.OpenFiles = mol_state_1.StateAction.build({
     display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
     from: objects_1.PluginStateObject.Root,
@@ -30,50 +65,20 @@ exports.OpenFiles = mol_state_1.StateAction.build({
     }
 })(function (_a, plugin) {
     var params = _a.params, state = _a.state;
-    return mol_task_1.Task.create('Open Files', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Open Files', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     plugin.behaviors.layout.leftPanelTabName.next('data');
-                    return [4 /*yield*/, state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-                            var processFile, _i, _a, file, zippedFiles, _b, _c, _d, _e, _f, fn, filedata, asset, e_1;
-                            return (0, tslib_1.__generator)(this, function (_g) {
+                    return [4 /*yield*/, state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+                            var _i, _a, file, zippedFiles, _b, _c, _d, _e, _f, fn, filedata, asset, format, e_1;
+                            return tslib_1.__generator(this, function (_g) {
                                 switch (_g.label) {
                                     case 0:
                                         if (params.files === null) {
                                             plugin.log.error('No file(s) selected');
                                             return [2 /*return*/];
                                         }
-                                        processFile = function (file) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-                                            var info, isBinary, data, provider, parsed;
-                                            var _a, _b;
-                                            return (0, tslib_1.__generator)(this, function (_c) {
-                                                switch (_c.label) {
-                                                    case 0:
-                                                        info = (0, file_info_1.getFileInfo)(file.file);
-                                                        isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
-                                                        return [4 /*yield*/, plugin.builders.data.readFile({ file: file, isBinary: isBinary })];
-                                                    case 1:
-                                                        data = (_c.sent()).data;
-                                                        provider = params.format.name === 'auto'
-                                                            ? plugin.dataFormats.auto(info, (_a = data.cell) === null || _a === void 0 ? void 0 : _a.obj)
-                                                            : plugin.dataFormats.get(params.format.params);
-                                                        if (!provider) {
-                                                            plugin.log.warn("OpenFiles: could not find data provider for '".concat(info.name, ".").concat(info.ext, "'"));
-                                                            return [2 /*return*/];
-                                                        }
-                                                        return [4 /*yield*/, provider.parse(plugin, data)];
-                                                    case 2:
-                                                        parsed = _c.sent();
-                                                        if (!params.visuals) return [3 /*break*/, 4];
-                                                        return [4 /*yield*/, ((_b = provider.visuals) === null || _b === void 0 ? void 0 : _b.call(provider, plugin, parsed))];
-                                                    case 3:
-                                                        _c.sent();
-                                                        _c.label = 4;
-                                                    case 4: return [2 /*return*/];
-                                                }
-                                            });
-                                        }); };
                                         _i = 0, _a = params.files;
                                         _g.label = 1;
                                     case 1:
@@ -94,8 +99,10 @@ exports.OpenFiles = mol_state_1.StateAction.build({
                                     case 5:
                                         if (!(_d < _e.length)) return [3 /*break*/, 8];
                                         _f = _e[_d], fn = _f[0], filedata = _f[1];
+                                        if (!(filedata instanceof Uint8Array) || filedata.length === 0)
+                                            return [3 /*break*/, 7];
                                         asset = assets_1.Asset.File(new File([filedata], fn));
-                                        return [4 /*yield*/, processFile(asset)];
+                                        return [4 /*yield*/, processFile(asset, plugin, 'auto', params.visuals)];
                                     case 6:
                                         _g.sent();
                                         _g.label = 7;
@@ -103,7 +110,9 @@ exports.OpenFiles = mol_state_1.StateAction.build({
                                         _d++;
                                         return [3 /*break*/, 5];
                                     case 8: return [3 /*break*/, 11];
-                                    case 9: return [4 /*yield*/, processFile(file)];
+                                    case 9:
+                                        format = params.format.name === 'auto' ? 'auto' : params.format.params;
+                                        return [4 /*yield*/, processFile(file, plugin, format, params.visuals)];
                                     case 10:
                                         _g.sent();
                                         _g.label = 11;
@@ -131,7 +140,7 @@ exports.DownloadFile = mol_state_1.StateAction.build({
     display: { name: 'Download File', description: 'Load one or more file from an URL' },
     from: objects_1.PluginStateObject.Root,
     params: function (a, ctx) {
-        var options = ctx.dataFormats.options;
+        var options = tslib_1.__spreadArray(tslib_1.__spreadArray([], ctx.dataFormats.options, true), [['zip', 'Zip']], false);
         return {
             url: param_definition_1.ParamDefinition.Url(''),
             format: param_definition_1.ParamDefinition.Select(options[0][0], options),
@@ -141,41 +150,65 @@ exports.DownloadFile = mol_state_1.StateAction.build({
     }
 })(function (_a, plugin) {
     var params = _a.params, state = _a.state;
-    return mol_task_1.Task.create('Open Files', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Open Files', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     plugin.behaviors.layout.leftPanelTabName.next('data');
-                    return [4 /*yield*/, state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-                            var provider, data, parsed, e_2;
-                            var _a;
-                            return (0, tslib_1.__generator)(this, function (_b) {
-                                switch (_b.label) {
+                    return [4 /*yield*/, state.transaction(function () { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+                            var data, zippedFiles, _i, _a, _b, fn, filedata, asset, provider, data, parsed, e_2;
+                            var _c, _d;
+                            return tslib_1.__generator(this, function (_e) {
+                                switch (_e.label) {
                                     case 0:
-                                        _b.trys.push([0, 5, , 6]);
+                                        _e.trys.push([0, 12, , 13]);
+                                        if (!(params.format === 'zip')) return [3 /*break*/, 7];
+                                        return [4 /*yield*/, plugin.builders.data.download({ url: params.url, isBinary: true })];
+                                    case 1:
+                                        data = _e.sent();
+                                        return [4 /*yield*/, (0, zip_1.unzip)(taskCtx, ((_c = data.obj) === null || _c === void 0 ? void 0 : _c.data).buffer)];
+                                    case 2:
+                                        zippedFiles = _e.sent();
+                                        _i = 0, _a = Object.entries(zippedFiles);
+                                        _e.label = 3;
+                                    case 3:
+                                        if (!(_i < _a.length)) return [3 /*break*/, 6];
+                                        _b = _a[_i], fn = _b[0], filedata = _b[1];
+                                        if (!(filedata instanceof Uint8Array) || filedata.length === 0)
+                                            return [3 /*break*/, 5];
+                                        asset = assets_1.Asset.File(new File([filedata], fn));
+                                        return [4 /*yield*/, processFile(asset, plugin, 'auto', params.visuals)];
+                                    case 4:
+                                        _e.sent();
+                                        _e.label = 5;
+                                    case 5:
+                                        _i++;
+                                        return [3 /*break*/, 3];
+                                    case 6: return [3 /*break*/, 11];
+                                    case 7:
                                         provider = plugin.dataFormats.get(params.format);
                                         if (!provider) {
                                             plugin.log.warn("DownloadFile: could not find data provider for '".concat(params.format, "'"));
                                             return [2 /*return*/];
                                         }
                                         return [4 /*yield*/, plugin.builders.data.download({ url: params.url, isBinary: params.isBinary })];
-                                    case 1:
-                                        data = _b.sent();
+                                    case 8:
+                                        data = _e.sent();
                                         return [4 /*yield*/, provider.parse(plugin, data)];
-                                    case 2:
-                                        parsed = _b.sent();
-                                        if (!params.visuals) return [3 /*break*/, 4];
-                                        return [4 /*yield*/, ((_a = provider.visuals) === null || _a === void 0 ? void 0 : _a.call(provider, plugin, parsed))];
-                                    case 3:
-                                        _b.sent();
-                                        _b.label = 4;
-                                    case 4: return [3 /*break*/, 6];
-                                    case 5:
-                                        e_2 = _b.sent();
+                                    case 9:
+                                        parsed = _e.sent();
+                                        if (!params.visuals) return [3 /*break*/, 11];
+                                        return [4 /*yield*/, ((_d = provider.visuals) === null || _d === void 0 ? void 0 : _d.call(provider, plugin, parsed))];
+                                    case 10:
+                                        _e.sent();
+                                        _e.label = 11;
+                                    case 11: return [3 /*break*/, 13];
+                                    case 12:
+                                        e_2 = _e.sent();
                                         console.error(e_2);
                                         plugin.log.error("Error downloading '".concat(typeof params.url === 'string' ? params.url : params.url.url, "'"));
-                                        return [3 /*break*/, 6];
-                                    case 6: return [2 /*return*/];
+                                        return [3 /*break*/, 13];
+                                    case 13: return [2 /*return*/];
                                 }
                             });
                         }); }).runInContext(taskCtx)];

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -9,7 +9,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject } from '../objects';
 export declare const PdbDownloadProvider: {
     rcsb: PD.Group<PD.Normalize<{
-        encoding: "bcif" | "cif";
+        encoding: "cif" | "bcif";
     }>>;
     pdbe: PD.Group<PD.Normalize<{
         variant: "updated" | "updated-bcif" | "updtaed-bcif" | "archival";
@@ -26,6 +26,12 @@ declare const DownloadStructure: StateAction<PluginStateObject.Root, void, PD.No
         isBinary: any;
         options: any;
     }>, "url"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
+    }>, "modelarchive"> | PD.NamedParams<PD.Normalize<{
         provider: any;
         options: any;
     }>, "pdb"> | PD.NamedParams<PD.Normalize<{
@@ -37,12 +43,6 @@ declare const DownloadStructure: StateAction<PluginStateObject.Root, void, PD.No
     }>, "swissmodel"> | PD.NamedParams<PD.Normalize<{
         id: any;
         options: any;
-    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
-        id: any;
-        options: any;
-    }>, "modelarchive"> | PD.NamedParams<PD.Normalize<{
-        id: any;
-        options: any;
     }>, "pubchem">;
 }>>;
 export declare const UpdateTrajectory: StateAction<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, void, PD.Normalize<{
@@ -65,3 +65,12 @@ export declare const AddTrajectory: StateAction<PluginStateObject.Root, void, PD
     model: string;
     coordinates: string;
 }>>;
+export declare const LoadTrajectory: StateAction<PluginStateObject.Root, void, PD.Normalize<{
+    source: PD.NamedParams<PD.Normalize<{
+        model: any;
+        coordinates: any;
+    }>, "url"> | PD.NamedParams<PD.Normalize<{
+        model: any;
+        coordinates: any;
+    }>, "file">;
+}>>;