molstar 3.2.0 → 3.4.0

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

@@ -16,7 +16,7 @@ var data_source_1 = require("../../mol-util/data-source");
 var object_1 = require("../../mol-util/object");
 var version_1 = require("../../mol-plugin/version");
 var PluginStateSnapshotManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(PluginStateSnapshotManager, _super);
+    tslib_1.__extends(PluginStateSnapshotManager, _super);
     function PluginStateSnapshotManager(plugin) {
         var _this = _super.call(this, {
             current: void 0,
@@ -30,9 +30,9 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
             changed: _this.ev()
         };
         _this.timeoutHandle = void 0;
-        _this.next = function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        _this.next = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var next, snapshot, delay;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         this.timeoutHandle = void 0;
@@ -146,9 +146,9 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
         return this.state.entries.get(idx).snapshot.id;
     };
     PluginStateSnapshotManager.prototype.setStateSnapshot = function (snapshot) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var entries, _i, _a, e, current, entry, next;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         if (snapshot.version !== version_1.PLUGIN_VERSION) {
@@ -216,9 +216,9 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
         };
     };
     PluginStateSnapshotManager.prototype.serialize = function (options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var json, state, zipDataObj, assets, _i, _a, _b, asset, file, _c, _d, _e, index, data, zipFile;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
                         json = JSON.stringify(this.getStateSnapshot({ params: options === null || options === void 0 ? void 0 : options.params }), null, 2);
@@ -263,9 +263,9 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
         });
     };
     PluginStateSnapshotManager.prototype.open = function (file) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var fn, data, snapshot, data, assets_1, stateFile, stateData, file_1, json, _a, _b, _i, json_1, _c, id, asset, snapshot, e_1;
-            return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var fn, data, snapshot, data, assetData_1, stateFile, stateData, file_1, json, _a, _b, _i, json_1, _c, id, asset, snapshot, e_1;
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0:
                         _d.trys.push([0, 8, , 9]);
@@ -288,12 +288,12 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
                     case 2: return [4 /*yield*/, this.plugin.runTask((0, data_source_1.readFromFile)(file, 'zip'))];
                     case 3:
                         data = _d.sent();
-                        assets_1 = Object.create(null);
+                        assetData_1 = Object.create(null);
                         (0, object_1.objectForEach)(data, function (v, k) {
                             if (k === 'state.json' || k === 'assets.json')
                                 return;
                             var name = k.substring(k.indexOf('/') + 1);
-                            assets_1[name] = new File([v], name);
+                            assetData_1[name] = v;
                         });
                         stateFile = new File([data['state.json']], 'state.json');
                         return [4 /*yield*/, this.plugin.runTask((0, data_source_1.readFromFile)(stateFile, 'string'))];
@@ -307,7 +307,7 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
                         json = _b.apply(_a, [_d.sent()]);
                         for (_i = 0, json_1 = json; _i < json_1.length; _i++) {
                             _c = json_1[_i], id = _c[0], asset = _c[1];
-                            this.plugin.managers.asset.set(asset, assets_1[id]);
+                            this.plugin.managers.asset.set(asset, new File([assetData_1[id]], asset.name));
                         }
                         _d.label = 6;
                     case 6:
@@ -364,7 +364,7 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
 exports.PluginStateSnapshotManager = PluginStateSnapshotManager;
 (function (PluginStateSnapshotManager) {
     function Entry(snapshot, params) {
-        return (0, tslib_1.__assign)({ timestamp: +new Date(), snapshot: snapshot }, params);
+        return tslib_1.__assign({ timestamp: +new Date(), snapshot: snapshot }, params);
     }
     PluginStateSnapshotManager.Entry = Entry;
     function isStateSnapshot(x) {
@@ -374,4 +374,3 @@ exports.PluginStateSnapshotManager = PluginStateSnapshotManager;
     PluginStateSnapshotManager.isStateSnapshot = isStateSnapshot;
 })(PluginStateSnapshotManager || (PluginStateSnapshotManager = {}));
 exports.PluginStateSnapshotManager = PluginStateSnapshotManager;
-//# sourceMappingURL=snapshots.js.map

package/lib/commonjs/mol-plugin-state/manager/structure/component.js

@@ -31,7 +31,7 @@ var structure_substance_1 = require("../../helpers/structure-substance");
 var material_1 = require("../../../mol-util/material");
 var clip_1 = require("../../../mol-util/clip");
 var StructureComponentManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StructureComponentManager, _super);
+    tslib_1.__extends(StructureComponentManager, _super);
     function StructureComponentManager(plugin) {
         var _this = _super.call(this, { options: param_definition_1.ParamDefinition.getDefaultValues(StructureComponentManager.OptionsParams) }) || this;
         _this.plugin = plugin;
@@ -55,10 +55,10 @@ var StructureComponentManager = /** @class */ (function (_super) {
         configurable: true
     });
     StructureComponentManager.prototype.setOptions = function (options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var interactionChanged, update, _i, _a, s, _b, _c, c;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 interactionChanged = options.interactions !== this.state.options.interactions;
                 this.updateState({ options: options });
                 this.events.optionsUpdated.next(void 0);
@@ -70,8 +70,8 @@ var StructureComponentManager = /** @class */ (function (_super) {
                         this.updateReprParams(update, c);
                     }
                 }
-                return [2 /*return*/, this.plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                return [2 /*return*/, this.plugin.dataTransaction(function () { 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*/, update.commit()];
                                 case 1:
@@ -117,10 +117,10 @@ var StructureComponentManager = /** @class */ (function (_super) {
     };
     StructureComponentManager.prototype.updateInterationProps = function () {
         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 _i, _d, s, interactionParams, oldParams, pd, params;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_e) {
+            return tslib_1.__generator(this, function (_e) {
                 switch (_e.label) {
                     case 0:
                         _i = 0, _d = this.currentStructures;
@@ -161,9 +161,9 @@ var StructureComponentManager = /** @class */ (function (_super) {
     };
     StructureComponentManager.prototype.applyPreset = function (structures, provider, params) {
         var _this = this;
-        return this.plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return this.plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _i, structures_1, s, preset;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         _i = 0, structures_1 = structures;
@@ -251,9 +251,9 @@ var StructureComponentManager = /** @class */ (function (_super) {
     };
     StructureComponentManager.prototype.modifyByCurrentSelection = function (components, action) {
         var _this = this;
-        return this.plugin.runTask(mol_task_1.Task.create('Modify Component', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return this.plugin.runTask(mol_task_1.Task.create('Modify Component', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var b, _i, components_2, c, selection;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         b = this.dataState.build();
@@ -385,9 +385,9 @@ var StructureComponentManager = /** @class */ (function (_super) {
         var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, ignoreLight = _a.ignoreLight, material = _a.materialStyle, clip = _a.clipObjects;
         var ignoreHydrogens = !showHydrogens;
         var typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, ignoreLight: ignoreLight, material: material, clip: clip };
-        return this.plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return this.plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _i, components_9, component;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         _i = 0, components_9 = components;
@@ -414,10 +414,10 @@ var StructureComponentManager = /** @class */ (function (_super) {
         var _this = this;
         if (structure.components.length === 0)
             return;
-        return this.plugin.runTask(mol_task_1.Task.create('Find Component', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return this.plugin.runTask(mol_task_1.Task.create('Find Component', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var data, sel, _a, _b, _i, _c, c, comp;
             var _d, _e;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
                         data = (_d = structure.cell.obj) === null || _d === void 0 ? void 0 : _d.data;
@@ -441,12 +441,12 @@ var StructureComponentManager = /** @class */ (function (_super) {
         }); }));
     };
     StructureComponentManager.prototype.add = function (params, structures) {
-        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 [2 /*return*/, this.plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
+                return [2 /*return*/, this.plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var xs, _a, showHydrogens, quality, ignoreLight, material, clip, ignoreHydrogens, typeParams, componentKey, _i, xs_1, s, component;
-                        return (0, tslib_1.__generator)(this, function (_b) {
+                        return tslib_1.__generator(this, function (_b) {
                             switch (_b.label) {
                                 case 0:
                                     xs = structures || this.currentStructures;
@@ -496,19 +496,19 @@ var StructureComponentManager = /** @class */ (function (_super) {
         });
     };
     StructureComponentManager.prototype.applyTheme = function (params, structures) {
-        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 [2 /*return*/, this.plugin.dataTransaction(function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
+                return [2 /*return*/, this.plugin.dataTransaction(function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var xs, getLoci, _i, xs_2, s, p, p, p, p;
                         var _this = this;
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                        return tslib_1.__generator(this, function (_a) {
                             switch (_a.label) {
                                 case 0:
                                     xs = structures || this.currentStructures;
                                     if (xs.length === 0)
                                         return [2 /*return*/];
-                                    getLoci = function (s) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () { var _a, _b; return (0, tslib_1.__generator)(this, function (_c) {
+                                    getLoci = function (s) { return tslib_1.__awaiter(_this, void 0, void 0, function () { var _a, _b; return tslib_1.__generator(this, function (_c) {
                                         switch (_c.label) {
                                             case 0:
                                                 _b = (_a = structure_1.StructureSelection).toLociWithSourceUnits;
@@ -637,7 +637,7 @@ exports.StructureComponentManager = StructureComponentManager;
     };
     function getAddParams(plugin, params) {
         var options = plugin.query.structure.registry.options;
-        params = (0, tslib_1.__assign)({ pivot: plugin.managers.structure.component.pivotStructure, allowNone: true, hideSelection: false, checkExisting: false }, params);
+        params = tslib_1.__assign({ pivot: plugin.managers.structure.component.pivotStructure, allowNone: true, hideSelection: false, checkExisting: false }, params);
         return {
             selection: param_definition_1.ParamDefinition.Select(options[1][0], options, { isHidden: params === null || params === void 0 ? void 0 : params.hideSelection }),
             representation: getRepresentationTypesSelect(plugin, params === null || params === void 0 ? void 0 : params.pivot, (params === null || params === void 0 ? void 0 : params.allowNone) ? [['none', '< Create Later >']] : []),
@@ -680,9 +680,8 @@ exports.StructureComponentManager = StructureComponentManager;
     }
     StructureComponentManager.getRepresentationTypes = getRepresentationTypes;
     function getRepresentationTypesSelect(plugin, pivot, custom, label) {
-        var types = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], custom, true), getRepresentationTypes(plugin, pivot), true);
+        var types = tslib_1.__spreadArray(tslib_1.__spreadArray([], custom, true), getRepresentationTypes(plugin, pivot), true);
         return param_definition_1.ParamDefinition.Select(types[0][0], types, { label: label });
     }
 })(StructureComponentManager || (StructureComponentManager = {}));
 exports.StructureComponentManager = StructureComponentManager;
-//# sourceMappingURL=component.js.map

package/lib/commonjs/mol-plugin-state/manager/structure/focus.js

@@ -19,7 +19,7 @@ var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var geometry_1 = require("../../../mol-math/geometry");
 var HISTORY_CAPACITY = 8;
 var StructureFocusManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StructureFocusManager, _super);
+    tslib_1.__extends(StructureFocusManager, _super);
     function StructureFocusManager(plugin) {
         var _this = _super.call(this, { history: [] }) || this;
         _this.plugin = plugin;
@@ -65,7 +65,7 @@ var StructureFocusManager = /** @class */ (function (_super) {
                 var structure = obj.data;
                 if (current && current.loci.structure === oldData) {
                     var loci = structure_1.StructureElement.Loci.remap(current.loci, structure);
-                    _this.state.current = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, current), { loci: loci });
+                    _this.state.current = tslib_1.__assign(tslib_1.__assign({}, current), { loci: loci });
                     _this.behaviors.current.next(_this.state.current);
                     loci_1.Loci.getBoundingSphere(loci, sphere);
                     var camera = (_b = _this.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.camera;
@@ -173,4 +173,3 @@ var StructureFocusManager = /** @class */ (function (_super) {
     return StructureFocusManager;
 }(component_1.StatefulPluginComponent));
 exports.StructureFocusManager = StructureFocusManager;
-//# sourceMappingURL=focus.js.map

package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js

@@ -50,7 +50,7 @@ function StructureVolumeStreamingRef(cell, structure) {
 function componentKey(cell) {
     if (!cell.transform.tags)
         return cell.transform.ref;
-    return (0, tslib_1.__spreadArray)([], cell.transform.tags, true).sort().join();
+    return tslib_1.__spreadArray([], cell.transform.tags, true).sort().join();
 }
 function StructureComponentRef(cell, structure) {
     return { kind: 'structure-component', cell: cell, version: cell.transform.version, structure: structure, key: componentKey(cell), representations: [] };
@@ -253,4 +253,3 @@ function doPreOrder(tree, state) {
     _doPreOrder(ctx, tree.root);
     return ctx.state;
 }
-//# sourceMappingURL=hierarchy-state.js.map

package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.js

@@ -15,7 +15,7 @@ var set_1 = require("../../../mol-util/set");
 var component_1 = require("../../component");
 var hierarchy_state_1 = require("./hierarchy-state");
 var StructureHierarchyManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StructureHierarchyManager, _super);
+    tslib_1.__extends(StructureHierarchyManager, _super);
     function StructureHierarchyManager(plugin) {
         var _this = _super.call(this) || this;
         _this.plugin = plugin;
@@ -135,7 +135,7 @@ var StructureHierarchyManager = /** @class */ (function (_super) {
         if (this.state.syncedTree === this.dataState.tree) {
             if (notify && !this.state.notified) {
                 this.state.notified = true;
-                this.behaviors.selection.next((0, tslib_1.__assign)({ hierarchy: this.state.hierarchy }, this.state.selection));
+                this.behaviors.selection.next(tslib_1.__assign({ hierarchy: this.state.hierarchy }, this.state.selection));
             }
             return;
         }
@@ -215,9 +215,9 @@ var StructureHierarchyManager = /** @class */ (function (_super) {
     };
     StructureHierarchyManager.prototype.applyPreset = function (trajectories, provider, params) {
         var _this = this;
-        return this.plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return this.plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _i, trajectories_1, t;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         _i = 0, trajectories_1 = trajectories;
@@ -243,13 +243,13 @@ var StructureHierarchyManager = /** @class */ (function (_super) {
         }); });
     };
     StructureHierarchyManager.prototype.updateStructure = function (s, params) {
-        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: return [4 /*yield*/, this.plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                    case 0: return [4 /*yield*/, this.plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                             var root, children;
-                            return (0, tslib_1.__generator)(this, function (_a) {
+                            return tslib_1.__generator(this, function (_a) {
                                 switch (_a.label) {
                                     case 0:
                                         root = mol_state_1.StateTree.getDecoratorRoot(this.dataState.tree, s.cell.transform.ref);
@@ -348,4 +348,3 @@ exports.StructureHierarchyManager = StructureHierarchyManager;
     StructureHierarchyManager.getSelectedStructuresDescription = getSelectedStructuresDescription;
 })(StructureHierarchyManager = exports.StructureHierarchyManager || (exports.StructureHierarchyManager = {}));
 exports.StructureHierarchyManager = StructureHierarchyManager;
-//# sourceMappingURL=hierarchy.js.map

package/lib/commonjs/mol-plugin-state/manager/structure/measurement.js

@@ -26,7 +26,7 @@ exports.StructureMeasurementParams = {
 };
 var DefaultStructureMeasurementOptions = param_definition_1.ParamDefinition.getDefaultValues(exports.StructureMeasurementParams);
 var StructureMeasurementManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StructureMeasurementManager, _super);
+    tslib_1.__extends(StructureMeasurementManager, _super);
     function StructureMeasurementManager(plugin) {
         var _this = _super.call(this, { labels: [], distances: [], angles: [], dihedrals: [], orientations: [], planes: [], options: DefaultStructureMeasurementOptions }) || this;
         _this.plugin = plugin;
@@ -57,9 +57,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         return builder.toRoot().group(transforms_1.StateTransforms.Misc.CreateGroup, { label: "Measurements" }, { tags: exports.MeasurementGroupTag });
     };
     StructureMeasurementManager.prototype.setOptions = function (options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var update, _i, _a, cell, _b, _c, cell, _d, _e, cell, _f, _g, cell;
-            return (0, tslib_1.__generator)(this, function (_h) {
+            return tslib_1.__generator(this, function (_h) {
                 switch (_h.label) {
                     case 0:
                         if (this.updateState({ options: options }))
@@ -95,9 +95,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addDistance = function (a, b, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var cellA, cellB, dependsOn, update, state;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         cellA = this.plugin.helpers.substructureParent.get(a.structure);
@@ -116,7 +116,7 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
                             isTransitive: true,
                             label: 'Distance'
                         }, { dependsOn: dependsOn, tags: options === null || options === void 0 ? void 0 : options.selectionTags })
-                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsDistance3D, (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ customText: (options === null || options === void 0 ? void 0 : options.customText) || '', unitLabel: this.state.options.distanceUnitLabel, textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.lineParams), options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
+                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsDistance3D, tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ customText: (options === null || options === void 0 ? void 0 : options.customText) || '', unitLabel: this.state.options.distanceUnitLabel, textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.lineParams), options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
                         state = this.plugin.state.data;
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
                     case 1:
@@ -127,9 +127,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addAngle = function (a, b, c, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var cellA, cellB, cellC, dependsOn, update, state;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         cellA = this.plugin.helpers.substructureParent.get(a.structure);
@@ -151,7 +151,7 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
                             isTransitive: true,
                             label: 'Angle'
                         }, { dependsOn: dependsOn, tags: options === null || options === void 0 ? void 0 : options.selectionTags })
-                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsAngle3D, (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ customText: (options === null || options === void 0 ? void 0 : options.customText) || '', textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.lineParams), options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
+                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsAngle3D, tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ customText: (options === null || options === void 0 ? void 0 : options.customText) || '', textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.lineParams), options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
                         state = this.plugin.state.data;
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
                     case 1:
@@ -162,9 +162,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addDihedral = function (a, b, c, d, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var cellA, cellB, cellC, cellD, dependsOn, update, state;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         cellA = this.plugin.helpers.substructureParent.get(a.structure);
@@ -189,7 +189,7 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
                             isTransitive: true,
                             label: 'Dihedral'
                         }, { dependsOn: dependsOn, tags: options === null || options === void 0 ? void 0 : options.selectionTags })
-                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsDihedral3D, (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ customText: (options === null || options === void 0 ? void 0 : options.customText) || '', textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.lineParams), options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
+                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsDihedral3D, tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ customText: (options === null || options === void 0 ? void 0 : options.customText) || '', textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.lineParams), options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
                         state = this.plugin.state.data;
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
                     case 1:
@@ -200,9 +200,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addLabel = function (a, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var cellA, dependsOn, update, state;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         cellA = this.plugin.helpers.substructureParent.get(a.structure);
@@ -218,7 +218,7 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
                             isTransitive: true,
                             label: 'Label'
                         }, { dependsOn: dependsOn, tags: options === null || options === void 0 ? void 0 : options.selectionTags })
-                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsLabel3D, (0, tslib_1.__assign)((0, tslib_1.__assign)({ textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
+                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsLabel3D, tslib_1.__assign(tslib_1.__assign({ textColor: this.state.options.textColor }, options === null || options === void 0 ? void 0 : options.labelParams), options === null || options === void 0 ? void 0 : options.visualParams), { tags: options === null || options === void 0 ? void 0 : options.reprTags });
                         state = this.plugin.state.data;
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
                     case 1:
@@ -229,9 +229,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addOrientation = function (locis) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var selections, dependsOn, i, il, l, cell, update, state;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         selections = [];
@@ -264,9 +264,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addPlane = function (locis) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var selections, dependsOn, i, il, l, cell, update, state;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         selections = [];
@@ -299,9 +299,9 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         });
     };
     StructureMeasurementManager.prototype.addOrderLabels = function (locis) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var update, current, _i, current_1, obj, order, _a, locis_1, loci, cell, dependsOn, state;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         update = this.getGroup();
@@ -373,4 +373,3 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
     return StructureMeasurementManager;
 }(component_1.StatefulPluginComponent));
 exports.StructureMeasurementManager = StructureMeasurementManager;
-//# sourceMappingURL=measurement.js.map

package/lib/commonjs/mol-plugin-state/manager/structure/selection.js

@@ -24,7 +24,7 @@ var util_1 = require("../../../mol-data/util");
 var boundaryHelper = new boundary_helper_1.BoundaryHelper('98');
 var HISTORY_CAPACITY = 24;
 var StructureSelectionManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StructureSelectionManager, _super);
+    tslib_1.__extends(StructureSelectionManager, _super);
     function StructureSelectionManager(plugin) {
         var _this = _super.call(this, { entries: new Map(), additionsHistory: [], stats: SelectionStats() }) || this;
         _this.plugin = plugin;
@@ -464,9 +464,9 @@ var StructureSelectionManager = /** @class */ (function (_super) {
     StructureSelectionManager.prototype.fromSelectionQuery = function (modifier, query, applyGranularity) {
         var _this = this;
         if (applyGranularity === void 0) { applyGranularity = true; }
-        this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _i, _a, s, loci;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         _i = 0, _a = this.applicableStructures;
@@ -553,4 +553,3 @@ function getElementRange(structure, ref, ext) {
             indices: int_1.OrderedSet.ofRange(min, max)
         }]);
 }
-//# sourceMappingURL=selection.js.map

package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy-state.js

@@ -130,4 +130,3 @@ function doPreOrder(tree, state) {
     _doPreOrder(ctx, tree.root);
     return ctx.state;
 }
-//# sourceMappingURL=hierarchy-state.js.map

package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy.js

@@ -13,7 +13,7 @@ var hierarchy_state_1 = require("./hierarchy-state");
 var volume_representation_params_1 = require("../../helpers/volume-representation-params");
 var transforms_1 = require("../../transforms");
 var VolumeHierarchyManager = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(VolumeHierarchyManager, _super);
+    tslib_1.__extends(VolumeHierarchyManager, _super);
     function VolumeHierarchyManager(plugin) {
         var _this = _super.call(this) || this;
         _this.plugin = plugin;
@@ -143,4 +143,3 @@ exports.VolumeHierarchyManager = VolumeHierarchyManager;
     VolumeHierarchyManager.getRepresentationTypes = getRepresentationTypes;
 })(VolumeHierarchyManager = exports.VolumeHierarchyManager || (exports.VolumeHierarchyManager = {}));
 exports.VolumeHierarchyManager = VolumeHierarchyManager;
-//# sourceMappingURL=hierarchy.js.map

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>
@@ -23,6 +23,8 @@ import { CubeFile } from '../mol-io/reader/cube/parser';
 import { DxFile } from '../mol-io/reader/dx/parser';
 import { Color } from '../mol-util/color/color';
 import { Asset } from '../mol-util/assets';
+import { PrmtopFile } from '../mol-io/reader/prmtop/parser';
+import { TopFile } from '../mol-io/reader/top/parser';
 export declare type TypeClass = 'root' | 'data' | 'prop';
 export declare namespace PluginStateObject {
     export type Any = StateObject<any, TypeInfo>;
@@ -313,6 +315,50 @@ export declare namespace PluginStateObject {
         };
         export class Psf extends Psf_base {
         }
+        const Prmtop_base: {
+            new (data: PrmtopFile, props?: {
+                label: string;
+                description?: string | undefined;
+            } | undefined): {
+                id: import("../mol-util/uuid").UUID;
+                type: TypeInfo;
+                label: string;
+                description?: string | undefined;
+                data: PrmtopFile;
+            };
+            type: TypeInfo;
+            is(obj?: StateObject<any, StateObject.Type<any>> | undefined): obj is {
+                id: import("../mol-util/uuid").UUID;
+                type: TypeInfo;
+                label: string;
+                description?: string | undefined;
+                data: PrmtopFile;
+            };
+        };
+        export class Prmtop extends Prmtop_base {
+        }
+        const Top_base: {
+            new (data: TopFile, props?: {
+                label: string;
+                description?: string | undefined;
+            } | undefined): {
+                id: import("../mol-util/uuid").UUID;
+                type: TypeInfo;
+                label: string;
+                description?: string | undefined;
+                data: TopFile;
+            };
+            type: TypeInfo;
+            is(obj?: StateObject<any, StateObject.Type<any>> | undefined): obj is {
+                id: import("../mol-util/uuid").UUID;
+                type: TypeInfo;
+                label: string;
+                description?: string | undefined;
+                data: TopFile;
+            };
+        };
+        export class Top extends Top_base {
+        }
         const Ply_base: {
             new (data: PlyFile, props?: {
                 label: string;