molstar 3.3.1 → 3.4.0

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js

@@ -26,7 +26,7 @@ exports.RCSBAssemblySymmetry = behavior_1.PluginBehavior.create({
         description: 'Assembly Symmetry data calculated with BioJava, obtained via RCSB PDB.'
     },
     ctor: /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(class_1, _super);
+        tslib_1.__extends(class_1, _super);
         function class_1() {
             var _this = _super !== null && _super.apply(this, arguments) || this;
             _this.provider = prop_1.AssemblySymmetryProvider;
@@ -80,9 +80,9 @@ exports.InitAssemblySymmetry3D = mol_state_1.StateAction.build({
     isApplicable: function (a) { return prop_1.AssemblySymmetry.isApplicable(a.data); }
 })(function (_a, plugin) {
     var a = _a.a, ref = _a.ref, state = _a.state;
-    return mol_task_1.Task.create('Init Assembly Symmetry', function (ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    return mol_task_1.Task.create('Init Assembly Symmetry', function (ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var propCtx, assemblySymmetryData, symmetryIndex, e_1, tree;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     _a.trys.push([0, 3, , 4]);
@@ -120,7 +120,7 @@ var AssemblySymmetry3D = objects_1.PluginStateTransform.BuiltIn({
     from: objects_1.PluginStateObject.Molecule.Structure,
     to: objects_1.PluginStateObject.Shape.Representation3D,
     params: function (a) {
-        return (0, tslib_1.__assign)({}, representation_1.AssemblySymmetryParams);
+        return tslib_1.__assign({}, representation_1.AssemblySymmetryParams);
     }
 })({
     canAutoUpdate: function (_a) {
@@ -130,10 +130,10 @@ var AssemblySymmetry3D = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Assembly Symmetry', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Assembly Symmetry', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var assemblySymmetry, repr, type, kind, symbol;
             var _a;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, prop_1.AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data)];
                     case 1:
@@ -142,7 +142,7 @@ var AssemblySymmetry3D = objects_1.PluginStateTransform.BuiltIn({
                         if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
                             return [2 /*return*/, mol_state_1.StateObject.Null];
                         }
-                        repr = (0, representation_1.AssemblySymmetryRepresentation)((0, tslib_1.__assign)({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return representation_1.AssemblySymmetryParams; });
+                        repr = (0, representation_1.AssemblySymmetryRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return representation_1.AssemblySymmetryParams; });
                         return [4 /*yield*/, repr.createOrUpdate(params, a.data).runInContext(ctx)];
                     case 2:
                         _b.sent();
@@ -155,9 +155,9 @@ var AssemblySymmetry3D = objects_1.PluginStateTransform.BuiltIn({
     update: function (_a, plugin) {
         var _this = this;
         var a = _a.a, b = _a.b, newParams = _a.newParams;
-        return mol_task_1.Task.create('Assembly Symmetry', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Assembly Symmetry', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var assemblySymmetry, props, type, kind, symbol;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, prop_1.AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data)];
                     case 1:
@@ -168,7 +168,7 @@ var AssemblySymmetry3D = objects_1.PluginStateTransform.BuiltIn({
                             // because that keeps the old object
                             return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Recreate];
                         }
-                        props = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, b.data.repr.props), newParams);
+                        props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
                         return [4 /*yield*/, b.data.repr.createOrUpdate(props, a.data).runInContext(ctx)];
                     case 2:
                         _a.sent();
@@ -187,7 +187,7 @@ var AssemblySymmetry3D = objects_1.PluginStateTransform.BuiltIn({
 });
 exports.AssemblySymmetry3D = AssemblySymmetry3D;
 //
-exports.AssemblySymmetryPresetParams = (0, tslib_1.__assign)({}, representation_preset_1.StructureRepresentationPresetProvider.CommonParams);
+exports.AssemblySymmetryPresetParams = tslib_1.__assign({}, representation_preset_1.StructureRepresentationPresetProvider.CommonParams);
 exports.AssemblySymmetryPreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
     id: 'preset-structure-representation-rcsb-assembly-symmetry',
     display: {
@@ -200,10 +200,10 @@ exports.AssemblySymmetryPreset = (0, representation_preset_1.StructureRepresenta
     params: function () { return exports.AssemblySymmetryPresetParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, assemblySymmetry, colorTheme, preset;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -211,9 +211,9 @@ exports.AssemblySymmetryPreset = (0, representation_preset_1.StructureRepresenta
                         if (!structureCell || !structure)
                             return [2 /*return*/, {}];
                         if (!!prop_1.AssemblySymmetryDataProvider.get(structure).value) return [3 /*break*/, 2];
-                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Assembly Symmetry', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Assembly Symmetry', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                                 var propCtx, assemblySymmetryData, symmetryIndex;
-                                return (0, tslib_1.__generator)(this, function (_a) {
+                                return tslib_1.__generator(this, function (_a) {
                                     switch (_a.label) {
                                         case 0:
                                             propCtx = { runtime: runtime, assetManager: plugin.managers.asset };
@@ -236,10 +236,10 @@ exports.AssemblySymmetryPreset = (0, representation_preset_1.StructureRepresenta
                     case 3:
                         assemblySymmetry = _b.sent();
                         colorTheme = assemblySymmetry.isOk ? Tag.Cluster : undefined;
-                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__assign(tslib_1.__assign({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
                     case 4:
                         preset = _b.sent();
-                        return [2 /*return*/, { components: preset.components, representations: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, preset.representations), { assemblySymmetry: assemblySymmetry }) }];
+                        return [2 /*return*/, { components: preset.components, representations: tslib_1.__assign(tslib_1.__assign({}, preset.representations), { assemblySymmetry: assemblySymmetry }) }];
                 }
             });
         });

package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js

@@ -25,7 +25,7 @@ function getAsymId(unit) {
 function clusterMemberKey(asymId, operList) {
     return "".concat(asymId, "-").concat(operList.join('|'));
 }
-exports.AssemblySymmetryClusterColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ colorList: 'red-yellow-blue' }));
+exports.AssemblySymmetryClusterColorThemeParams = tslib_1.__assign({}, (0, palette_1.getPaletteParams)({ colorList: 'red-yellow-blue' }));
 function getAssemblySymmetryClusterColorThemeParams(ctx) {
     var params = param_definition_1.ParamDefinition.clone(exports.AssemblySymmetryClusterColorThemeParams);
     return params;
@@ -45,7 +45,7 @@ function AssemblySymmetryClusterColorTheme(ctx, props) {
             var members = clusters[i].members;
             for (var j = 0, jl = members.length; j < jl; ++j) {
                 var asymId = members[j].asym_id;
-                var operList = (0, tslib_1.__spreadArray)([], members[j].pdbx_struct_oper_list_ids || [], true);
+                var operList = tslib_1.__spreadArray([], members[j].pdbx_struct_oper_list_ids || [], true);
                 clusterByMember_1.set(clusterMemberKey(asymId, operList), i);
                 if (operList.length === 0) {
                     operList.push('1'); // TODO hack assuming '1' is the id of the identity operator

package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js

@@ -59,9 +59,9 @@ var AssemblySymmetry;
     AssemblySymmetry.isApplicable = isApplicable;
     function fetch(ctx, structure, props) {
         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 client, variables, result, value;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         if (!isApplicable(structure))
@@ -172,12 +172,12 @@ exports.AssemblySymmetryDataProvider = custom_structure_property_1.CustomStructu
     defaultParams: exports.AssemblySymmetryDataParams,
     getParams: function (data) { return exports.AssemblySymmetryDataParams; },
     isApplicable: function (data) { return AssemblySymmetry.isApplicable(data); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.AssemblySymmetryDataParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.AssemblySymmetryDataParams)), props);
                     return [4 /*yield*/, AssemblySymmetry.fetch(ctx, data, p)];
                 case 1: return [2 /*return*/, _a.sent()];
             }
@@ -186,7 +186,7 @@ exports.AssemblySymmetryDataProvider = custom_structure_property_1.CustomStructu
 });
 //
 function getAssemblySymmetryParams(data) {
-    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.AssemblySymmetryDataParams), { symmetryIndex: getSymmetrySelectParam(data) });
+    return tslib_1.__assign(tslib_1.__assign({}, exports.AssemblySymmetryDataParams), { symmetryIndex: getSymmetrySelectParam(data) });
 }
 exports.AssemblySymmetryParams = getAssemblySymmetryParams();
 exports.AssemblySymmetryProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
@@ -199,12 +199,12 @@ exports.AssemblySymmetryProvider = custom_structure_property_1.CustomStructurePr
     defaultParams: exports.AssemblySymmetryParams,
     getParams: getAssemblySymmetryParams,
     isApplicable: function (data) { return AssemblySymmetry.isApplicable(data); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p, assemblySymmetryData, assemblySymmetry;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(getAssemblySymmetryParams(data))), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(getAssemblySymmetryParams(data))), props);
                     return [4 /*yield*/, exports.AssemblySymmetryDataProvider.attach(ctx, data, p)];
                 case 1:
                     _a.sent();

package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js

@@ -46,20 +46,20 @@ function axesColorHelp(value) {
         ? { description: 'Color axes by their order', legend: OrderColorsLegend }
         : {};
 }
-var SharedParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), { scale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }) });
-var AxesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { axesColor: param_definition_1.ParamDefinition.MappedStatic('byOrder', {
+var SharedParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { scale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }) });
+var AxesParams = tslib_1.__assign(tslib_1.__assign({}, SharedParams), { axesColor: param_definition_1.ParamDefinition.MappedStatic('byOrder', {
         byOrder: param_definition_1.ParamDefinition.EmptyGroup(),
         uniform: param_definition_1.ParamDefinition.Group({
             colorValue: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange),
         }, { isFlat: true })
     }, { help: axesColorHelp }) });
-var CageParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { cageColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange) });
+var CageParams = tslib_1.__assign(tslib_1.__assign({}, SharedParams), { cageColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange) });
 var AssemblySymmetryVisuals = {
     // cage should come before 'axes' so that the representative loci uses the cage shape
-    'cage': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getCageShape, mesh_1.Mesh.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
-    'axes': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getAxesShape, mesh_1.Mesh.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
+    'cage': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getCageShape, mesh_1.Mesh.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
+    'axes': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getAxesShape, mesh_1.Mesh.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
 };
-exports.AssemblySymmetryParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, AxesParams), CageParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['axes', 'cage'], param_definition_1.ParamDefinition.objectToOptions(AssemblySymmetryVisuals)) });
+exports.AssemblySymmetryParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, AxesParams), CageParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['axes', 'cage'], param_definition_1.ParamDefinition.objectToOptions(AssemblySymmetryVisuals)) });
 //
 function getAssemblyName(s) {
     var _a;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js

@@ -20,7 +20,7 @@ var objects_1 = require("../../../mol-plugin-state/objects");
 var mol_task_1 = require("../../../mol-task");
 var icons_1 = require("../../../mol-plugin-ui/controls/icons");
 var AssemblySymmetryControls = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(AssemblySymmetryControls, _super);
+    tslib_1.__extends(AssemblySymmetryControls, _super);
     function AssemblySymmetryControls() {
         var _this = _super !== null && _super.apply(this, arguments) || this;
         _this.paramsOnChange = function (options) {
@@ -72,10 +72,10 @@ var AssemblySymmetryControls = /** @class */ (function (_super) {
         var pivot = this.pivot;
         if (!pivot.cell.parent)
             return null;
-        return (0, jsx_runtime_1.jsx)(apply_action_1.ApplyActionControl, { state: pivot.cell.parent, action: EnableAssemblySymmetry3D, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: { header: 'Enable', icon: icons_1.CheckSvg } }, void 0);
+        return (0, jsx_runtime_1.jsx)(apply_action_1.ApplyActionControl, { state: pivot.cell.parent, action: EnableAssemblySymmetry3D, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: { header: 'Enable', icon: icons_1.CheckSvg } });
     };
     AssemblySymmetryControls.prototype.renderNoSymmetries = function () {
-        return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-row-text' }, { children: (0, jsx_runtime_1.jsx)("div", { children: "No Symmetries for Assembly" }, void 0) }), void 0);
+        return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-row-text' }, { children: (0, jsx_runtime_1.jsx)("div", { children: "No Symmetries for Assembly" }) }));
     };
     Object.defineProperty(AssemblySymmetryControls.prototype, "params", {
         get: function () {
@@ -96,7 +96,7 @@ var AssemblySymmetryControls = /** @class */ (function (_super) {
                 return prop_1.AssemblySymmetryProvider.props(structure);
             }
             else {
-                return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(prop_1.AssemblySymmetryProvider.defaultParams)), { symmetryIndex: -1 });
+                return tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(prop_1.AssemblySymmetryProvider.defaultParams)), { symmetryIndex: -1 });
             }
         },
         enumerable: false,
@@ -104,9 +104,9 @@ var AssemblySymmetryControls = /** @class */ (function (_super) {
     });
     AssemblySymmetryControls.prototype.updateAssemblySymmetry = function (values) {
         var _a, _b, _c, _d;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var s, currValues, b, pd, params, _i, _e, components, name_1;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
                         s = this.pivot;
@@ -183,7 +183,7 @@ var AssemblySymmetryControls = /** @class */ (function (_super) {
         configurable: true
     });
     AssemblySymmetryControls.prototype.renderParams = function () {
-        return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: this.params, values: this.values, onChangeValues: this.paramsOnChange }, void 0) }, void 0);
+        return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: this.params, values: this.values, onChangeValues: this.paramsOnChange }) });
     };
     AssemblySymmetryControls.prototype.renderControls = function () {
         if (!this.pivot)
@@ -201,8 +201,8 @@ var EnableAssemblySymmetry3D = mol_state_1.StateAction.build({
     from: objects_1.PluginStateObject.Molecule.Structure,
 })(function (_a, plugin) {
     var a = _a.a, ref = _a.ref, state = _a.state;
-    return mol_task_1.Task.create('Enable Assembly Symmetry', function (ctx) { 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('Enable Assembly Symmetry', function (ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, behavior_1.AssemblySymmetryPreset.apply(ref, Object.create(null), plugin)];
                 case 1:

package/lib/commonjs/extensions/rcsb/validation-report/behavior.js

@@ -31,7 +31,7 @@ exports.RCSBValidationReport = behavior_1.PluginBehavior.create({
         description: 'Data from wwPDB Validation Report, obtained via RCSB PDB.'
     },
     ctor: /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(class_1, _super);
+        tslib_1.__extends(class_1, _super);
         function class_1() {
             var _this = _super !== null && _super.apply(this, arguments) || this;
             _this.provider = prop_1.ValidationReportProvider;
@@ -291,18 +291,18 @@ exports.ValidationReportGeometryQualityPreset = (0, representation_preset_1.Stru
     params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, colorTheme, _b, components, representations, clashes, _c, update, builder, typeParams, color, clashesBallAndStick, clashesRepr;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
                         structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
                         if (!structureCell || !structure)
                             return [2 /*return*/, {}];
-                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Validation Report', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                                return (0, tslib_1.__generator)(this, function (_a) {
+                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Validation Report', function (runtime) { 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*/, prop_1.ValidationReportProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, structure.models[0])];
                                         case 1:
@@ -314,7 +314,7 @@ exports.ValidationReportGeometryQualityPreset = (0, representation_preset_1.Stru
                     case 1:
                         _d.sent();
                         colorTheme = geometry_quality_1.GeometryQualityColorThemeProvider.name;
-                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__assign(tslib_1.__assign({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
                     case 2:
                         _b = _d.sent(), components = _b.components, representations = _b.representations;
                         return [4 /*yield*/, plugin.builders.structure.tryCreateComponentFromExpression(structureCell, hasClash.expression, 'clashes', { label: 'Clashes' })];
@@ -328,7 +328,7 @@ exports.ValidationReportGeometryQualityPreset = (0, representation_preset_1.Stru
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 4:
                         _d.sent();
-                        return [2 /*return*/, { components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, components), { clashes: clashes }), representations: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, representations), { clashesBallAndStick: clashesBallAndStick, clashesRepr: clashesRepr }) }];
+                        return [2 /*return*/, { components: tslib_1.__assign(tslib_1.__assign({}, components), { clashes: clashes }), representations: tslib_1.__assign(tslib_1.__assign({}, representations), { clashesBallAndStick: clashesBallAndStick, clashesRepr: clashesRepr }) }];
                 }
             });
         });
@@ -346,18 +346,18 @@ exports.ValidationReportDensityFitPreset = (0, representation_preset_1.Structure
     params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, colorTheme;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
                         structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
                         if (!structureCell || !structure)
                             return [2 /*return*/, {}];
-                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Validation Report', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                                return (0, tslib_1.__generator)(this, function (_a) {
+                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Validation Report', function (runtime) { 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*/, prop_1.ValidationReportProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, structure.models[0])];
                                         case 1:
@@ -369,7 +369,7 @@ exports.ValidationReportDensityFitPreset = (0, representation_preset_1.Structure
                     case 1:
                         _b.sent();
                         colorTheme = density_fit_1.DensityFitColorThemeProvider.name;
-                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__assign(tslib_1.__assign({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
                     case 2: return [2 /*return*/, _b.sent()];
                 }
             });
@@ -388,18 +388,18 @@ exports.ValidationReportRandomCoilIndexPreset = (0, representation_preset_1.Stru
     params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, colorTheme;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
                         structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
                         if (!structureCell || !structure)
                             return [2 /*return*/, {}];
-                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Validation Report', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                                return (0, tslib_1.__generator)(this, function (_a) {
+                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Validation Report', function (runtime) { 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*/, prop_1.ValidationReportProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, structure.models[0])];
                                         case 1:
@@ -411,7 +411,7 @@ exports.ValidationReportRandomCoilIndexPreset = (0, representation_preset_1.Stru
                     case 1:
                         _b.sent();
                         colorTheme = random_coil_index_1.RandomCoilIndexColorThemeProvider.name;
-                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__assign(tslib_1.__assign({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
                     case 2: return [2 /*return*/, _b.sent()];
                 }
             });

package/lib/commonjs/extensions/rcsb/validation-report/prop.js

@@ -47,9 +47,9 @@ var ValidationReport;
     }
     ValidationReport.fromXml = fromXml;
     function fetch(ctx, model, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var url, xml;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         url = assets_1.Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.baseUrl));
@@ -63,9 +63,9 @@ var ValidationReport;
     }
     ValidationReport.fetch = fetch;
     function open(ctx, model, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var xml;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (props.input === null)
@@ -80,8 +80,8 @@ var ValidationReport;
     }
     ValidationReport.open = open;
     function obtain(ctx, model, props) {
-        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) {
                 switch (props.source.name) {
                     case 'file': return [2 /*return*/, open(ctx, model, props.source.params)];
                     case 'server': return [2 /*return*/, fetch(ctx, model, props.source.params)];
@@ -132,12 +132,12 @@ exports.ValidationReportProvider = custom_model_property_1.CustomModelProperty.c
     defaultParams: exports.ValidationReportParams,
     getParams: function (data) { return exports.ValidationReportParams; },
     isApplicable: function (data) { return ValidationReport.isApplicable(data); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValidationReportParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValidationReportParams)), props);
                     return [4 /*yield*/, ValidationReport.obtain(ctx, data, p)];
                 case 1: return [2 /*return*/, _a.sent()];
             }
@@ -241,9 +241,9 @@ exports.ClashesProvider = custom_structure_property_1.CustomStructureProperty.cr
     defaultParams: {},
     getParams: function (data) { return ({}); },
     isApplicable: function (data) { return true; },
-    obtain: function (ctx, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var validationReport;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, exports.ValidationReportProvider.attach(ctx, data.models[0])];
                 case 1:
@@ -389,7 +389,7 @@ function parseValidationReportXml(xml, model) {
                 var atomB = index.findAtomOnResidue(rI, getItem(bo, 'atom1'));
                 addIndex(idx, atomA, bondOutliers.index);
                 addIndex(idx, atomB, bondOutliers.index);
-                bondOutliers.data.push((0, tslib_1.__assign)({ tag: 'bond-outlier', atomA: atomA, atomB: atomB }, getMolInfo(bo)));
+                bondOutliers.data.push(tslib_1.__assign({ tag: 'bond-outlier', atomA: atomA, atomB: atomB }, getMolInfo(bo)));
             }
             var molAngleOutliers = g.getElementsByTagName('angle-outlier');
             if (molAngleOutliers.length)
@@ -403,7 +403,7 @@ function parseValidationReportXml(xml, model) {
                 addIndex(idx, atomA, angleOutliers.index);
                 addIndex(idx, atomB, angleOutliers.index);
                 addIndex(idx, atomC, angleOutliers.index);
-                angleOutliers.data.push((0, tslib_1.__assign)({ tag: 'angle-outlier', atomA: atomA, atomB: atomB, atomC: atomC }, getMolInfo(ao)));
+                angleOutliers.data.push(tslib_1.__assign({ tag: 'angle-outlier', atomA: atomA, atomB: atomB, atomC: atomC }, getMolInfo(ao)));
             }
             var planeOutliers = g.getElementsByTagName('plane-outlier');
             if (planeOutliers.length)
@@ -427,7 +427,7 @@ function parseValidationReportXml(xml, model) {
                 var atomB = index.findAtomOnResidue(rI, atoms[1]);
                 addIndex(idx, atomA, bondOutliers.index);
                 addIndex(idx, atomB, bondOutliers.index);
-                bondOutliers.data.push((0, tslib_1.__assign)({ tag: 'mog-bond-outlier', atomA: atomA, atomB: atomB }, getMogInfo(mbo)));
+                bondOutliers.data.push(tslib_1.__assign({ tag: 'mog-bond-outlier', atomA: atomA, atomB: atomB }, getMogInfo(mbo)));
             }
             var mogAngleOutliers = g.getElementsByTagName('mog-angle-outlier');
             if (mogAngleOutliers.length)
@@ -442,7 +442,7 @@ function parseValidationReportXml(xml, model) {
                 addIndex(idx, atomA, angleOutliers.index);
                 addIndex(idx, atomB, angleOutliers.index);
                 addIndex(idx, atomC, angleOutliers.index);
-                angleOutliers.data.push((0, tslib_1.__assign)({ tag: 'mog-angle-outlier', atomA: atomA, atomB: atomB, atomC: atomC }, getMogInfo(mao)));
+                angleOutliers.data.push(tslib_1.__assign({ tag: 'mog-angle-outlier', atomA: atomA, atomB: atomB, atomC: atomC }, getMogInfo(mao)));
             }
         }
         var clashes_1 = g.getElementsByTagName('clash');

package/lib/commonjs/extensions/rcsb/validation-report/representation.js

@@ -55,7 +55,7 @@ function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, me
     }
     return m;
 }
-exports.IntraUnitClashParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
+exports.IntraUnitClashParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
 function IntraUnitClashVisual(materialId) {
     return (0, units_visual_1.UnitsMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitClashParams),
@@ -156,7 +156,7 @@ function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
     }
     return m;
 }
-exports.InterUnitClashParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
+exports.InterUnitClashParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
 function InterUnitClashVisual(materialId) {
     return (0, complex_visual_1.ComplexMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitClashParams),
@@ -231,7 +231,7 @@ var ClashesVisuals = {
     'intra-clash': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit clash cylinder', ctx, getParams, IntraUnitClashVisual); },
     'inter-clash': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit clash cylinder', ctx, getParams, InterUnitClashVisual); },
 };
-exports.ClashesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.IntraUnitClashParams), exports.InterUnitClashParams), { unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-clash', 'inter-clash'], param_definition_1.ParamDefinition.objectToOptions(ClashesVisuals)) });
+exports.ClashesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, exports.IntraUnitClashParams), exports.InterUnitClashParams), { unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-clash', 'inter-clash'], param_definition_1.ParamDefinition.objectToOptions(ClashesVisuals)) });
 function getClashesParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.ClashesParams);
 }

package/lib/commonjs/extensions/zenodo/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+export declare const ZenodoImport: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/commonjs/extensions/zenodo/index.js

@@ -0,0 +1,35 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ZenodoImport = void 0;
+var tslib_1 = require("tslib");
+var behavior_1 = require("../../mol-plugin/behavior/behavior");
+var ui_1 = require("./ui");
+exports.ZenodoImport = behavior_1.PluginBehavior.create({
+    name: 'extension-zenodo-import',
+    category: 'misc',
+    display: {
+        name: 'Zenodo Export'
+    },
+    ctor: /** @class */ (function (_super) {
+        tslib_1.__extends(class_1, _super);
+        function class_1() {
+            return _super !== null && _super.apply(this, arguments) || this;
+        }
+        class_1.prototype.register = function () {
+            this.ctx.customImportControls.set('zenodo-import', ui_1.ZenodoImportUI);
+        };
+        class_1.prototype.update = function () {
+            return false;
+        };
+        class_1.prototype.unregister = function () {
+            this.ctx.customImportControls.delete('zenodo-import');
+        };
+        return class_1;
+    }(behavior_1.PluginBehavior.Handler)),
+    params: function () { return ({}); }
+});