molstar 3.3.1 → 3.6.0

package/lib/commonjs/extensions/model-export/index.js

@@ -16,7 +16,7 @@ exports.ModelExport = behavior_1.PluginBehavior.create({
         name: 'Model Export'
     },
     ctor: /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(class_1, _super);
+        tslib_1.__extends(class_1, _super);
         function class_1() {
             return _super !== null && _super.apply(this, arguments) || this;
         }

package/lib/commonjs/extensions/model-export/ui.js

@@ -17,7 +17,7 @@ var use_behavior_1 = require("../../mol-plugin-ui/hooks/use-behavior");
 var param_definition_1 = require("../../mol-util/param-definition");
 var export_1 = require("./export");
 var ModelExportUI = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(ModelExportUI, _super);
+    tslib_1.__extends(ModelExportUI, _super);
     function ModelExportUI() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
@@ -29,7 +29,7 @@ var ModelExportUI = /** @class */ (function (_super) {
         };
     };
     ModelExportUI.prototype.renderControls = function () {
-        return (0, jsx_runtime_1.jsx)(ExportControls, { plugin: this.plugin }, void 0);
+        return (0, jsx_runtime_1.jsx)(ExportControls, { plugin: this.plugin });
     };
     return ModelExportUI;
 }(base_1.CollapsableControls));
@@ -53,8 +53,8 @@ function ExportControls(_a) {
     if (hierarchy.structures.length > 1) {
         label = 'Export (as ZIP)';
     }
-    var onExport = function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    var onExport = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     setExporting(true);
@@ -72,5 +72,5 @@ function ExportControls(_a) {
             }
         });
     }); };
-    return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: Params, values: params, onChangeValues: setParams, isDisabled: isBusy || exporting }, void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: onExport, style: { marginTop: 1 }, disabled: isBusy || hierarchy.structures.length === 0 || exporting, commit: hierarchy.structures.length ? 'on' : 'off' }, { children: label }), void 0)] }, void 0);
+    return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: Params, values: params, onChangeValues: setParams, isDisabled: isBusy || exporting }), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: onExport, style: { marginTop: 1 }, disabled: isBusy || hierarchy.structures.length === 0 || exporting, commit: hierarchy.structures.length ? 'on' : 'off' }, { children: label }))] });
 }

package/lib/commonjs/extensions/mp4-export/controls.js

@@ -16,7 +16,7 @@ exports.Mp4AnimationParams = {
     quantization: param_definition_1.ParamDefinition.Numeric(18, { min: 10, max: 51 }, { description: 'Lower is better, but slower.' })
 };
 var Mp4Controls = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(Mp4Controls, _super);
+    tslib_1.__extends(Mp4Controls, _super);
     function Mp4Controls(plugin) {
         var _this = _super.call(this) || this;
         _this.plugin = plugin;
@@ -45,7 +45,7 @@ var Mp4Controls = /** @class */ (function (_super) {
         this.behaviors.canApply.next((_b = (_a = anim.canApply) === null || _a === void 0 ? void 0 : _a.call(anim, this.plugin)) !== null && _b !== void 0 ? _b : { canApply: true });
     };
     Mp4Controls.prototype.setCurrentParams = function (values) {
-        this.behaviors.current.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.behaviors.current.value), { values: values }));
+        this.behaviors.current.next(tslib_1.__assign(tslib_1.__assign({}, this.behaviors.current.value), { values: values }));
     };
     Object.defineProperty(Mp4Controls.prototype, "current", {
         get: function () {
@@ -56,16 +56,16 @@ var Mp4Controls = /** @class */ (function (_super) {
     });
     Mp4Controls.prototype.render = function () {
         var _this = this;
-        var task = mol_task_1.Task.create('Export Animation', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        var task = mol_task_1.Task.create('Export Animation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var resolution, anim, movie, filename, e_1;
             var _a, _b, _c;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0:
                         _d.trys.push([0, 2, , 3]);
                         resolution = (_a = this.plugin.helpers.viewportScreenshot) === null || _a === void 0 ? void 0 : _a.getSizeAndViewport();
                         anim = this.current;
-                        return [4 /*yield*/, (0, encoder_1.encodeMp4Animation)(this.plugin, ctx, (0, tslib_1.__assign)((0, tslib_1.__assign)({ animation: {
+                        return [4 /*yield*/, (0, encoder_1.encodeMp4Animation)(this.plugin, ctx, tslib_1.__assign(tslib_1.__assign({ animation: {
                                     definition: anim.anim,
                                     params: anim.values,
                                 } }, resolution), { quantizationParameter: this.behaviors.params.value.quantization, pass: (_b = this.plugin.helpers.viewportScreenshot) === null || _b === void 0 ? void 0 : _b.imagePass }))];

package/lib/commonjs/extensions/mp4-export/encoder.js

@@ -7,13 +7,13 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.encodeMp4Animation = void 0;
 var tslib_1 = require("tslib");
-var HME = (0, tslib_1.__importStar)(require("h264-mp4-encoder"));
+var HME = tslib_1.__importStar(require("h264-mp4-encoder"));
 var model_1 = require("../../mol-plugin-state/animation/model");
 function encodeMp4Animation(plugin, ctx, params) {
     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 durationMs, encoder, width, height, vw, vh, normalizedViewport, loop, canvasProps, wasAnimating, stoppedAnimation, finalized, fps, N, dt, i, image;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0: return [4 /*yield*/, ctx.update({ message: 'Initializing...', isIndeterminate: true })];
                 case 1:
@@ -33,7 +33,7 @@ function encodeMp4Animation(plugin, ctx, params) {
                         vw -= 1;
                     if (vh % 2 !== 0)
                         vh -= 1;
-                    normalizedViewport = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.viewport), { width: vw, height: vh });
+                    normalizedViewport = tslib_1.__assign(tslib_1.__assign({}, params.viewport), { width: vw, height: vh });
                     encoder.width = vw;
                     encoder.height = vh;
                     if (params.quantizationParameter)

package/lib/commonjs/extensions/mp4-export/index.js

@@ -16,7 +16,7 @@ exports.Mp4Export = behavior_1.PluginBehavior.create({
         name: 'MP4 Animation Export'
     },
     ctor: /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(class_1, _super);
+        tslib_1.__extends(class_1, _super);
         function class_1() {
             return _super !== null && _super.apply(this, arguments) || this;
         }

package/lib/commonjs/extensions/mp4-export/ui.js

@@ -17,15 +17,15 @@ var parameters_1 = require("../../mol-plugin-ui/controls/parameters");
 var download_1 = require("../../mol-util/download");
 var controls_1 = require("./controls");
 var Mp4EncoderUI = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(Mp4EncoderUI, _super);
+    tslib_1.__extends(Mp4EncoderUI, _super);
     function Mp4EncoderUI() {
         var _this = _super !== null && _super.apply(this, arguments) || this;
         _this.save = function () {
             (0, download_1.download)(new Blob([_this.state.data.movie]), _this.state.data.filename);
         };
-        _this.generate = function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        _this.generate = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var data, e_1;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         _a.trys.push([0, 2, , 3]);
@@ -62,7 +62,7 @@ var Mp4EncoderUI = /** @class */ (function (_super) {
     };
     Mp4EncoderUI.prototype.downloadControls = function () {
         var _this = this;
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: "Rendering successful!" }), void 0) }), void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: icons_1.GetAppSvg, onClick: this.save, style: { marginTop: 1 } }, { children: "Save Animation" }), void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: function () { return _this.setState({ data: void 0 }); }, style: { marginTop: 6 } }, { children: "Clear" }), void 0)] }, void 0);
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: "Rendering successful!" })) })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.GetAppSvg, onClick: this.save, style: { marginTop: 1 } }, { children: "Save Animation" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: function () { return _this.setState({ data: void 0 }); }, style: { marginTop: 6 } }, { children: "Clear" }))] });
     };
     Mp4EncoderUI.prototype.renderControls = function () {
         var _a;
@@ -73,7 +73,7 @@ var Mp4EncoderUI = /** @class */ (function (_super) {
         var current = ctrl.behaviors.current.value;
         var info = ctrl.behaviors.info.value;
         var canApply = ctrl.behaviors.canApply.value;
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: ctrl.behaviors.animations.value, values: { current: current === null || current === void 0 ? void 0 : current.anim.name }, onChangeValues: function (xs) { return ctrl.setCurrent(xs.current); }, isDisabled: this.state.busy }, void 0), current && (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: current.params, values: current.values, onChangeValues: function (xs) { return ctrl.setCurrentParams(xs); }, isDisabled: this.state.busy }, void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: ["Resolution: ", info.width, "x", info.height, (0, jsx_runtime_1.jsx)("br", {}, void 0), "Adjust in viewport using ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CameraOutlinedSvg, inline: true }, void 0)] }), void 0) }), void 0), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: controls_1.Mp4AnimationParams, values: ctrl.behaviors.params.value, onChangeValues: function (xs) { return ctrl.behaviors.params.next(xs); }, isDisabled: this.state.busy }, void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.generate, style: { marginTop: 1 }, disabled: this.state.busy || !canApply.canApply, commit: canApply.canApply ? 'on' : 'off' }, { children: canApply.canApply ? 'Render' : (_a = canApply.reason) !== null && _a !== void 0 ? _a : 'Invalid params/state' }), void 0)] }, void 0);
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: ctrl.behaviors.animations.value, values: { current: current === null || current === void 0 ? void 0 : current.anim.name }, onChangeValues: function (xs) { return ctrl.setCurrent(xs.current); }, isDisabled: this.state.busy }), current && (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: current.params, values: current.values, onChangeValues: function (xs) { return ctrl.setCurrentParams(xs); }, isDisabled: this.state.busy }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-help-description', style: { textAlign: 'center' } }, { children: ["Resolution: ", info.width, "x", info.height, (0, jsx_runtime_1.jsx)("br", {}), "Adjust in viewport using ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CameraOutlinedSvg, inline: true })] })) })), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: controls_1.Mp4AnimationParams, values: ctrl.behaviors.params.value, onChangeValues: function (xs) { return ctrl.behaviors.params.next(xs); }, isDisabled: this.state.busy }), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.generate, style: { marginTop: 1 }, disabled: this.state.busy || !canApply.canApply, commit: canApply.canApply ? 'on' : 'off' }, { children: canApply.canApply ? 'Render' : (_a = canApply.reason) !== null && _a !== void 0 ? _a : 'Invalid params/state' }))] });
     };
     Mp4EncoderUI.prototype.componentDidMount = function () {
         var _this = this;

package/lib/commonjs/extensions/pdbe/preferred-assembly.js

@@ -54,9 +54,9 @@ var PDBePreferredAssembly;
         return (0, schema_1.toTable)(PDBePreferredAssembly.Schema.pdbe_preferred_assembly, cat).assembly_id.value(0) || getFirstFromModel(model);
     }
     function attachFromCifOrApi(model, params) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var asmName, data;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (model.customProperties.has(PDBePreferredAssembly.Descriptor))

package/lib/commonjs/extensions/pdbe/struct-ref-domain.js

@@ -64,9 +64,9 @@ var PDBeStructRefDomain;
         return (0, schema_1.toTable)(PDBeStructRefDomain.Schema.pdbe_struct_ref_domain, cat);
     }
     function attachFromCifOrApi(model, params) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var table, info, data;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (model.customProperties.has(PDBeStructRefDomain.Descriptor))

package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js

@@ -21,7 +21,7 @@ exports.PDBeStructureQualityReport = behavior_1.PluginBehavior.create({
         description: 'Data from wwPDB Validation Report, obtained via PDBe.'
     },
     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.StructureQualityReportProvider;

package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js

@@ -39,7 +39,7 @@ var StructureQualityReport;
         pdbe_structure_quality_report: {
             updated_datetime_utc: db_1.Column.Schema.str
         },
-        pdbe_structure_quality_report_issues: (0, tslib_1.__assign)((0, tslib_1.__assign)({ id: db_1.Column.Schema.int }, mmcif_extras_1.mmCIF_residueId_schema), { pdbx_PDB_model_num: db_1.Column.Schema.int, issue_type_group_id: db_1.Column.Schema.int }),
+        pdbe_structure_quality_report_issues: tslib_1.__assign(tslib_1.__assign({ id: db_1.Column.Schema.int }, mmcif_extras_1.mmCIF_residueId_schema), { pdbx_PDB_model_num: db_1.Column.Schema.int, issue_type_group_id: db_1.Column.Schema.int }),
         pdbe_structure_quality_report_issue_types: {
             group_id: db_1.Column.Schema.int,
             issue_type: db_1.Column.Schema.str
@@ -52,9 +52,9 @@ var StructureQualityReport;
     }
     StructureQualityReport.fromJson = fromJson;
     function fromServer(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, json, data;
-            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.serverUrl));
@@ -80,9 +80,9 @@ var StructureQualityReport;
     }
     StructureQualityReport.fromCif = fromCif;
     function fromCifOrServer(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 cif;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 cif = fromCif(ctx, model, props);
                 return [2 /*return*/, cif ? { value: cif } : fromServer(ctx, model, props)];
             });
@@ -158,12 +158,12 @@ exports.StructureQualityReportProvider = custom_model_property_1.CustomModelProp
     defaultParams: exports.StructureQualityReportParams,
     getParams: function (data) { return exports.StructureQualityReportParams; },
     isApplicable: function (data) { return StructureQualityReport.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.StructureQualityReportParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.StructureQualityReportParams)), props);
                     return [4 /*yield*/, StructureQualityReport.fromCifOrServer(ctx, data, p)];
                 case 1: return [2 /*return*/, _a.sent()];
             }

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts

@@ -24,6 +24,7 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;

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.d.ts

@@ -16,6 +16,7 @@ export declare const AssemblySymmetryParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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: