molstar 3.3.1 → 3.6.0

package/lib/commonjs/extensions/anvil/prop.js

@@ -17,7 +17,7 @@ var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var base_1 = require("../../mol-script/runtime/query/base");
 var symbol_1 = require("../../mol-script/language/symbol");
 var type_1 = require("../../mol-script/language/type");
-exports.MembraneOrientationParams = (0, tslib_1.__assign)({}, algorithm_1.ANVILParams);
+exports.MembraneOrientationParams = tslib_1.__assign({}, algorithm_1.ANVILParams);
 var MembraneOrientation;
 (function (MembraneOrientation) {
     var Tag;
@@ -52,13 +52,13 @@ exports.MembraneOrientationProvider = custom_structure_property_1.CustomStructur
     defaultParams: exports.MembraneOrientationParams,
     getParams: function (data) { return exports.MembraneOrientationParams; },
     isApplicable: function (data) { return true; },
-    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;
         var _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.MembraneOrientationParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.MembraneOrientationParams)), props);
                     _a = {};
                     return [4 /*yield*/, computeAnvil(ctx, data, p)];
                 case 1: return [2 /*return*/, (_a.value = _b.sent(), _a)];
@@ -67,12 +67,12 @@ exports.MembraneOrientationProvider = custom_structure_property_1.CustomStructur
     }); }
 });
 function computeAnvil(ctx, data, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, 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(algorithm_1.ANVILParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(algorithm_1.ANVILParams)), props);
                     return [4 /*yield*/, (0, algorithm_1.computeANVIL)(data, p).runInContext(ctx.runtime)];
                 case 1: return [2 /*return*/, _a.sent()];
             }

package/lib/commonjs/extensions/anvil/representation.d.ts

@@ -18,6 +18,7 @@ declare const BilayerPlanesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -98,6 +99,7 @@ export declare const MembraneOrientationParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 };
@@ -134,6 +136,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 };
@@ -170,6 +173,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 }, "membrane-orientation">;

package/lib/commonjs/extensions/anvil/representation.js

@@ -29,13 +29,13 @@ var SharedParams = {
     color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgrey),
     radiusFactor: param_definition_1.ParamDefinition.Numeric(1.2, { min: 0.1, max: 3.0, step: 0.01 }, { description: 'Scale the radius of the membrane layer' })
 };
-var BilayerPlanesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), SharedParams), { sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }) });
-var BilayerRimsParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), linesSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 50, step: 0.01 }), dashedLines: param_definition_1.ParamDefinition.Boolean(false) });
+var BilayerPlanesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }) });
+var BilayerRimsParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), linesSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 50, step: 0.01 }), dashedLines: param_definition_1.ParamDefinition.Boolean(false) });
 var MembraneOrientationVisuals = {
-    'bilayer-planes': function (ctx, getParams) { return (0, representation_3.ShapeRepresentation)(getBilayerPlanes, mesh_1.Mesh.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); }, modifyProps: function (p) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, p), { alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false })); } }); },
-    'bilayer-rims': function (ctx, getParams) { return (0, representation_3.ShapeRepresentation)(getBilayerRims, lines_1.Lines.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); }
+    'bilayer-planes': function (ctx, getParams) { return (0, representation_3.ShapeRepresentation)(getBilayerPlanes, mesh_1.Mesh.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); }, modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false })); } }); },
+    'bilayer-rims': function (ctx, getParams) { return (0, representation_3.ShapeRepresentation)(getBilayerRims, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); }
 };
-exports.MembraneOrientationParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, BilayerPlanesParams), BilayerRimsParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['bilayer-planes', 'bilayer-rims'], param_definition_1.ParamDefinition.objectToOptions(MembraneOrientationVisuals)) });
+exports.MembraneOrientationParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, BilayerPlanesParams), BilayerRimsParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['bilayer-planes', 'bilayer-rims'], param_definition_1.ParamDefinition.objectToOptions(MembraneOrientationVisuals)) });
 function getMembraneOrientationParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.MembraneOrientationParams);
 }

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

@@ -19,7 +19,7 @@ exports.CellPack = behavior_1.PluginBehavior.create({
         description: 'CellPack Model Loading and Viewing.'
     },
     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/cellpack/model.js

@@ -32,6 +32,7 @@ var color_1 = require("../../mol-util/color");
 var object_1 = require("../../mol-util/object");
 var data_source_1 = require("../../mol-util/data-source");
 var names_1 = require("../../mol-util/color/names");
+var schema_1 = require("../../mol-model-formats/structure/basic/schema");
 function getCellPackModelUrl(fileName, baseUrl) {
     return "".concat(baseUrl, "/results/").concat(fileName);
 }
@@ -44,9 +45,9 @@ var TrajectoryCache = /** @class */ (function () {
     return TrajectoryCache;
 }());
 function getModel(plugin, id, ingredient, baseUrl, trajCache, location, file) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var assetManager, modelIndex, surface, trajectory, assets, text, cif, binary, cif, text, pdb, data, e_1, _a, mmcif, asset, _b, mmcif, asset, data, model;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     assetManager = plugin.managers.asset;
@@ -159,9 +160,9 @@ function getModel(plugin, id, ingredient, baseUrl, trajCache, location, file) {
 }
 function getStructure(plugin, model, source, props) {
     if (props === void 0) { props = {}; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var structure, assembly, query, sel, asymIds, compiled, result;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     structure = structure_1.Structure.ofModel(model);
@@ -353,20 +354,21 @@ function getCifCurve(name, transforms, model) {
     };
 }
 function getCurve(plugin, name, ingredient, transforms, model) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var cif, curveModelTask, curveModel;
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     cif = getCifCurve(name, transforms, model);
-                    curveModelTask = mol_task_1.Task.create('Curve Model', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        var format, models;
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                    curveModelTask = mol_task_1.Task.create('Curve Model', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                        var format, basic, models;
+                        return tslib_1.__generator(this, function (_a) {
                             switch (_a.label) {
                                 case 0:
                                     format = mmcif_1.MmcifFormat.fromFrame(cif);
-                                    return [4 /*yield*/, (0, parser_1.createModels)(format.data.db, format, ctx)];
+                                    basic = (0, schema_1.createBasic)(format.data.db, true);
+                                    return [4 /*yield*/, (0, parser_1.createModels)(basic, format, ctx)];
                                 case 1:
                                     models = _a.sent();
                                     return [2 /*return*/, models.representative];
@@ -383,9 +385,9 @@ function getCurve(plugin, name, ingredient, transforms, model) {
     });
 }
 function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, trajCache, location) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var name, source, results, nbCurve, file, _a, model, assets, structure, bu, legacy, pcp, structureMean, m1, o, m, p, q, m;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     name = ingredient.name, source = ingredient.source, results = ingredient.results, nbCurve = ingredient.nbCurve;
@@ -469,9 +471,9 @@ function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, tr
 }
 function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles) {
     var _this = this;
-    return mol_task_1.Task.create('Create Packing Structure', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Packing Structure', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var ingredients, location, name, assets, trajCache, structures, colors, _a, _b, _i, iName, ingredientStructure, c, units, offsetInvariantId, offsetChainGroupId, _c, structures_1, s, maxInvariantId, maxChainGroupId, _d, _e, u, invariantId, chainGroupId, structure, i, il;
-        return (0, tslib_1.__generator)(this, function (_f) {
+        return tslib_1.__generator(this, function (_f) {
             switch (_f.label) {
                 case 0:
                     ingredients = packing.ingredients, location = packing.location, name = packing.name;
@@ -565,9 +567,9 @@ function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles)
 }
 exports.createStructureFromCellPack = createStructureFromCellPack;
 function handleHivRna(plugin, packings, baseUrl) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var i, il, url, json, points, curve0, j, jl;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     i = 0, il = packings.length;
@@ -601,9 +603,9 @@ function handleHivRna(plugin, packings, baseUrl) {
     });
 }
 function loadMembrane(plugin, name, state, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var file, fileName, _i, _a, f, cifileName, _b, _c, f, legacy_membrane, geometry_membrane, b, url, url, url, url, props, membrane, membraneParams, membrane, membraneParams;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0:
                     file = undefined;
@@ -709,9 +711,9 @@ function loadMembrane(plugin, name, state, params) {
     });
 }
 function handleMembraneSpheres(state, primitives) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var nSpheres, j;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     nSpheres = primitives.positions.length / 3;
@@ -738,9 +740,9 @@ function handleMembraneSpheres(state, primitives) {
     });
 }
 function loadPackings(plugin, runtime, state, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ingredientFiles, cellPackJson, resultsFile, url, file, modelFile, data, cellPackBuilder, cellPackObject, packings, i, il, p, packing, packingParams;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     ingredientFiles = params.ingredients || [];
@@ -889,8 +891,8 @@ exports.LoadCellPackModel = mol_state_1.StateAction.build({
     from: objects_1.PluginStateObject.Root
 })(function (_a, ctx) {
     var state = _a.state, params = _a.params;
-    return mol_task_1.Task.create('CellPack Loader', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('CellPack Loader', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, loadPackings(ctx, taskCtx, state, params)];
                 case 1:

package/lib/commonjs/extensions/cellpack/preset.js

@@ -22,10 +22,10 @@ exports.CellpackPackingPreset = (0, representation_preset_1.StructureRepresentat
     display: { name: 'CellPack Packing' },
     params: function () { return exports.CellpackPackingPresetParams; },
     apply: function (ref, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, reprProps, components, color, _a, update, builder, typeParams, representations;
             var _b;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -51,7 +51,7 @@ exports.CellpackPackingPreset = (0, representation_preset_1.StructureRepresentat
                         color = generate_1.CellPackGenerateColorThemeProvider.name;
                         _a = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, {}), update = _a.update, builder = _a.builder, typeParams = _a.typeParams;
                         representations = {
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: params.representation, typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), reprProps), color: color }, { tag: 'polymer' })
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: params.representation, typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), reprProps), color: color }, { tag: 'polymer' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 2:
@@ -71,10 +71,10 @@ exports.CellpackMembranePreset = (0, representation_preset_1.StructureRepresenta
     display: { name: 'CellPack Membrane' },
     params: function () { return exports.CellpackMembranePresetParams; },
     apply: function (ref, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, reprProps, components, _a, update, builder, typeParams, representations;
             var _b;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -95,7 +95,7 @@ exports.CellpackMembranePreset = (0, representation_preset_1.StructureRepresenta
                         }
                         _a = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, {}), update = _a.update, builder = _a.builder, typeParams = _a.typeParams;
                         representations = {
-                            membrane: builder.buildRepresentation(update, components.membrane, { type: 'gaussian-surface', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), reprProps), color: 'uniform', colorParams: { value: names_1.ColorNames.lightgrey } }, { tag: 'all' })
+                            membrane: builder.buildRepresentation(update, components.membrane, { type: 'gaussian-surface', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), reprProps), color: 'uniform', colorParams: { value: names_1.ColorNames.lightgrey } }, { tag: 'all' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 2:

package/lib/commonjs/extensions/cellpack/property.js

@@ -20,10 +20,10 @@ exports.CellPackInfoProvider = custom_structure_property_1.CustomStructureProper
     defaultParams: CellPackInfoParams,
     getParams: function (data) { return CellPackInfoParams; },
     isApplicable: function (data) { return true; },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, {
-                    value: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, CellPackInfoParams.info.defaultValue), props.info)
+                    value: tslib_1.__assign(tslib_1.__assign({}, CellPackInfoParams.info.defaultValue), props.info)
                 }];
         });
     }); }

package/lib/commonjs/extensions/cellpack/representation.d.ts

@@ -44,6 +44,7 @@ export declare const MBParams: {
     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/cellpack/representation.js

@@ -19,11 +19,11 @@ var mesh_builder_1 = require("../../mol-geo/geometry/mesh/mesh-builder");
 var sphere_1 = require("../../mol-geo/primitive/sphere");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var representation_2 = require("../../mol-repr/representation");
-var MembraneSphereParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), { cellColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), cellScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), radius: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), center: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(0, 0, 0)), quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params.quality), { isEssential: false }) });
+var MembraneSphereParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { cellColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), cellScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), radius: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), center: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(0, 0, 0)), quality: tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params.quality), { isEssential: false }) });
 var MembraneSphereVisuals = {
     'mesh': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getMBShape, mesh_1.Mesh.Utils); },
 };
-exports.MBParams = (0, tslib_1.__assign)({}, MembraneSphereParams);
+exports.MBParams = tslib_1.__assign({}, MembraneSphereParams);
 function getMBMesh(data, props, mesh) {
     var state = mesh_builder_1.MeshBuilder.createState(256, 128, mesh);
     var radius = props.radius;

package/lib/commonjs/extensions/cellpack/state.js

@@ -23,7 +23,7 @@ var binary_1 = require("../../mol-io/common/binary");
 var util_1 = require("./util");
 exports.DefaultCellPackBaseUrl = 'https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0';
 var CellPack = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(CellPack, _super);
+    tslib_1.__extends(CellPack, _super);
     function CellPack() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
@@ -45,9 +45,9 @@ var ParseCellPack = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params, cache = _a.cache;
-        return mol_task_1.Task.create('Parse CellPack', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Parse CellPack', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var cell, counter_id, fiber_counter_id, comp_counter, packings, compartments, cytoplasme, iName, name_1, _a, surface, interior, filename, compartment, iName, iName, options, resultsAsset, url, results, buffer, numbers, ninst, npoints, ncurve, offset, pos, quat, i, x, y, z, ingr_id, pid, ctr_pos, ctr_info, curve_ids, counter, ctr_points, prev_ctype, prev_cid, i, x, y, z, cid, ctype, pid_1, cname_1, pid_2, cname_2, pid, cname;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         cell = a.data;
@@ -220,9 +220,9 @@ var ParseCellPack = objects_1.PluginStateTransform.BuiltIn({
         }); });
     },
     dispose: function (_a) {
-        var _b, _c;
+        var _b;
         var cache = _a.cache;
-        (_c = (_b = cache) === null || _b === void 0 ? void 0 : _b.asset) === null || _c === void 0 ? void 0 : _c.dispose();
+        (_b = cache === null || cache === void 0 ? void 0 : cache.asset) === null || _b === void 0 ? void 0 : _b.dispose();
     },
 });
 exports.ParseCellPack = ParseCellPack;
@@ -243,9 +243,9 @@ var StructureFromCellpack = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params, cache = _a.cache;
-        return mol_task_1.Task.create('Structure from CellPack', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Structure from CellPack', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var packing, ingredientFiles, _i, _a, file, _b, structure, assets, colors;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         packing = a.data.packings[params.packing];
@@ -303,9 +303,9 @@ var StructureFromAssemblies = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Build Structure', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Build Structure', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var model, initial_structure, structures, structure, symmetry, _i, _a, a_1, s, builder, offsetInvariantId, _b, structures_1, s, maxInvariantId, _c, _d, u, invariantId, i, il;
-            return (0, tslib_1.__generator)(this, function (_e) {
+            return tslib_1.__generator(this, function (_e) {
                 switch (_e.label) {
                     case 0:
                         model = a.data;
@@ -377,15 +377,15 @@ exports.CreateCompartmentSphere = CreateTransformer({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Compartment Sphere', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Compartment Sphere', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var data, repr;
             var _a;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         data = params;
-                        repr = (0, representation_1.MBRepresentation)((0, tslib_1.__assign)({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return (representation_1.MBParams); });
-                        return [4 /*yield*/, repr.createOrUpdate((0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { quality: 'custom', xrayShaded: true, doubleSided: true }), data).runInContext(ctx)];
+                        repr = (0, representation_1.MBRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return (representation_1.MBParams); });
+                        return [4 /*yield*/, repr.createOrUpdate(tslib_1.__assign(tslib_1.__assign({}, params), { quality: 'custom', xrayShaded: true, doubleSided: true }), data).runInContext(ctx)];
                     case 1:
                         _b.sent();
                         return [2 /*return*/, new objects_1.PluginStateObject.Shape.Representation3D({ repr: repr, sourceData: a }, { label: data.label })];

package/lib/commonjs/extensions/cellpack/util.js

@@ -13,9 +13,9 @@ var parser_1 = require("../../mol-io/reader/pdb/parser");
 var assets_1 = require("../../mol-util/assets");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function parseCif(plugin, data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var comp, parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     comp = cif_1.CIF.parse(data);
@@ -31,9 +31,9 @@ function parseCif(plugin, data) {
 }
 exports.parseCif = parseCif;
 function parsePDBfile(plugin, data, id) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var comp, parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     comp = (0, parser_1.parsePDB)(data, id);
@@ -49,10 +49,10 @@ function parsePDBfile(plugin, data, id) {
 }
 exports.parsePDBfile = parsePDBfile;
 function downloadCif(plugin, url, isBinary, assetManager) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var type, asset;
         var _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     type = isBinary ? 'binary' : 'string';
@@ -67,10 +67,10 @@ function downloadCif(plugin, url, isBinary, assetManager) {
     });
 }
 function downloadPDB(plugin, url, id, assetManager) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var asset;
         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*/, assetManager.resolve(assets_1.Asset.getUrlAsset(assetManager, url), 'string').run()];
                 case 1:
@@ -83,9 +83,9 @@ function downloadPDB(plugin, url, id, assetManager) {
     });
 }
 function getFromPdb(plugin, pdbId, assetManager) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _a, cif, asset;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, downloadCif(plugin, "https://models.rcsb.org/".concat(pdbId, ".bcif"), true, assetManager)];
                 case 1:
@@ -97,10 +97,10 @@ function getFromPdb(plugin, pdbId, assetManager) {
 }
 exports.getFromPdb = getFromPdb;
 function getFromOPM(plugin, pdbId, assetManager) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var asset;
         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*/, plugin.runTask(assetManager.resolve(assets_1.Asset.getUrlAsset(assetManager, "https://opm-assets.storage.googleapis.com/pdb/".concat(pdbId.toLowerCase(), ".pdb")), 'string'))];
                 case 1:
@@ -114,9 +114,9 @@ function getFromOPM(plugin, pdbId, assetManager) {
 }
 exports.getFromOPM = getFromOPM;
 function getFromCellPackDB(plugin, id, baseUrl, assetManager) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var isBinary, _a, cif, asset, name_1;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     if (!(id.toLowerCase().endsWith('.cif') || id.toLowerCase().endsWith('.bcif'))) return [3 /*break*/, 2];

package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js

@@ -28,18 +28,18 @@ exports.DnatcoConfalPyramidsPreset = (0, representation_preset_1.StructureRepres
     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, model, _b, components, representations, pyramids, _c, update, builder, typeParams, pyramidsRepr;
             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);
                         model = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data.model;
                         if (!structureCell || !model)
                             return [2 /*return*/, {}];
-                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Confal Pyramids', 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('Confal Pyramids', 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*/, property_1.ConfalPyramidsProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, model)];
                                         case 1:
@@ -50,7 +50,7 @@ exports.DnatcoConfalPyramidsPreset = (0, representation_preset_1.StructureRepres
                             }); }))];
                     case 1:
                         _d.sent();
-                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, (0, tslib_1.__assign)({}, params), plugin)];
+                        return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__assign({}, params), plugin)];
                     case 2:
                         _b = _d.sent(), components = _b.components, representations = _b.representations;
                         return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(structureCell, 'nucleic', { label: 'Confal Pyramids' })];
@@ -62,7 +62,7 @@ exports.DnatcoConfalPyramidsPreset = (0, representation_preset_1.StructureRepres
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 4:
                         _d.sent();
-                        return [2 /*return*/, { components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, components), { pyramids: pyramids }), representations: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, representations), { pyramidsRepr: pyramidsRepr }) }];
+                        return [2 /*return*/, { components: tslib_1.__assign(tslib_1.__assign({}, components), { pyramids: pyramids }), representations: tslib_1.__assign(tslib_1.__assign({}, representations), { pyramidsRepr: pyramidsRepr }) }];
                 }
             });
         });
@@ -76,7 +76,7 @@ exports.DnatcoConfalPyramids = behavior_1.PluginBehavior.create({
         description: 'Schematic depiction of conformer class and confal value.',
     },
     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 = property_1.ConfalPyramidsProvider;