molstar 3.3.0 → 3.5.0

package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js

@@ -8,11 +8,11 @@ var jsx_runtime_1 = require("react/jsx-runtime");
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-var ReactDOM = (0, tslib_1.__importStar)(require("react-dom"));
+var ReactDOM = tslib_1.__importStar(require("react-dom"));
 var plugin_1 = require("../../../mol-plugin-ui/plugin");
 var update_transform_1 = require("../../../mol-plugin-ui/state/update-transform");
 var helpers_1 = require("../helpers");
 function volumeStreamingControls(plugin, parent) {
-    ReactDOM.render((0, jsx_runtime_1.jsx)(plugin_1.PluginContextContainer, (0, tslib_1.__assign)({ plugin: plugin }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.TransformUpdaterControl, { nodeRef: helpers_1.StateElements.VolumeStreaming }, void 0) }), void 0), parent);
+    ReactDOM.render((0, jsx_runtime_1.jsx)(plugin_1.PluginContextContainer, tslib_1.__assign({ plugin: plugin }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.TransformUpdaterControl, { nodeRef: helpers_1.StateElements.VolumeStreaming }) })), parent);
 }
 exports.volumeStreamingControls = volumeStreamingControls;

package/lib/commonjs/examples/task.js

@@ -10,13 +10,13 @@ var tslib_1 = require("tslib");
 var mol_task_1 = require("../mol-task");
 var now_1 = require("../mol-util/now");
 function test1() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var t, r;
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    t = mol_task_1.Task.create('test', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
+                    t = mol_task_1.Task.create('test', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () { return tslib_1.__generator(this, function (_a) {
                         return [2 /*return*/, 1];
                     }); }); });
                     return [4 /*yield*/, t.run()];
@@ -45,8 +45,8 @@ function messageTree(root, prefix) {
 }
 function createTask(delayMs, r) {
     var _this = this;
-    return mol_task_1.Task.create('delayed value ' + r, function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('delayed value ' + r, function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     ctx.update("Processing delayed ".concat(r, " after ").concat(delayMs, "ms"), true);
@@ -65,8 +65,8 @@ function createTask(delayMs, r) {
 }
 function abortAfter(delay) {
     var _this = this;
-    return mol_task_1.Task.create('abort after ' + delay, function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('abort after ' + delay, function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, mol_task_1.Scheduler.delay(delay)];
                 case 1:
@@ -79,9 +79,9 @@ function abortAfter(delay) {
 exports.abortAfter = abortAfter;
 function testTree() {
     var _this = this;
-    return mol_task_1.Task.create('test o', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('test o', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var c1, c2, c3, r, _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0: return [4 /*yield*/, mol_task_1.Scheduler.delay(250)];
                 case 1:
@@ -143,16 +143,16 @@ function processChunk(n, state) {
     state.current = toProcess;
     return toProcess - start;
 }
-exports.ms = (0, mol_task_1.MultistepTask)('ms-task', ['step 1', 'step 2', 'step 3'], function (p, step, ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+exports.ms = (0, mol_task_1.MultistepTask)('ms-task', ['step 1', 'step 2', 'step 3'], function (p, step, ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
     var child;
-    return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__generator(this, function (_a) {
         switch (_a.label) {
             case 0: return [4 /*yield*/, step(0)];
             case 1:
                 _a.sent();
-                child = mol_task_1.Task.create('chunked', function (ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+                child = mol_task_1.Task.create('chunked', function (ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
                     var s;
-                    return (0, tslib_1.__generator)(this, function (_a) {
+                    return tslib_1.__generator(this, function (_a) {
                         switch (_a.label) {
                             case 0: return [4 /*yield*/, (0, mol_task_1.chunkedSubtask)(ctx, 25, { i: 0, current: 0, total: 125 }, processChunk, function (ctx, s, p) { return ctx.update('chunk test ' + p); })];
                             case 1:
@@ -196,9 +196,9 @@ exports.abortingObserver = abortingObserver;
 function logP(p) { console.log(messageTree(p.root)); }
 exports.logP = logP;
 function test() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var m, 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]);

package/lib/commonjs/extensions/alpha-orbitals/collocation.js

@@ -13,9 +13,9 @@ var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var array_1 = require("../../mol-util/array");
 var spherical_functions_1 = require("./spherical-functions");
 function sphericalCollocation(grid, orbital, taskCtx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _a, basis, sphericalOrder, cutoffThreshold, baseCount, _i, _b, atom, _c, _d, shell, _e, _f, L, matrix, baseIndex, _g, _h, atom, _j, _k, shell, amIndex, _l, _m, L, alpha;
-        return (0, tslib_1.__generator)(this, function (_o) {
+        return tslib_1.__generator(this, function (_o) {
             switch (_o.label) {
                 case 0:
                     _a = grid.params, basis = _a.basis, sphericalOrder = _a.sphericalOrder, cutoffThreshold = _a.cutoffThreshold;

package/lib/commonjs/extensions/alpha-orbitals/data-model.js

@@ -25,7 +25,7 @@ function initCubeGrid(params) {
     var count = geometry.length;
     var box = geometry_1.Box3D.expand((0, geometry_1.Box3D)(), geometry_1.Box3D.fromVec3Array((0, geometry_1.Box3D)(), geometry), linear_algebra_1.Vec3.create(expand, expand, expand));
     var size = geometry_1.Box3D.size((0, linear_algebra_1.Vec3)(), box);
-    var spacingThresholds = typeof spacing === 'number' ? [[0, spacing]] : (0, tslib_1.__spreadArray)([], spacing, true);
+    var spacingThresholds = typeof spacing === 'number' ? [[0, spacing]] : tslib_1.__spreadArray([], spacing, true);
     spacingThresholds.sort(function (a, b) { return b[0] - a[0]; });
     var s = 0.4;
     for (var i = 0; i <= spacingThresholds.length; i++) {

package/lib/commonjs/extensions/alpha-orbitals/density.js

@@ -14,9 +14,9 @@ var data_model_1 = require("./data-model");
 var compute_1 = require("./gpu/compute");
 function createSphericalCollocationDensityGrid(params, orbitals, webgl) {
     var _this = this;
-    return mol_task_1.Task.create('Spherical Collocation Grid', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Spherical Collocation Grid', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var cubeGrid, matrix, grid, isovalues;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     cubeGrid = (0, data_model_1.initCubeGrid)(params);

package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js

@@ -34,13 +34,13 @@ var Orbitals = (0, grid3d_1.createGrid3dComputeRenderable)({
     }
 });
 var Density = (0, grid3d_1.createGrid3dComputeRenderable)({
-    schema: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, Schema), { uOccupancy: (0, schema_1.UniformSpec)('f') }),
+    schema: tslib_1.__assign(tslib_1.__assign({}, Schema), { uOccupancy: (0, schema_1.UniformSpec)('f') }),
     loopBounds: ['uNCenters', 'uMaxCoeffs'],
     mainCode: shader_frag_1.MAIN,
     utilCode: shader_frag_1.UTILS,
     returnCode: 'current + uOccupancy * v * v',
     values: function (params) {
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, createTextureData(params.grid, params.orbitals[0])), { uOccupancy: 0 });
+        return tslib_1.__assign(tslib_1.__assign({}, createTextureData(params.grid, params.orbitals[0])), { uOccupancy: 0 });
     },
     cumulative: {
         states: function (params) {

package/lib/commonjs/extensions/alpha-orbitals/orbitals.js

@@ -18,9 +18,9 @@ var compute_1 = require("./gpu/compute");
 // setDebugMode(true);
 function createSphericalCollocationGrid(params, orbital, webgl) {
     var _this = this;
-    return mol_task_1.Task.create('Spherical Collocation Grid', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Spherical Collocation Grid', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var cubeGrid, matrix, grid, isovalues;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     cubeGrid = (0, data_model_1.initCubeGrid)(params);

package/lib/commonjs/extensions/alpha-orbitals/transforms.js

@@ -20,7 +20,7 @@ var representation_1 = require("../../mol-plugin-state/transforms/representation
 var data_model_1 = require("./data-model");
 var density_1 = require("./density");
 var BasisAndOrbitals = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(BasisAndOrbitals, _super);
+    tslib_1.__extends(BasisAndOrbitals, _super);
     function BasisAndOrbitals() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
@@ -97,18 +97,18 @@ exports.CreateOrbitalVolume = objects_1.PluginStateTransform.BuiltIn({
     to: objects_1.PluginStateObject.Volume.Data,
     params: function (a) {
         if (!a) {
-            return (0, tslib_1.__assign)({ index: param_definition_1.ParamDefinition.Numeric(0) }, CreateOrbitalVolumeParamBase);
+            return tslib_1.__assign({ index: param_definition_1.ParamDefinition.Numeric(0) }, CreateOrbitalVolumeParamBase);
         }
-        return (0, tslib_1.__assign)({ index: param_definition_1.ParamDefinition.Select(0, a.data.orbitals.map(function (o, i) { return [i, "[".concat(i + 1, "] ").concat(o.energy.toFixed(4))]; })) }, CreateOrbitalVolumeParamBase);
+        return tslib_1.__assign({ index: param_definition_1.ParamDefinition.Select(0, a.data.orbitals.map(function (o, i) { return [i, "[".concat(i + 1, "] ").concat(o.energy.toFixed(4))]; })) }, CreateOrbitalVolumeParamBase);
     }
 })({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Orbital Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Orbital Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var data, volume;
             var _a, _b, _c, _d, _e;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0: return [4 /*yield*/, (0, orbitals_1.createSphericalCollocationGrid)({
                             basis: a.data.basis,
@@ -144,10 +144,10 @@ exports.CreateOrbitalDensityVolume = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Orbital Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Orbital Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var data, volume;
             var _a, _b, _c, _d, _e;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0: return [4 /*yield*/, (0, density_1.createSphericalCollocationDensityGrid)({
                             basis: a.data.basis,
@@ -194,10 +194,10 @@ exports.CreateOrbitalRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, srcParams = _a.params;
-        return mol_task_1.Task.create('Orbitals Representation 3D', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Orbitals Representation 3D', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var params, propertyCtx, provider, props, repr;
             var _a;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         params = volumeParams(plugin, a, srcParams);
@@ -210,7 +210,7 @@ exports.CreateOrbitalRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
                         _b.label = 2;
                     case 2:
                         props = params.type.params || {};
-                        repr = provider.factory((0, tslib_1.__assign)({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.volume.themes), provider.getParams);
+                        repr = provider.factory(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.volume.themes), provider.getParams);
                         repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
                         return [4 /*yield*/, repr.createOrUpdate(props, a.data).runInContext(ctx)];
                     case 3:
@@ -224,13 +224,13 @@ exports.CreateOrbitalRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
     update: function (_a, plugin) {
         var _this = this;
         var a = _a.a, b = _a.b, srcParams = _a.newParams;
-        return mol_task_1.Task.create('Orbitals Representation 3D', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Orbitals Representation 3D', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var newParams, props;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         newParams = volumeParams(plugin, a, srcParams);
-                        props = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, b.data.repr.props), newParams.type.params);
+                        props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams.type.params);
                         b.data.repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
                         return [4 /*yield*/, b.data.repr.createOrUpdate(props, a.data).runInContext(ctx)];
                     case 1:

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

@@ -48,8 +48,8 @@ var TMDET_DEFINITION = new Set(['LEU', 'ILE', 'VAL', 'PHE', 'MET', 'GLY', 'TRP',
  */
 function computeANVIL(structure, props) {
     var _this = this;
-    return mol_task_1.Task.create('Compute Membrane Orientation', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Compute Membrane Orientation', 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*/, calculate(runtime, structure, props)];
                 case 1: return [2 /*return*/, _a.sent()];
@@ -74,12 +74,12 @@ var v3sub = linear_algebra_1.Vec3.sub;
 var v3zero = linear_algebra_1.Vec3.zero;
 var centroidHelper = new centroid_helper_1.CentroidHelper();
 function initialize(structure, props, accessibleSurfaceArea) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         function isPartOfEntity(l) {
             return !structure_1.Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_seq_id.valueKind(l.unit.residueIndex[l.element]) === 0;
         }
         var l, _a, label_atom_id, label_comp_id, x, y, z, asaCutoff, offsets, exposed, hydrophobic, definition, vec, i, il, unit, elements, j, jl, eI, centroid, k, kl, extent;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             l = structure_1.StructureElement.Location.create(structure);
             _a = structure_1.StructureProperties.atom, label_atom_id = _a.label_atom_id, label_comp_id = _a.label_comp_id, x = _a.x, y = _a.y, z = _a.z;
             asaCutoff = props.asaCutoff / 100;
@@ -128,17 +128,17 @@ function initialize(structure, props, accessibleSurfaceArea) {
                 centroidHelper.radiusStep(vec);
             }
             extent = 1.2 * Math.sqrt(centroidHelper.radiusSq);
-            return [2 /*return*/, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, props), { structure: structure, offsets: offsets, exposed: exposed, hydrophobic: hydrophobic, centroid: centroid, extent: extent, large: offsets.length > LARGE_CA_THRESHOLD })];
+            return [2 /*return*/, tslib_1.__assign(tslib_1.__assign({}, props), { structure: structure, offsets: offsets, exposed: exposed, hydrophobic: hydrophobic, centroid: centroid, extent: extent, large: offsets.length > LARGE_CA_THRESHOLD })];
         });
     });
 }
 function calculate(runtime, structure, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var asaProps, accessibleSurfaceArea, ctx, initialHphobHphil, initialMembrane, refinedMembrane, membrane, normalVector, center, extent;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    asaProps = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(accessible_surface_area_1.AccessibleSurfaceAreaParams)), { probeSize: 4.0, traceOnly: true, numberOfSpherePoints: 184 });
+                    asaProps = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(accessible_surface_area_1.AccessibleSurfaceAreaParams)), { probeSize: 4.0, traceOnly: true, numberOfSpherePoints: 184 });
                     return [4 /*yield*/, shrake_rupley_1.AccessibleSurfaceArea.compute(structure, asaProps).runInContext(runtime)];
                 case 1:
                     accessibleSurfaceArea = _a.sent();
@@ -203,9 +203,9 @@ var MembraneCandidate;
     MembraneCandidate.scored = scored;
 })(MembraneCandidate || (MembraneCandidate = {}));
 function findMembrane(runtime, message, ctx, spherePoints, initialStats) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var centroid, stepSize, minThickness, maxThickness, large, membrane, qmax, diam, n, nl, spherePoint, diamNorm, sliceStats, qvartemp, i, il, c1, c2, stats, jmax, width, widthl, i, il, hphob, hphil, j, ij, stats, qvaltest;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     centroid = ctx.centroid, stepSize = ctx.stepSize, minThickness = ctx.minThickness, maxThickness = ctx.maxThickness, large = ctx.large;
@@ -274,9 +274,9 @@ function findMembrane(runtime, message, ctx, spherePoints, initialStats) {
 }
 /** Adjust membrane thickness by maximizing the number of membrane segments. */
 function adjustThickness(runtime, message, ctx, membrane, initialHphobHphil) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var minThickness, large, step, maxThickness, maxNos, optimalThickness, n, nl, p, temp, nos;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     minThickness = ctx.minThickness, large = ctx.large;
@@ -296,7 +296,7 @@ function adjustThickness(runtime, message, ctx, membrane, initialHphobHphil) {
                     _a.sent();
                     _a.label = 3;
                 case 3:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, ctx), { maxThickness: maxThickness, stepSize: step });
+                    p = tslib_1.__assign(tslib_1.__assign({}, ctx), { maxThickness: maxThickness, stepSize: step });
                     return [4 /*yield*/, findMembrane(runtime, void 0, p, [membrane.spherePoint], initialHphobHphil)];
                 case 4:
                     temp = _a.sent();

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

@@ -29,7 +29,7 @@ exports.ANVILMembraneOrientation = behavior_1.PluginBehavior.create({
         description: 'Data calculated with ANVIL algorithm.'
     },
     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.MembraneOrientationProvider;
@@ -98,7 +98,7 @@ var MembraneOrientation3D = 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.MembraneOrientationParams);
+        return tslib_1.__assign({}, representation_1.MembraneOrientationParams);
     }
 })({
     canAutoUpdate: function (_a) {
@@ -108,15 +108,15 @@ var MembraneOrientation3D = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a, plugin) {
         var _this = this;
         var a = _a.a, params = _a.params;
-        return mol_task_1.Task.create('Membrane Orientation', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Membrane Orientation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var repr;
             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.MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data)];
                     case 1:
                         _b.sent();
-                        repr = (0, representation_1.MembraneOrientationRepresentation)((0, tslib_1.__assign)({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return representation_1.MembraneOrientationParams; });
+                        repr = (0, representation_1.MembraneOrientationRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return representation_1.MembraneOrientationParams; });
                         return [4 /*yield*/, repr.createOrUpdate(params, a.data).runInContext(ctx)];
                     case 2:
                         _b.sent();
@@ -128,14 +128,14 @@ var MembraneOrientation3D = 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('Membrane Orientation', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Membrane Orientation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var props;
-            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.MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data)];
                     case 1:
                         _a.sent();
-                        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();
@@ -162,10 +162,10 @@ exports.MembraneOrientationPreset = (0, representation_preset_1.StructureReprese
     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, membraneOrientation, 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);
@@ -173,8 +173,8 @@ exports.MembraneOrientationPreset = (0, representation_preset_1.StructureReprese
                         if (!structureCell || !structure)
                             return [2 /*return*/, {}];
                         if (!!prop_1.MembraneOrientationProvider.get(structure).value) return [3 /*break*/, 2];
-                        return [4 /*yield*/, plugin.runTask(mol_task_1.Task.create('Membrane Orientation', 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('Membrane Orientation', 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.MembraneOrientationProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, structure)];
                                         case 1:
@@ -190,10 +190,10 @@ exports.MembraneOrientationPreset = (0, representation_preset_1.StructureReprese
                     case 3:
                         membraneOrientation = _b.sent();
                         colorTheme = hydrophobicity_1.HydrophobicityColorThemeProvider.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 4:
                         preset = _b.sent();
-                        return [2 /*return*/, { components: preset.components, representations: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, preset.representations), { membraneOrientation: membraneOrientation }) }];
+                        return [2 /*return*/, { components: preset.components, representations: tslib_1.__assign(tslib_1.__assign({}, preset.representations), { membraneOrientation: membraneOrientation }) }];
                 }
             });
         });

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.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;
         }