molstar 3.2.0 → 3.4.0

package/lib/commonjs/examples/proteopedia-wrapper/helpers.js

@@ -11,9 +11,9 @@ var symmetry_1 = require("../../mol-model-formats/structure/property/symmetry");
 var ModelInfo;
 (function (ModelInfo) {
     function getPreferredAssembly(ctx, model) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var id, src, json, data, assemblies, _i, assemblies_1, asm, e_1;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (model.entryId.length <= 3)
@@ -47,9 +47,9 @@ var ModelInfo;
         });
     }
     function get(ctx, model, checkPreferred) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var residueCount, residueOffsets, chainIndex, pref, hetResidues, hetMap, rI, cI, eI, entityType, comp_id, lig, preferredAssemblyId, symmetry;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         residueCount = model.atomicHierarchy.residues._rowCount;
@@ -106,4 +106,3 @@ var StateElements;
     StateElements["HetGroupFocus"] = "het-group-focus";
     StateElements["HetGroupFocusGroup"] = "het-group-focus-group";
 })(StateElements = exports.StateElements || (exports.StateElements = {}));
-//# sourceMappingURL=helpers.js.map

package/lib/commonjs/examples/proteopedia-wrapper/index.js

@@ -6,7 +6,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var ReactDOM = (0, tslib_1.__importStar)(require("react-dom"));
+var ReactDOM = tslib_1.__importStar(require("react-dom"));
 var canvas3d_1 = require("../../mol-canvas3d/canvas3d");
 var model_index_1 = require("../../mol-plugin-state/animation/built-in/model-index");
 var structure_representation_params_1 = require("../../mol-plugin-state/helpers/structure-representation-params");
@@ -60,9 +60,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
             }
         };
         this.coloring = {
-            evolutionaryConservation: function (params) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            evolutionaryConservation: function (params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var state, tree, colorTheme;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             if (!(!params || !params.keepStyle)) return [3 /*break*/, 2];
@@ -75,10 +75,10 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
                             tree = state.build();
                             colorTheme = { name: annotation_1.EvolutionaryConservation.propertyProvider.descriptor.name, params: this.plugin.representation.structure.themes.colorThemeRegistry.get(annotation_1.EvolutionaryConservation.propertyProvider.descriptor.name).defaultValues };
                             if (!params || !!params.sequence) {
-                                tree.to(helpers_1.StateElements.SequenceVisual).update(transforms_1.StateTransforms.Representation.StructureRepresentation3D, function (old) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, old), { colorTheme: colorTheme })); });
+                                tree.to(helpers_1.StateElements.SequenceVisual).update(transforms_1.StateTransforms.Representation.StructureRepresentation3D, function (old) { return (tslib_1.__assign(tslib_1.__assign({}, old), { colorTheme: colorTheme })); });
                             }
                             if (params && !!params.het) {
-                                tree.to(helpers_1.StateElements.HetVisual).update(transforms_1.StateTransforms.Representation.StructureRepresentation3D, function (old) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, old), { colorTheme: colorTheme })); });
+                                tree.to(helpers_1.StateElements.HetVisual).update(transforms_1.StateTransforms.Representation.StructureRepresentation3D, function (old) { return (tslib_1.__assign(tslib_1.__assign({}, old), { colorTheme: colorTheme })); });
                             }
                             return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: tree })];
                         case 3:
@@ -90,9 +90,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         };
         this.experimentalDataElement = void 0;
         this.experimentalData = {
-            init: function (parent) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            init: function (parent) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var asm, params;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             asm = this.state.select(helpers_1.StateElements.Assembly)[0].obj;
@@ -127,9 +127,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
                 commands_1.PluginCommands.State.Update(_this.plugin, { state: _this.state, tree: update });
                 commands_1.PluginCommands.Camera.Reset(_this.plugin, {});
             },
-            focusFirst: function (compId, options) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            focusFirst: function (compId, options) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var update, core, surroundings, group, asm, coreSel, waters, exclude, onlySurroundings, focus, sphere, radius, snapshot;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             if (!this.state.transforms.has(helpers_1.StateElements.Assembly))
@@ -196,9 +196,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
             },
             download: function (type, params) {
                 if (type === void 0) { type = 'molj'; }
-                return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var data;
-                    return (0, tslib_1.__generator)(this, function (_a) {
+                    return tslib_1.__generator(this, function (_a) {
                         switch (_a.label) {
                             case 0: return [4 /*yield*/, this.plugin.managers.snapshot.serialize({ type: type, params: params })];
                             case 1:
@@ -211,16 +211,16 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
             },
             fetch: function (url, type) {
                 if (type === void 0) { type = 'molj'; }
-                return (0, tslib_1.__awaiter)(_this, void 0, void 0, 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, 3, , 4]);
                                 return [4 /*yield*/, this.plugin.runTask(this.plugin.fetch({ url: url, type: 'binary' }))];
                             case 1:
                                 data = _a.sent();
-                                this.loadedParams = (0, tslib_1.__assign)({}, this.emptyLoadedParams);
+                                this.loadedParams = tslib_1.__assign({}, this.emptyLoadedParams);
                                 return [4 /*yield*/, this.plugin.managers.snapshot.open(new File([data], "state.".concat(type)))];
                             case 2: return [2 /*return*/, _a.sent()];
                             case 3:
@@ -235,13 +235,13 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         };
     }
     MolStarProteopediaWrapper.prototype.init = function (target, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var _a, customColoring;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
                                     model_index_1.AnimateModelIndex
                                 ], layout: {
                                     initial: {
@@ -370,9 +370,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         return cell.obj.data;
     };
     MolStarProteopediaWrapper.prototype.doInfo = function (checkPreferredAssembly) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var model, info;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         model = this.getObj('model');
@@ -392,9 +392,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
     };
     MolStarProteopediaWrapper.prototype.load = function (_a) {
         var url = _a.url, _b = _a.format, format = _b === void 0 ? 'cif' : _b, _c = _a.assemblyId, assemblyId = _c === void 0 ? '' : _c, _d = _a.isBinary, isBinary = _d === void 0 ? false : _d, representationStyle = _a.representationStyle;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var loadType, state, modelTree, info, asmId, structureTree, tree, info, asmId, props_1;
-            return (0, tslib_1.__generator)(this, function (_e) {
+            return tslib_1.__generator(this, function (_e) {
                 switch (_e.label) {
                     case 0:
                         loadType = 'full';
@@ -438,7 +438,7 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
                                 params: {}
                             }
                         };
-                        tree.to(helpers_1.StateElements.Assembly).update(transforms_1.StateTransforms.Model.StructureFromModel, function (p) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, p), props_1)); });
+                        tree.to(helpers_1.StateElements.Assembly).update(transforms_1.StateTransforms.Model.StructureFromModel, function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), props_1)); });
                         return [4 /*yield*/, this.applyState(tree)];
                     case 7:
                         _e.sent();
@@ -453,9 +453,9 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         });
     };
     MolStarProteopediaWrapper.prototype.updateStyle = function (style, partial) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var tree;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         tree = this.visual(style, partial);
@@ -473,7 +473,7 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         if (!this.plugin.canvas3d)
             return;
         var renderer = this.plugin.canvas3d.props.renderer;
-        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, renderer), { backgroundColor: (0, color_1.Color)(color) }) } });
+        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: tslib_1.__assign(tslib_1.__assign({}, renderer), { backgroundColor: (0, color_1.Color)(color) }) } });
     };
     MolStarProteopediaWrapper.prototype.toggleSpin = function () {
         if (!this.plugin.canvas3d)
@@ -481,7 +481,7 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         var trackball = this.plugin.canvas3d.props.trackball;
         commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, {
             settings: {
-                trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { animate: trackball.animate.name === 'spin'
+                trackball: tslib_1.__assign(tslib_1.__assign({}, trackball), { animate: trackball.animate.name === 'spin'
                         ? { name: 'off', params: {} }
                         : { name: 'spin', params: { speed: 1 } } })
             }
@@ -495,4 +495,3 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
     return MolStarProteopediaWrapper;
 }());
 window.MolStarProteopediaWrapper = MolStarProteopediaWrapper;
-//# sourceMappingURL=index.js.map

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

@@ -8,12 +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;
-//# sourceMappingURL=controls.js.map

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]);
@@ -218,4 +218,3 @@ function test() {
 }
 test();
 // testObs();
-//# sourceMappingURL=task.js.map

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;
@@ -131,4 +131,3 @@ function getRadiusBox(grid, center, radius) {
     linear_algebra_1.Vec3.min(max, max, linear_algebra_1.Vec3.subScalar((0, linear_algebra_1.Vec3)(), grid.dimensions, 1));
     return [min, max];
 }
-//# sourceMappingURL=collocation.js.map

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++) {
@@ -66,4 +66,3 @@ function createGrid(gridInfo, values, axisOrder) {
     return grid;
 }
 exports.createGrid = createGrid;
-//# sourceMappingURL=data-model.js.map

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);
@@ -110,4 +110,3 @@ function computeDensityIsocontourValues(input, cumulativeThreshold) {
     };
 }
 exports.computeDensityIsocontourValues = computeDensityIsocontourValues;
-//# sourceMappingURL=density.js.map

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) {
@@ -154,4 +154,3 @@ function createTextureData(grid, orbital) {
         tAlpha: { width: baseCount, height: 1, array: alpha },
     };
 }
-//# sourceMappingURL=compute.js.map

package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js

@@ -8,4 +8,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MAIN = exports.UTILS = void 0;
 exports.UTILS = "\nfloat L1(vec3 p, float a0, float a1, float a2) {\n    return a0 * p.z + a1 * p.x + a2 * p.y;\n}\n\nfloat L2(vec3 p, float a0, float a1, float a2, float a3, float a4) {\n    float x = p.x, y = p.y, z = p.z;\n    float xx = x * x, yy = y * y, zz = z * z;\n    return (\n        a0 * (-0.5 * xx - 0.5 * yy + zz) +\n        a1 * (1.7320508075688772 * x * z) +\n        a2 * (1.7320508075688772 * y * z) +\n        a3 * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +\n        a4 * (1.7320508075688772 * x * y)\n    );\n}\n\nfloat L3(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6) {\n    float x = p.x, y = p.y, z = p.z;\n    float xx = x * x, yy = y * y, zz = z * z;\n    float xxx = xx * x, yyy = yy * y, zzz = zz * z;\n    return (\n        a0 * (-1.5 * xx * z - 1.5 * yy * z + zzz) +\n        a1 * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +\n        a2 * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +\n        a3 * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +\n        a4 * (3.872983346207417 * x * y * z) +\n        a5 * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +\n        a6 * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)\n    );\n}\n\nfloat L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6, float a7, float a8) {\n    float x = p.x, y = p.y, z = p.z;\n    float xx = x * x, yy = y * y, zz = z * z;\n    float xxx = xx * x, yyy = yy * y, zzz = zz * z;\n    float xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;\n    return (\n        a0 * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +\n        a1 * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +\n        a2 * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +\n        a3 * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +\n        a4 * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +\n        a5 * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +\n        a6 * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +\n        a7 * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +\n        a8 * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)\n    );\n}\n\nfloat alpha(float offset, float f) {\n    #ifdef WEBGL1\n        // in webgl1, the value is in the alpha channel!\n        return texture2D(tAlpha, vec2(offset * f, 0.5)).a;\n    #else\n        return texture2D(tAlpha, vec2(offset * f, 0.5)).x;\n    #endif\n}\n\nfloat Y(int L, vec3 X, float aO, float fA) {\n    if (L == 0) {\n        return alpha(aO, fA);\n    } else if (L == 1) {\n        return L1(X,\n            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA)\n        );\n    } else if (L == 2) {\n        return L2(X,\n            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA)\n        );\n    } else if (L == 3) {\n        return L3(X,\n            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),\n            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA)\n        );\n    } else if (L == 4) {\n        return L4(X,\n            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),\n            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA), alpha(aO + 7.0, fA), alpha(aO + 8.0, fA)\n        );\n    }\n    // TODO: do we need L > 4?\n    return 0.0;\n}\n\n#ifndef WEBGL1\n    float R(float R2, int start, int end, float fCoeff) {\n        float gauss = 0.0;\n        for (int i = start; i < end; i++) {\n            vec2 c = texture2D(tCoeff, vec2(float(i) * fCoeff, 0.5)).xy;\n            gauss += c.x * exp(-c.y * R2);\n        }\n        return gauss;\n    }\n#else\n    float R(float R2, int start, int end, float fCoeff) {\n        float gauss = 0.0;\n        int o = start;\n        for (int i = 0; i < uMaxCoeffs; i++) {\n            if (o >= end) break;\n\n            vec2 c = texture2D(tCoeff, vec2(float(o) * fCoeff, 0.5)).xy;\n            gauss += c.x * exp(-c.y * R2);\n            o++;\n        }\n        return gauss;\n    }\n#endif\n";
 exports.MAIN = "\n    float fCenter = 1.0 / float(uNCenters - 1);\n    float fCoeff = 1.0 / float(uNCoeff - 1);\n    float fA = 1.0 / float(uNAlpha - 1);\n\n    float v = 0.0;\n\n    for (int i = 0; i < uNCenters; i++) {\n        vec2 cCoord = vec2(float(i) * fCenter, 0.5);\n\n        vec4 center = texture2D(tCenters, cCoord);\n        vec3 X = xyz - center.xyz;\n        float R2 = dot(X, X);\n\n        // center.w is squared cutoff radius\n        if (R2 > center.w) {\n            continue;\n        }\n\n        vec4 info = texture2D(tInfo, cCoord);\n\n        int L = int(info.x);\n        float aO = info.y;\n        int coeffStart = int(info.z);\n        int coeffEnd = int(info.w);\n\n        v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);\n    }\n";
-//# sourceMappingURL=shader.frag.js.map

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);
@@ -118,4 +118,3 @@ function computeOrbitalIsocontourValues(input, cumulativeThreshold) {
     };
 }
 exports.computeOrbitalIsocontourValues = computeOrbitalIsocontourValues;
-//# sourceMappingURL=orbitals.js.map

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

@@ -63,4 +63,3 @@ function L4(alpha, x, y, z) {
         alpha[7] * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
         alpha[8] * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy));
 }
-//# sourceMappingURL=spherical-functions.js.map

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:
@@ -258,4 +258,3 @@ function volumeParams(plugin, volume, params) {
         colorParams: { value: params.color }
     });
 }
-//# sourceMappingURL=transforms.js.map

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();
@@ -575,4 +575,3 @@ function setLocation(l, structure, serialIndex) {
     l.element = structure.serialMapping.elementIndices[serialIndex];
     return l;
 }
-//# sourceMappingURL=algorithm.js.map