molstar 3.3.1 → 3.4.0

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;
         }

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.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;