molstar 3.2.0 → 3.4.0

package/lib/commonjs/mol-plugin-state/animation/built-in/camera-rock.js

@@ -31,9 +31,9 @@ exports.AnimateCameraRock = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var snapshot, phase, angle, position;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 if (t.current === 0) {
                     return [2 /*return*/, { kind: 'next', state: animState }];
                 }
@@ -50,7 +50,7 @@ exports.AnimateCameraRock = model_1.PluginStateAnimation.create({
                 quat_1.Quat.setAxisAngle(_rot, _axis, angle);
                 vec3_1.Vec3.transformQuat(_dir, _dir, _rot);
                 position = vec3_1.Vec3.add((0, vec3_1.Vec3)(), snapshot.target, _dir);
-                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, snapshot), { position: position }), durationMs: 0 });
+                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: tslib_1.__assign(tslib_1.__assign({}, snapshot), { position: position }), durationMs: 0 });
                 if (phase >= 0.99999) {
                     return [2 /*return*/, { kind: 'finished' }];
                 }
@@ -59,4 +59,3 @@ exports.AnimateCameraRock = model_1.PluginStateAnimation.create({
         });
     }
 });
-//# sourceMappingURL=camera-rock.js.map

package/lib/commonjs/mol-plugin-state/animation/built-in/camera-spin.js

@@ -30,9 +30,9 @@ exports.AnimateCameraSpin = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var snapshot, phase, angle, position;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 if (t.current === 0) {
                     return [2 /*return*/, { kind: 'next', state: animState }];
                 }
@@ -49,7 +49,7 @@ exports.AnimateCameraSpin = model_1.PluginStateAnimation.create({
                 quat_1.Quat.setAxisAngle(_rot, _axis, angle);
                 vec3_1.Vec3.transformQuat(_dir, _dir, _rot);
                 position = vec3_1.Vec3.add((0, vec3_1.Vec3)(), snapshot.target, _dir);
-                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, snapshot), { position: position }), durationMs: 0 });
+                (_b = ctx.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.requestCameraReset({ snapshot: tslib_1.__assign(tslib_1.__assign({}, snapshot), { position: position }), durationMs: 0 });
                 if (phase >= 0.99999) {
                     return [2 /*return*/, { kind: 'finished' }];
                 }
@@ -58,4 +58,3 @@ exports.AnimateCameraSpin = model_1.PluginStateAnimation.create({
         });
     }
 });
-//# sourceMappingURL=camera-spin.js.map

package/lib/commonjs/mol-plugin-state/animation/built-in/explode-units.js

@@ -21,9 +21,9 @@ exports.AnimateUnitsExplode = model_1.PluginStateAnimation.create({
     }); },
     initialState: function () { return ({ t: 0 }); },
     setup: function (_, __, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, reprs, update, changed, _i, reprs_1, r, explodes;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 state = plugin.state.data;
                 reprs = state.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D));
                 update = state.build();
@@ -57,9 +57,9 @@ exports.AnimateUnitsExplode = model_1.PluginStateAnimation.create({
         return update.commit();
     },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, anims, update, d, newTime, _i, anims_1, m;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         state = ctx.plugin.state.data;
@@ -83,4 +83,3 @@ exports.AnimateUnitsExplode = model_1.PluginStateAnimation.create({
         });
     }
 });
-//# sourceMappingURL=explode-units.js.map

package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.js

@@ -69,9 +69,9 @@ exports.AnimateModelIndex = model_1.PluginStateAnimation.create({
     },
     initialState: function () { return ({}); },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, models, update, params, palindromeDirections, isEnd, allSingles, _loop_1, _i, models_3, m;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         // limit fps
@@ -169,4 +169,3 @@ exports.AnimateModelIndex = model_1.PluginStateAnimation.create({
         });
     }
 });
-//# sourceMappingURL=model-index.js.map

package/lib/commonjs/mol-plugin-state/animation/built-in/spin-structure.js

@@ -23,9 +23,9 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
     initialState: function () { return ({ t: 0 }); },
     getDuration: function (p) { return ({ kind: 'fixed', durationMs: p.durationInMs }); },
     setup: function (_, __, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, reprs, update, changed, _i, reprs_1, r, spins;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 state = plugin.state.data;
                 reprs = state.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D));
                 update = state.build();
@@ -60,9 +60,9 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, anims, update, d, newTime, _i, anims_1, m;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         state = ctx.plugin.state.data;
@@ -75,7 +75,7 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
                         newTime = (animState.t + d) % 1;
                         for (_i = 0, anims_1 = anims; _i < anims_1.length; _i++) {
                             m = anims_1[_i];
-                            update.to(m).update((0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = m.params) === null || _a === void 0 ? void 0 : _a.values), { t: newTime }));
+                            update.to(m).update(tslib_1.__assign(tslib_1.__assign({}, (_a = m.params) === null || _a === void 0 ? void 0 : _a.values), { t: newTime }));
                         }
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(ctx.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
                     case 1:
@@ -86,4 +86,3 @@ exports.AnimateStructureSpin = model_1.PluginStateAnimation.create({
         });
     }
 });
-//# sourceMappingURL=spin-structure.js.map

package/lib/commonjs/mol-plugin-state/animation/built-in/state-interpolation.js

@@ -23,9 +23,9 @@ exports.AnimateStateInterpolation = model_1.PluginStateAnimation.create({
     },
     initialState: function () { return ({}); },
     apply: function (animState, t, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var snapshots, currentT, srcIndex, tarIndex, _src, _tar, src, tar, state, update, _i, src_1, s, _a, tar_1, t_1, e, f, oldState, newState;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         snapshots = ctx.plugin.managers.snapshot.state.entries;
@@ -78,4 +78,3 @@ exports.AnimateStateInterpolation = model_1.PluginStateAnimation.create({
         });
     }
 });
-//# sourceMappingURL=state-interpolation.js.map

package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js

@@ -11,8 +11,8 @@ var model_1 = require("../model");
 function setPartialSnapshot(plugin, entry, first) {
     var _a;
     if (first === void 0) { first = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_b) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     if (!entry.snapshot.data) return [3 /*break*/, 2];
@@ -68,9 +68,9 @@ exports.AnimateStateSnapshots = model_1.PluginStateAnimation.create({
     },
     apply: function (animState, t, ctx) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var ctime, i, _i, _b, s;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 if (t.current >= animState.totalDuration) {
                     return [2 /*return*/, { kind: 'finished' }];
                 }
@@ -89,9 +89,8 @@ exports.AnimateStateSnapshots = model_1.PluginStateAnimation.create({
                     return [2 /*return*/, { kind: 'skip' }];
                 }
                 setPartialSnapshot(ctx.plugin, animState.snapshots[i]);
-                return [2 /*return*/, { kind: 'next', state: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, animState), { currentIndex: i }) }];
+                return [2 /*return*/, { kind: 'next', state: tslib_1.__assign(tslib_1.__assign({}, animState), { currentIndex: i }) }];
             });
         });
     }
 });
-//# sourceMappingURL=state-snapshots.js.map

package/lib/commonjs/mol-plugin-state/animation/helpers.js

@@ -85,4 +85,3 @@ function spinStructure(structure, unitTransforms, t, axis, origin) {
     }
 }
 exports.spinStructure = spinStructure;
-//# sourceMappingURL=helpers.js.map

package/lib/commonjs/mol-plugin-state/animation/model.js

@@ -23,4 +23,3 @@ var PluginStateAnimation;
     PluginStateAnimation.getDuration = getDuration;
 })(PluginStateAnimation || (PluginStateAnimation = {}));
 exports.PluginStateAnimation = PluginStateAnimation;
-//# sourceMappingURL=model.js.map

package/lib/commonjs/mol-plugin-state/builder/data.js

@@ -34,9 +34,9 @@ var DataBuilder = /** @class */ (function () {
     };
     DataBuilder.prototype.readFile = function (params, options) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var data, fileInfo;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, this.dataState.build().toRoot().apply(data_1.ReadFile, params, options).commit({ revertOnError: true })];
                     case 1:
@@ -50,4 +50,3 @@ var DataBuilder = /** @class */ (function () {
     return DataBuilder;
 }());
 exports.DataBuilder = DataBuilder;
-//# sourceMappingURL=data.js.map

package/lib/commonjs/mol-plugin-state/builder/preset-provider.js

@@ -5,4 +5,3 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-//# sourceMappingURL=preset-provider.js.map

package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js

@@ -28,7 +28,7 @@ exports.TrajectoryHierarchyPresetProvider = TrajectoryHierarchyPresetProvider;
     }); };
 })(TrajectoryHierarchyPresetProvider = exports.TrajectoryHierarchyPresetProvider || (exports.TrajectoryHierarchyPresetProvider = {}));
 var CommonParams = TrajectoryHierarchyPresetProvider.CommonParams;
-var DefaultParams = function (a, plugin) { return ((0, tslib_1.__assign)({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))), showUnitcell: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)), structure: param_definition_1.ParamDefinition.Optional(root_structure_1.RootStructureDefinition.getParams(void 0, 'assembly').type), representationPresetParams: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(representation_preset_1.StructureRepresentationPresetProvider.CommonParams)) }, CommonParams(a, plugin))); };
+var DefaultParams = function (a, plugin) { return (tslib_1.__assign({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))), showUnitcell: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)), structure: param_definition_1.ParamDefinition.Optional(root_structure_1.RootStructureDefinition.getParams(void 0, 'assembly').type), representationPresetParams: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(representation_preset_1.StructureRepresentationPresetProvider.CommonParams)) }, CommonParams(a, plugin))); };
 var defaultPreset = TrajectoryHierarchyPresetProvider({
     id: 'preset-trajectory-default',
     display: {
@@ -40,9 +40,9 @@ var defaultPreset = TrajectoryHierarchyPresetProvider({
     },
     params: DefaultParams,
     apply: function (trajectory, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var builder, model, modelProperties, structure, structureProperties, unitcell, _a, representationPreset, representation;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         builder = plugin.builders.structure;
@@ -85,7 +85,7 @@ var defaultPreset = TrajectoryHierarchyPresetProvider({
         });
     }
 });
-var AllModelsParams = function (a, plugin) { return ((0, tslib_1.__assign)({ useDefaultIfSingleModel: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)), representationPresetParams: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(representation_preset_1.StructureRepresentationPresetProvider.CommonParams)) }, CommonParams(a, plugin))); };
+var AllModelsParams = function (a, plugin) { return (tslib_1.__assign({ useDefaultIfSingleModel: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)), representationPresetParams: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(representation_preset_1.StructureRepresentationPresetProvider.CommonParams)) }, CommonParams(a, plugin))); };
 var allModels = TrajectoryHierarchyPresetProvider({
     id: 'preset-trajectory-all-models',
     display: {
@@ -98,9 +98,9 @@ var allModels = TrajectoryHierarchyPresetProvider({
     params: AllModelsParams,
     apply: function (trajectory, params, plugin) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var tr, builder, models, structures, i, model, modelProperties, structure, structureProperties, quality, representationPreset;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         tr = (_b = (_a = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, trajectory)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data;
@@ -144,11 +144,11 @@ var allModels = TrajectoryHierarchyPresetProvider({
         });
     }
 });
-var CrystalSymmetryParams = function (a, plugin) { return ((0, tslib_1.__assign)({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))) }, CommonParams(a, plugin))); };
+var CrystalSymmetryParams = function (a, plugin) { return (tslib_1.__assign({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))) }, CommonParams(a, plugin))); };
 function applyCrystalSymmetry(props, trajectory, params, plugin) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var builder, model, modelProperties, structure, structureProperties, unitcell, representationPreset, representation;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     builder = plugin.builders.structure;
@@ -197,8 +197,8 @@ var unitcell = TrajectoryHierarchyPresetProvider({
     },
     params: CrystalSymmetryParams,
     apply: function (trajectory, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        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*/, applyCrystalSymmetry({ ijkMin: linear_algebra_1.Vec3.create(0, 0, 0), ijkMax: linear_algebra_1.Vec3.create(0, 0, 0) }, trajectory, params, plugin)];
                     case 1: return [2 /*return*/, _a.sent()];
@@ -218,8 +218,8 @@ var supercell = TrajectoryHierarchyPresetProvider({
     },
     params: CrystalSymmetryParams,
     apply: function (trajectory, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        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*/, applyCrystalSymmetry({ ijkMin: linear_algebra_1.Vec3.create(-1, -1, -1), ijkMax: linear_algebra_1.Vec3.create(1, 1, 1), theme: 'operator-hkl' }, trajectory, params, plugin)];
                     case 1: return [2 /*return*/, _a.sent()];
@@ -228,7 +228,7 @@ var supercell = TrajectoryHierarchyPresetProvider({
         });
     }
 });
-var CrystalContactsParams = function (a, plugin) { return ((0, tslib_1.__assign)({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))) }, CommonParams(a, plugin))); };
+var CrystalContactsParams = function (a, plugin) { return (tslib_1.__assign({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))) }, CommonParams(a, plugin))); };
 var crystalContacts = TrajectoryHierarchyPresetProvider({
     id: 'preset-trajectory-crystal-contacts',
     display: {
@@ -240,9 +240,9 @@ var crystalContacts = TrajectoryHierarchyPresetProvider({
     },
     params: CrystalContactsParams,
     apply: function (trajectory, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var builder, model, modelProperties, structure, structureProperties, unitcell, representationPreset, representation;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         builder = plugin.builders.structure;
@@ -288,4 +288,3 @@ exports.PresetTrajectoryHierarchy = {
     supercell: supercell,
     crystalContacts: crystalContacts,
 };
-//# sourceMappingURL=hierarchy-preset.js.map

package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.js

@@ -111,4 +111,3 @@ var TrajectoryHierarchyBuilder = /** @class */ (function () {
     return TrajectoryHierarchyBuilder;
 }());
 exports.TrajectoryHierarchyBuilder = TrajectoryHierarchyBuilder;
-//# sourceMappingURL=hierarchy.js.map

package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js

@@ -112,7 +112,7 @@ var auto = StructureRepresentationPresetProvider({
                 } // else fall through
             case structure_1.Structure.Size.Small:
                 // `showCarbohydrateSymbol: true` is nice, e.g., for PDB 1aga
-                return atomicDetail.apply(ref, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { showCarbohydrateSymbol: true }), plugin);
+                return atomicDetail.apply(ref, tslib_1.__assign(tslib_1.__assign({}, params), { showCarbohydrateSymbol: true }), plugin);
             default:
                 (0, type_helpers_1.assertUnreachable)(size);
         }
@@ -122,8 +122,8 @@ var empty = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-empty',
     display: { name: 'Empty', description: 'Removes all existing representations.' },
     apply: function (ref, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 return [2 /*return*/, {}];
             });
         });
@@ -139,10 +139,10 @@ var polymerAndLigand = StructureRepresentationPresetProvider({
     params: function () { return CommonParams; },
     apply: function (ref, params, plugin) {
         var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, structure, cartoonProps, waterType, lipidType, _l, update, builder, typeParams, color, symmetryColor, ballAndStickColor, representations;
             var _m;
-            return (0, tslib_1.__generator)(this, function (_o) {
+            return tslib_1.__generator(this, function (_o) {
                 switch (_o.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -182,14 +182,14 @@ var polymerAndLigand = StructureRepresentationPresetProvider({
                         lipidType = (((_f = (_e = (_d = components.lipid) === null || _d === void 0 ? void 0 : _d.obj) === null || _e === void 0 ? void 0 : _e.data) === null || _f === void 0 ? void 0 : _f.elementCount) || 0) > 20000 ? 'line' : 'ball-and-stick';
                         _l = reprBuilder(plugin, params, structure), update = _l.update, builder = _l.builder, typeParams = _l.typeParams, color = _l.color, symmetryColor = _l.symmetryColor, ballAndStickColor = _l.ballAndStickColor;
                         representations = {
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), cartoonProps), color: symmetryColor }, { tag: 'polymer' }),
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), cartoonProps), color: symmetryColor }, { tag: 'polymer' }),
                             ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: typeParams, color: color, colorParams: ballAndStickColor }, { tag: 'ligand' }),
                             nonStandard: builder.buildRepresentation(update, components.nonStandard, { type: 'ball-and-stick', typeParams: typeParams, color: color, colorParams: ballAndStickColor }, { tag: 'non-standard' }),
-                            branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { alpha: 0.3 }), color: color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
+                            branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { alpha: 0.3 }), color: color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
                             branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: typeParams, color: color }, { tag: 'branched-snfg-3d' }),
-                            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { alpha: 0.6 }), color: color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
+                            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { alpha: 0.6, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }), color: color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
                             ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams: typeParams, color: color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ion' }),
-                            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { alpha: 0.6 }), color: color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
+                            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { alpha: 0.6, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }), color: color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
                             coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams: typeParams, color: color || 'chain-id' }, { tag: 'coarse' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: false })];
@@ -213,10 +213,10 @@ var proteinAndNucleic = StructureRepresentationPresetProvider({
     params: function () { return CommonParams; },
     apply: function (ref, params, plugin) {
         var _a, _b, _c, _d;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, structure, cartoonProps, gaussianProps, _e, update, builder, typeParams, symmetryColor, representations;
             var _f;
-            return (0, tslib_1.__generator)(this, function (_g) {
+            return tslib_1.__generator(this, function (_g) {
                 switch (_g.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -240,8 +240,8 @@ var proteinAndNucleic = StructureRepresentationPresetProvider({
                         };
                         _e = reprBuilder(plugin, params, structure), update = _e.update, builder = _e.builder, typeParams = _e.typeParams, symmetryColor = _e.symmetryColor;
                         representations = {
-                            protein: builder.buildRepresentation(update, components.protein, { type: 'cartoon', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), cartoonProps), color: symmetryColor }, { tag: 'protein' }),
-                            nucleic: builder.buildRepresentation(update, components.nucleic, { type: 'gaussian-surface', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), gaussianProps), color: symmetryColor }, { tag: 'nucleic' })
+                            protein: builder.buildRepresentation(update, components.protein, { type: 'cartoon', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), cartoonProps), color: symmetryColor }, { tag: 'protein' }),
+                            nucleic: builder.buildRepresentation(update, components.nucleic, { type: 'gaussian-surface', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), gaussianProps), color: symmetryColor }, { tag: 'nucleic' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -264,10 +264,10 @@ var coarseSurface = StructureRepresentationPresetProvider({
     params: function () { return CommonParams; },
     apply: function (ref, params, plugin) {
         var _a, _b, _c, _d;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, structure, size, gaussianProps, _e, update, builder, typeParams, symmetryColor, representations;
             var _f;
-            return (0, tslib_1.__generator)(this, function (_g) {
+            return tslib_1.__generator(this, function (_g) {
                 switch (_g.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -306,8 +306,8 @@ var coarseSurface = StructureRepresentationPresetProvider({
                         }
                         _e = reprBuilder(plugin, params, structure), update = _e.update, builder = _e.builder, typeParams = _e.typeParams, symmetryColor = _e.symmetryColor;
                         representations = {
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'gaussian-surface', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), gaussianProps), color: symmetryColor }, { tag: 'polymer' }),
-                            lipid: builder.buildRepresentation(update, components.lipid, { type: 'gaussian-surface', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), gaussianProps), color: symmetryColor }, { tag: 'lipid' })
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'gaussian-surface', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), gaussianProps), color: symmetryColor }, { tag: 'polymer' }),
+                            lipid: builder.buildRepresentation(update, components.lipid, { type: 'gaussian-surface', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), gaussianProps), color: symmetryColor }, { tag: 'lipid' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -330,10 +330,10 @@ var polymerCartoon = StructureRepresentationPresetProvider({
     params: function () { return CommonParams; },
     apply: function (ref, params, plugin) {
         var _a, _b, _c, _d;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, structure, cartoonProps, _e, update, builder, typeParams, symmetryColor, representations;
             var _f;
-            return (0, tslib_1.__generator)(this, function (_g) {
+            return tslib_1.__generator(this, function (_g) {
                 switch (_g.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -350,7 +350,7 @@ var polymerCartoon = StructureRepresentationPresetProvider({
                         };
                         _e = reprBuilder(plugin, params, structure), update = _e.update, builder = _e.builder, typeParams = _e.typeParams, symmetryColor = _e.symmetryColor;
                         representations = {
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), cartoonProps), color: symmetryColor }, { tag: 'polymer' })
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), cartoonProps), color: symmetryColor }, { tag: 'polymer' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 2:
@@ -370,13 +370,13 @@ var atomicDetail = StructureRepresentationPresetProvider({
         name: 'Atomic Detail', group: BuiltInPresetGroupName,
         description: 'Shows everything in atomic detail with Ball & Stick.'
     },
-    params: function () { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, CommonParams), { showCarbohydrateSymbol: param_definition_1.ParamDefinition.Boolean(false) })); },
+    params: function () { return (tslib_1.__assign(tslib_1.__assign({}, CommonParams), { showCarbohydrateSymbol: param_definition_1.ParamDefinition.Boolean(false) })); },
     apply: function (ref, params, plugin) {
         var _a, _b, _c, _d, _e, _f;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, structure, highElementCount, lowResidueElementRatio, m, bondsGiven, atomicType, showCarbohydrateSymbol, _g, _h, _j, _k, update, builder, typeParams, color, ballAndStickColor, colorParams, representations;
             var _l, _m;
-            return (0, tslib_1.__generator)(this, function (_o) {
+            return tslib_1.__generator(this, function (_o) {
                 switch (_o.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -426,7 +426,7 @@ var atomicDetail = StructureRepresentationPresetProvider({
                         };
                         if (showCarbohydrateSymbol) {
                             Object.assign(representations, {
-                                snfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { alpha: 0.4, visuals: ['carbohydrate-symbol'] }), color: color }, { tag: 'snfg-3d' }),
+                                snfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { alpha: 0.4, visuals: ['carbohydrate-symbol'] }), color: color }, { tag: 'snfg-3d' }),
                             });
                         }
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
@@ -447,13 +447,13 @@ var illustrative = StructureRepresentationPresetProvider({
         name: 'Illustrative', group: 'Miscellaneous',
         description: '...'
     },
-    params: function () { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, CommonParams), { showCarbohydrateSymbol: param_definition_1.ParamDefinition.Boolean(false) })); },
+    params: function () { return (tslib_1.__assign(tslib_1.__assign({}, CommonParams), { showCarbohydrateSymbol: param_definition_1.ParamDefinition.Boolean(false) })); },
     apply: function (ref, params, plugin) {
         var _a, _b, _c, _d, _e;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, structure, _f, update, builder, typeParams, color, representations;
             var _g;
-            return (0, tslib_1.__generator)(this, function (_h) {
+            return tslib_1.__generator(this, function (_h) {
                 switch (_h.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -468,7 +468,7 @@ var illustrative = StructureRepresentationPresetProvider({
                         structure = structureCell.obj.data;
                         _f = reprBuilder(plugin, params, structure), update = _f.update, builder = _f.builder, typeParams = _f.typeParams, color = _f.color;
                         representations = {
-                            all: builder.buildRepresentation(update, components.all, { type: 'spacefill', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { ignoreLight: true }), color: 'illustrative' }, { tag: 'all' }),
+                            all: builder.buildRepresentation(update, components.all, { type: 'spacefill', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { ignoreLight: true }), color: 'illustrative' }, { tag: 'all' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 2:
@@ -500,4 +500,3 @@ exports.PresetStructureRepresentations = {
     'coarse-surface': coarseSurface,
     illustrative: illustrative,
 };
-//# sourceMappingURL=representation-preset.js.map

package/lib/commonjs/mol-plugin-state/builder/structure/representation.js

@@ -121,9 +121,9 @@ var StructureRepresentationBuilder = /** @class */ (function () {
         return this.plugin.runTask(task);
     };
     StructureRepresentationBuilder.prototype.addRepresentation = function (structure, props, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var repr, selector;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         repr = this.dataState.build();
@@ -153,4 +153,3 @@ var StructureRepresentationBuilder = /** @class */ (function () {
     return StructureRepresentationBuilder;
 }());
 exports.StructureRepresentationBuilder = StructureRepresentationBuilder;
-//# sourceMappingURL=representation.js.map

package/lib/commonjs/mol-plugin-state/builder/structure.js

@@ -30,9 +30,9 @@ var StructureBuilder = /** @class */ (function () {
         configurable: true
     });
     StructureBuilder.prototype.parseTrajectoryData = function (data, format) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var provider, trajectory;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         provider = typeof format === 'string' ? this.plugin.dataFormats.get(format) : format;
@@ -116,16 +116,16 @@ var StructureBuilder = /** @class */ (function () {
     /** returns undefined if the component is empty/null */
     StructureBuilder.prototype.tryCreateComponent = function (structure, params, key, tags) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, root, keyTag, component, selector;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         state = this.dataState;
                         root = state.build().to(structure);
                         keyTag = "structure-component-".concat(key);
                         component = root.applyOrUpdateTagged(keyTag, transforms_1.StateTransforms.Model.StructureComponent, params, {
-                            tags: tags ? (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], tags, true), [keyTag], false) : [keyTag]
+                            tags: tags ? tslib_1.__spreadArray(tslib_1.__spreadArray([], tags, true), [keyTag], false) : [keyTag]
                         });
                         return [4 /*yield*/, component.commit()];
                     case 1:
@@ -157,11 +157,11 @@ var StructureBuilder = /** @class */ (function () {
     };
     StructureBuilder.prototype.tryCreateComponentFromSelection = function (structure, selection, key, params) {
         var _this = this;
-        return this.plugin.runTask(mol_task_1.Task.create('Query Component', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return this.plugin.runTask(mol_task_1.Task.create('Query Component', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var _a, label, tags, structureData, transformParams, _b, _c, _d;
             var _e, _f;
             var _g, _h;
-            return (0, tslib_1.__generator)(this, function (_j) {
+            return tslib_1.__generator(this, function (_j) {
                 switch (_j.label) {
                     case 0:
                         _a = params || {}, label = _a.label, tags = _a.tags;
@@ -205,4 +205,3 @@ var StructureBuilder = /** @class */ (function () {
     return StructureBuilder;
 }());
 exports.StructureBuilder = StructureBuilder;
-//# sourceMappingURL=structure.js.map

package/lib/commonjs/mol-plugin-state/component.js

@@ -51,7 +51,7 @@ var PluginComponent = /** @class */ (function () {
 }());
 exports.PluginComponent = PluginComponent;
 var StatefulPluginComponent = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StatefulPluginComponent, _super);
+    tslib_1.__extends(StatefulPluginComponent, _super);
     function StatefulPluginComponent(initialState) {
         var _this = _super.call(this) || this;
         _this._state = initialState;
@@ -80,4 +80,3 @@ var StatefulPluginComponent = /** @class */ (function (_super) {
     return StatefulPluginComponent;
 }(PluginComponent));
 exports.StatefulPluginComponent = StatefulPluginComponent;
-//# sourceMappingURL=component.js.map