molstar 3.3.1 → 3.6.0

package/lib/commonjs/mol-plugin-state/formats/topology.d.ts

@@ -0,0 +1,73 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export declare const TopologyFormatCategory = "Topology";
+export { PsfProvider };
+declare const PsfProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Psf, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Psf, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Psf, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+};
+declare type PsfProvider = typeof PsfProvider;
+export { PrmtopProvider };
+declare const PrmtopProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Prmtop, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+};
+declare type PrmtopProvider = typeof PrmtopProvider;
+export { TopProvider };
+declare const TopProvider: {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Top, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Top, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Top, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+};
+declare type TopProvider = typeof TopProvider;
+export declare type TopologyProvider = PsfProvider;
+export declare const BuiltInTopologyFormats: readonly [readonly ["psf", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Psf, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Psf, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Psf, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+}], readonly ["prmtop", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Prmtop, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Prmtop, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+}], readonly ["top", {
+    label: string;
+    description: string;
+    category: string;
+    stringExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<{
+        format: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Format.Top, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Data.String, import("../objects").PluginStateObject.Format.Top, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+        topology: import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-state/transformer").StateTransformer<import("../objects").PluginStateObject.Format.Top, import("../objects").PluginStateObject.Molecule.Topology, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
+    }>;
+}]];
+export declare type BuiltInTopologyFormat = (typeof BuiltInTopologyFormats)[number][0];

package/lib/commonjs/mol-plugin-state/formats/topology.js

@@ -0,0 +1,87 @@
+"use strict";
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.BuiltInTopologyFormats = exports.TopProvider = exports.PrmtopProvider = exports.PsfProvider = exports.TopologyFormatCategory = void 0;
+var tslib_1 = require("tslib");
+var transforms_1 = require("../transforms");
+var provider_1 = require("./provider");
+exports.TopologyFormatCategory = 'Topology';
+var PsfProvider = (0, provider_1.DataFormatProvider)({
+    label: 'PSF',
+    description: 'PSF',
+    category: exports.TopologyFormatCategory,
+    stringExtensions: ['psf'],
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var format, topology;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    format = plugin.state.data.build()
+                        .to(data)
+                        .apply(transforms_1.StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
+                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromPsf);
+                    return [4 /*yield*/, format.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
+            }
+        });
+    }); }
+});
+exports.PsfProvider = PsfProvider;
+var PrmtopProvider = (0, provider_1.DataFormatProvider)({
+    label: 'PRMTOP',
+    description: 'PRMTOP',
+    category: exports.TopologyFormatCategory,
+    stringExtensions: ['prmtop', 'parm7'],
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var format, topology;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    format = plugin.state.data.build()
+                        .to(data)
+                        .apply(transforms_1.StateTransforms.Data.ParsePrmtop, {}, { state: { isGhost: true } });
+                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromPrmtop);
+                    return [4 /*yield*/, format.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
+            }
+        });
+    }); }
+});
+exports.PrmtopProvider = PrmtopProvider;
+var TopProvider = (0, provider_1.DataFormatProvider)({
+    label: 'TOP',
+    description: 'TOP',
+    category: exports.TopologyFormatCategory,
+    stringExtensions: ['top'],
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var format, topology;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    format = plugin.state.data.build()
+                        .to(data)
+                        .apply(transforms_1.StateTransforms.Data.ParseTop, {}, { state: { isGhost: true } });
+                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromTop);
+                    return [4 /*yield*/, format.commit()];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
+            }
+        });
+    }); }
+});
+exports.TopProvider = TopProvider;
+exports.BuiltInTopologyFormats = [
+    ['psf', PsfProvider],
+    ['prmtop', PrmtopProvider],
+    ['top', TopProvider],
+];

package/lib/commonjs/mol-plugin-state/formats/trajectory.js

@@ -28,10 +28,10 @@ exports.MmcifProvider = {
             return (0, provider_1.guessCifVariant)(info, data) === -1;
         return false;
     },
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var state, cif, trajectory;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;
@@ -61,10 +61,10 @@ exports.CifCoreProvider = {
             return (0, provider_1.guessCifVariant)(info, data) === 'coreCif';
         return false;
     },
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var state, cif, trajectory;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;
@@ -86,9 +86,9 @@ exports.CifCoreProvider = {
 };
 function directTrajectory(transformer, transformerParams) {
     var _this = this;
-    return function (plugin, data, params) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return function (plugin, data, params) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var state, trajectory;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     state = plugin.state.data;

package/lib/commonjs/mol-plugin-state/formats/volume.js

@@ -20,18 +20,18 @@ var util_1 = require("../../mol-plugin/behavior/dynamic/volume-streaming/util");
 var mol_task_1 = require("../../mol-task");
 exports.VolumeFormatCategory = 'Volume';
 function tryObtainRecommendedIsoValue(plugin, volume) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var entryId;
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             if (!volume)
                 return [2 /*return*/];
             entryId = volume.entryId;
             if (!entryId || !entryId.toLowerCase().startsWith('emd'))
                 return [2 /*return*/];
-            return [2 /*return*/, plugin.runTask(mol_task_1.Task.create('Try Set Recommended IsoValue', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            return [2 /*return*/, plugin.runTask(mol_task_1.Task.create('Try Set Recommended IsoValue', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var absIsoLevel, 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]);
@@ -60,9 +60,9 @@ function tryGetRecomendedIsoValue(volume) {
     return volume_1.Volume.adjustedIsoValue(volume, recommendedIsoValue.absoluteValue, 'absolute');
 }
 function defaultVisuals(plugin, data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var typeParams, isoValue, visual;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     typeParams = {};
@@ -84,9 +84,9 @@ exports.Ccp4Provider = (0, provider_1.DataFormatProvider)({
     description: 'CCP4/MRC/MAP',
     category: exports.VolumeFormatCategory,
     binaryExtensions: ['ccp4', 'mrc', 'map'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -110,9 +110,9 @@ exports.Dsn6Provider = (0, provider_1.DataFormatProvider)({
     description: 'DSN6/BRIX',
     category: exports.VolumeFormatCategory,
     binaryExtensions: ['dsn6', 'brix'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -137,9 +137,9 @@ exports.DxProvider = (0, provider_1.DataFormatProvider)({
     category: exports.VolumeFormatCategory,
     stringExtensions: ['dx'],
     binaryExtensions: ['dxbin'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -163,9 +163,9 @@ exports.CubeProvider = (0, provider_1.DataFormatProvider)({
     description: 'Cube',
     category: exports.VolumeFormatCategory,
     stringExtensions: ['cub', 'cube'],
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, volume, structure;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.build()
@@ -186,10 +186,10 @@ exports.CubeProvider = (0, provider_1.DataFormatProvider)({
             }
         });
     }); },
-    visuals: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    visuals: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var surfaces, volumeReprs, volumeData, volumePos, volumeNeg, volume, structure, structureReprs;
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     surfaces = plugin.build();
@@ -230,7 +230,7 @@ exports.CubeProvider = (0, provider_1.DataFormatProvider)({
                         if (r)
                             structureReprs.push(r);
                     });
-                    return [2 /*return*/, (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], volumeReprs, true), structureReprs, true)];
+                    return [2 /*return*/, tslib_1.__spreadArray(tslib_1.__spreadArray([], volumeReprs, true), structureReprs, true)];
             }
         });
     }); }
@@ -244,9 +244,9 @@ exports.DscifProvider = (0, provider_1.DataFormatProvider)({
     isApplicable: function (info, data) {
         return (0, provider_1.guessCifVariant)(info, data) === 'dscif' ? true : false;
     },
-    parse: function (plugin, data, params) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var cifCell, b, blocks, volumes, i, _i, blocks_1, block, entryId, _a, volumes_1, v;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, plugin.build().to(data).apply(transforms_1.StateTransforms.Data.ParseCif).commit()];
                 case 1:
@@ -282,9 +282,9 @@ exports.DscifProvider = (0, provider_1.DataFormatProvider)({
             }
         });
     }); },
-    visuals: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    visuals: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var volumes, tree, visuals, isoValue, posParams, negParams;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     volumes = data.volumes;

package/lib/commonjs/mol-plugin-state/helpers/root-structure.js

@@ -42,12 +42,12 @@ var RootStructureDefinition;
         var modes = {
             auto: param_definition_1.ParamDefinition.Group(CommonStructureParams),
             model: param_definition_1.ParamDefinition.Group(CommonStructureParams),
-            assembly: param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({ id: param_definition_1.ParamDefinition.Optional(model
+            assembly: param_definition_1.ParamDefinition.Group(tslib_1.__assign({ id: param_definition_1.ParamDefinition.Optional(model
                     ? param_definition_1.ParamDefinition.Select(assemblyIds.length ? assemblyIds[0][0] : '', assemblyIds, { label: 'Asm Id', description: 'Assembly Id' })
                     : param_definition_1.ParamDefinition.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' })) }, CommonStructureParams), { isFlat: true }),
-            'symmetry-mates': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({ radius: param_definition_1.ParamDefinition.Numeric(5, { min: 0, max: 50, step: 1 }) }, CommonStructureParams), { isFlat: true }),
-            'symmetry': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({ ijkMin: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(-1, -1, -1), { step: 1 }, { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }), ijkMax: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(1, 1, 1), { step: 1 }, { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }) }, CommonStructureParams), { isFlat: true }),
-            'symmetry-assembly': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({ generators: param_definition_1.ParamDefinition.ObjectList({
+            'symmetry-mates': param_definition_1.ParamDefinition.Group(tslib_1.__assign({ radius: param_definition_1.ParamDefinition.Numeric(5, { min: 0, max: 50, step: 1 }) }, CommonStructureParams), { isFlat: true }),
+            'symmetry': param_definition_1.ParamDefinition.Group(tslib_1.__assign({ ijkMin: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(-1, -1, -1), { step: 1 }, { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }), ijkMax: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(1, 1, 1), { step: 1 }, { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }) }, CommonStructureParams), { isFlat: true }),
+            'symmetry-assembly': param_definition_1.ParamDefinition.Group(tslib_1.__assign({ generators: param_definition_1.ParamDefinition.ObjectList({
                     operators: param_definition_1.ParamDefinition.ObjectList({
                         index: param_definition_1.ParamDefinition.Select(0, operatorOptions),
                         shift: param_definition_1.ParamDefinition.Vec3((0, linear_algebra_1.Vec3)(), { step: 1 }, { label: 'IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
@@ -84,9 +84,9 @@ var RootStructureDefinition;
     }
     RootStructureDefinition.canAutoUpdate = canAutoUpdate;
     function buildAssembly(plugin, ctx, model, id, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var asm, symmetry, base, label, s, objProps;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         asm = void 0;
@@ -120,9 +120,9 @@ var RootStructureDefinition;
         });
     }
     function buildSymmetry(ctx, model, ijkMin, ijkMax, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var base, s, objProps;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         base = structure_1.Structure.ofModel(model, props);
@@ -136,9 +136,9 @@ var RootStructureDefinition;
         });
     }
     function buildSymmetryMates(ctx, model, radius, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var base, s, objProps;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         base = structure_1.Structure.ofModel(model, props);
@@ -152,9 +152,9 @@ var RootStructureDefinition;
         });
     }
     function buildSymmetryAssembly(ctx, model, generators, symmetry, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var base, s, objProps;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         base = structure_1.Structure.ofModel(model, props);
@@ -168,9 +168,9 @@ var RootStructureDefinition;
         });
     }
     function create(plugin, ctx, model, params) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var props, symmetry, s, s;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 props = params === null || params === void 0 ? void 0 : params.params;
                 symmetry = symmetry_2.ModelSymmetry.Provider.get(model);
                 if (!symmetry || !params || params.name === 'model') {

package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js

@@ -15,13 +15,13 @@ var loci_1 = require("../../mol-model/loci");
 var clipping_1 = require("../../mol-theme/clipping");
 var ClippingManagerTag = 'clipping-controls';
 function setStructureClipping(plugin, components, groups, lociGetter, types) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, clippingCell) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, clippingCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var structure, loci, layer, bundleLayers, filtered, filtered;
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                        return tslib_1.__generator(this, function (_a) {
                             switch (_a.label) {
                                 case 0:
                                     if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -37,7 +37,7 @@ function setStructureClipping(plugin, components, groups, lociGetter, types) {
                                         groups: groups
                                     };
                                     if (clippingCell) {
-                                        bundleLayers = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], clippingCell.params.values.layers, true), [layer], false);
+                                        bundleLayers = tslib_1.__spreadArray(tslib_1.__spreadArray([], clippingCell.params.values.layers, true), [layer], false);
                                         filtered = getFilteredBundle(bundleLayers, structure);
                                         update.to(clippingCell).update(clipping_1.Clipping.toBundle(filtered));
                                     }
@@ -59,9 +59,9 @@ function setStructureClipping(plugin, components, groups, lociGetter, types) {
 }
 exports.setStructureClipping = setStructureClipping;
 function eachRepr(plugin, components, callback) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var state, update, _i, components_1, c, _a, _b, r, clipping;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;

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

@@ -14,6 +14,7 @@ var objects_1 = require("../objects");
 var structure_selection_query_1 = require("./structure-selection-query");
 var mol_state_1 = require("../../mol-state");
 var script_1 = require("../../mol-script/script");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 exports.StaticStructureComponentTypes = [
     'all',
     'polymer',
@@ -90,7 +91,7 @@ function createStructureComponent(a, params, cache) {
                     query = structure_selection_query_1.StructureSelectionQueries.coarse.query;
                     label = 'Coarse';
                     break;
-                default: throw new Error("".concat(params.type, " is a not valid complex element."));
+                default: (0, type_helpers_1.assertUnreachable)(params.type);
             }
             var result = query(new structure_1.QueryContext(a));
             component = structure_1.StructureSelection.unionStructure(result);

package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js

@@ -16,13 +16,13 @@ var color_1 = require("../../mol-util/color");
 var loci_1 = require("../../mol-model/loci");
 var OverpaintManagerTag = 'overpaint-controls';
 function setStructureOverpaint(plugin, components, color, lociGetter, types) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, overpaintCell) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, overpaintCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var structure, loci, layer, bundleLayers, filtered, filtered;
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                        return tslib_1.__generator(this, function (_a) {
                             switch (_a.label) {
                                 case 0:
                                     if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -39,7 +39,7 @@ function setStructureOverpaint(plugin, components, color, lociGetter, types) {
                                         clear: color === -1
                                     };
                                     if (overpaintCell) {
-                                        bundleLayers = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], overpaintCell.params.values.layers, true), [layer], false);
+                                        bundleLayers = tslib_1.__spreadArray(tslib_1.__spreadArray([], overpaintCell.params.values.layers, true), [layer], false);
                                         filtered = getFilteredBundle(bundleLayers, structure);
                                         update.to(overpaintCell).update(overpaint_1.Overpaint.toBundle(filtered));
                                     }
@@ -61,12 +61,12 @@ function setStructureOverpaint(plugin, components, color, lociGetter, types) {
 }
 exports.setStructureOverpaint = setStructureOverpaint;
 function clearStructureOverpaint(plugin, components, types) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, overpaintCell) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, overpaintCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                        return tslib_1.__generator(this, function (_a) {
                             if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
                                 return [2 /*return*/];
                             if (overpaintCell) {
@@ -84,9 +84,9 @@ function clearStructureOverpaint(plugin, components, types) {
 }
 exports.clearStructureOverpaint = clearStructureOverpaint;
 function eachRepr(plugin, components, callback) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var state, update, _i, components_1, c, _a, _b, r, overpaint;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;

package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -49,9 +49,9 @@ function StructureSelectionQuery(label, expression, props) {
         },
         ensureCustomProperties: props.ensureCustomProperties,
         getSelection: function (plugin, runtime, structure) {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var current, currentSelection;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             current = plugin.managers.structure.selection.getStructure(structure);
@@ -701,7 +701,7 @@ var StructureSelectionQueryRegistry = /** @class */ (function () {
         this.options = [];
         this.version = 1;
         // add built-in
-        (_a = this.list).push.apply(_a, (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Object.values(exports.StructureSelectionQueries), false), StandardAminoAcids.map(function (v) { return ResidueQuery(v, StructureSelectionCategory.AminoAcid); }), false), StandardNucleicBases.map(function (v) { return ResidueQuery(v, StructureSelectionCategory.NucleicBase); }), false));
+        (_a = this.list).push.apply(_a, tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], Object.values(exports.StructureSelectionQueries), false), StandardAminoAcids.map(function (v) { return ResidueQuery(v, StructureSelectionCategory.AminoAcid); }), false), StandardNucleicBases.map(function (v) { return ResidueQuery(v, StructureSelectionCategory.NucleicBase); }), false));
         (_b = this.options).push.apply(_b, this.list.map(function (q) { return [q, q.label, q.category]; }));
     }
     StructureSelectionQueryRegistry.prototype.add = function (q) {

package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js

@@ -16,13 +16,13 @@ var loci_1 = require("../../mol-model/loci");
 var material_1 = require("../../mol-util/material");
 var SubstanceManagerTag = 'substance-controls';
 function setStructureSubstance(plugin, components, material, lociGetter, types) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, substanceCell) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, substanceCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var structure, loci, layer, bundleLayers, filtered, filtered;
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                        return tslib_1.__generator(this, function (_a) {
                             switch (_a.label) {
                                 case 0:
                                     if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -39,7 +39,7 @@ function setStructureSubstance(plugin, components, material, lociGetter, types)
                                         clear: !material
                                     };
                                     if (substanceCell) {
-                                        bundleLayers = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], substanceCell.params.values.layers, true), [layer], false);
+                                        bundleLayers = tslib_1.__spreadArray(tslib_1.__spreadArray([], substanceCell.params.values.layers, true), [layer], false);
                                         filtered = getFilteredBundle(bundleLayers, structure);
                                         update.to(substanceCell).update(substance_1.Substance.toBundle(filtered));
                                     }
@@ -61,12 +61,12 @@ function setStructureSubstance(plugin, components, material, lociGetter, types)
 }
 exports.setStructureSubstance = setStructureSubstance;
 function clearStructureSubstance(plugin, components, types) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, substanceCell) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        return (0, tslib_1.__generator)(this, function (_a) {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, substanceCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                        return tslib_1.__generator(this, function (_a) {
                             if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
                                 return [2 /*return*/];
                             if (substanceCell) {
@@ -84,9 +84,9 @@ function clearStructureSubstance(plugin, components, types) {
 }
 exports.clearStructureSubstance = clearStructureSubstance;
 function eachRepr(plugin, components, callback) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var state, update, _i, components_1, c, _a, _b, r, substance;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     state = plugin.state.data;