molstar 3.3.1 → 3.6.0

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;

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, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }), 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, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }), 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:

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();

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;

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;

package/lib/commonjs/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts}

@@ -1,44 +1,48 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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 StructureFormatCategory = "Structure";
-export declare const PsfProvider: {
+export declare const CoordinatesFormatCategory = "Coordinates";
+export { DcdProvider };
+declare const DcdProvider: {
     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<{}>>>;
-    }>;
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 };
-export declare const DcdProvider: {
+declare type DcdProvider = typeof DcdProvider;
+export { XtcProvider };
+declare const XtcProvider: {
     label: string;
     description: string;
     category: string;
     binaryExtensions: string[];
     parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 };
-export declare const XtcProvider: {
+declare type XtcProvider = typeof XtcProvider;
+export { TrrProvider };
+declare const TrrProvider: {
     label: string;
     description: string;
     category: string;
     binaryExtensions: string[];
     parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 };
-export declare const BuiltInStructureFormats: readonly [readonly ["psf", {
+declare type TrrProvider = typeof TrrProvider;
+export { NctrajProvider };
+declare const NctrajProvider: {
     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 ["dcd", {
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+};
+declare type NctrajProvider = typeof NctrajProvider;
+export declare type CoordinatesProvider = DcdProvider | XtcProvider | TrrProvider;
+export declare const BuiltInCoordinatesFormats: readonly [readonly ["dcd", {
     label: string;
     description: string;
     category: string;
@@ -50,5 +54,17 @@ export declare const BuiltInStructureFormats: readonly [readonly ["psf", {
     category: string;
     binaryExtensions: string[];
     parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+}], readonly ["trr", {
+    label: string;
+    description: string;
+    category: string;
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+}], readonly ["nctraj", {
+    label: string;
+    description: string;
+    category: string;
+    binaryExtensions: string[];
+    parse: (plugin: import("../../mol-plugin/context").PluginContext, data: import("../../mol-state").StateObjectRef<import("../objects").PluginStateObject.Data.String | import("../objects").PluginStateObject.Data.Binary>) => Promise<import("../../mol-state").StateObjectSelector<import("../objects").PluginStateObject.Molecule.Coordinates, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
 }]];
-export declare type BuildInStructureFormat = (typeof BuiltInStructureFormats)[number][0];
+export declare type BuiltInCoordinatesFormat = (typeof BuiltInCoordinatesFormats)[number][0];

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

@@ -0,0 +1,70 @@
+"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.BuiltInCoordinatesFormats = exports.NctrajProvider = exports.TrrProvider = exports.XtcProvider = exports.DcdProvider = exports.CoordinatesFormatCategory = void 0;
+var transforms_1 = require("../transforms");
+var provider_1 = require("./provider");
+exports.CoordinatesFormatCategory = 'Coordinates';
+var DcdProvider = (0, provider_1.DataFormatProvider)({
+    label: 'DCD',
+    description: 'DCD',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['dcd'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromDcd);
+        return coordinates.commit();
+    }
+});
+exports.DcdProvider = DcdProvider;
+var XtcProvider = (0, provider_1.DataFormatProvider)({
+    label: 'XTC',
+    description: 'XTC',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['xtc'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromXtc);
+        return coordinates.commit();
+    }
+});
+exports.XtcProvider = XtcProvider;
+var TrrProvider = (0, provider_1.DataFormatProvider)({
+    label: 'TRR',
+    description: 'TRR',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['trr'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromTrr);
+        return coordinates.commit();
+    }
+});
+exports.TrrProvider = TrrProvider;
+var NctrajProvider = (0, provider_1.DataFormatProvider)({
+    label: 'NCTRAJ',
+    description: 'NCTRAJ',
+    category: exports.CoordinatesFormatCategory,
+    binaryExtensions: ['nc', 'nctraj'],
+    parse: function (plugin, data) {
+        var coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(transforms_1.StateTransforms.Model.CoordinatesFromNctraj);
+        return coordinates.commit();
+    }
+});
+exports.NctrajProvider = NctrajProvider;
+exports.BuiltInCoordinatesFormats = [
+    ['dcd', DcdProvider],
+    ['xtc', XtcProvider],
+    ['trr', TrrProvider],
+    ['nctraj', NctrajProvider],
+];

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 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>
@@ -13,10 +13,10 @@ export declare class DataFormatRegistry {
     private _extensions;
     private _binaryExtensions;
     private _options;
-    get types(): [string, string][];
+    get types(): [name: string, label: string][];
     get extensions(): Set<string>;
     get binaryExtensions(): Set<string>;
-    get options(): [string, string, string][];
+    get options(): [name: string, label: string, category: string][];
     constructor();
     private _clear;
     add(name: string, provider: DataFormatProvider): void;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 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>
@@ -10,7 +10,8 @@ exports.DataFormatRegistry = void 0;
 var trajectory_1 = require("./trajectory");
 var volume_1 = require("./volume");
 var shape_1 = require("./shape");
-var structure_1 = require("./structure");
+var topology_1 = require("./topology");
+var coordinates_1 = require("./coordinates");
 var DataFormatRegistry = /** @class */ (function () {
     function DataFormatRegistry() {
         this._list = [];
@@ -22,16 +23,20 @@ var DataFormatRegistry = /** @class */ (function () {
             var _a = BuiltInVolumeFormats_1[_i], id = _a[0], p = _a[1];
             this.add(id, p);
         }
-        for (var _b = 0, BuiltInStructureFormats_1 = structure_1.BuiltInStructureFormats; _b < BuiltInStructureFormats_1.length; _b++) {
-            var _c = BuiltInStructureFormats_1[_b], id = _c[0], p = _c[1];
+        for (var _b = 0, BuiltInTopologyFormats_1 = topology_1.BuiltInTopologyFormats; _b < BuiltInTopologyFormats_1.length; _b++) {
+            var _c = BuiltInTopologyFormats_1[_b], id = _c[0], p = _c[1];
             this.add(id, p);
         }
-        for (var _d = 0, BuiltInShapeFormats_1 = shape_1.BuiltInShapeFormats; _d < BuiltInShapeFormats_1.length; _d++) {
-            var _e = BuiltInShapeFormats_1[_d], id = _e[0], p = _e[1];
+        for (var _d = 0, BuiltInCoordinatesFormats_1 = coordinates_1.BuiltInCoordinatesFormats; _d < BuiltInCoordinatesFormats_1.length; _d++) {
+            var _e = BuiltInCoordinatesFormats_1[_d], id = _e[0], p = _e[1];
             this.add(id, p);
         }
-        for (var _f = 0, BuiltInTrajectoryFormats_1 = trajectory_1.BuiltInTrajectoryFormats; _f < BuiltInTrajectoryFormats_1.length; _f++) {
-            var _g = BuiltInTrajectoryFormats_1[_f], id = _g[0], p = _g[1];
+        for (var _f = 0, BuiltInShapeFormats_1 = shape_1.BuiltInShapeFormats; _f < BuiltInShapeFormats_1.length; _f++) {
+            var _g = BuiltInShapeFormats_1[_f], id = _g[0], p = _g[1];
+            this.add(id, p);
+        }
+        for (var _h = 0, BuiltInTrajectoryFormats_1 = trajectory_1.BuiltInTrajectoryFormats; _h < BuiltInTrajectoryFormats_1.length; _h++) {
+            var _j = BuiltInTrajectoryFormats_1[_h], id = _j[0], p = _j[1];
             this.add(id, p);
         }
     }

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

@@ -16,9 +16,9 @@ exports.PlyProvider = (0, provider_1.DataFormatProvider)({
     description: 'PLY',
     category: exports.ShapeFormatCategory,
     stringExtensions: ['ply'],
-    parse: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    parse: function (plugin, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var format, shape;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = plugin.state.data.build()