molstar 3.3.1 → 3.4.0

package/lib/apps/docking-viewer/viewport.js

@@ -316,7 +316,7 @@ var ViewportComponent = /** @class */ (function (_super) {
     ViewportComponent.prototype.render = function () {
         var _a, _b;
         var VPControls = ((_b = (_a = this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.viewport) === null || _b === void 0 ? void 0 : _b.controls) || ViewportControls;
-        return _jsxs(_Fragment, { children: [_jsx(Viewport, {}, void 0), this.showButtons && _jsxs("div", __assign({ className: 'msp-viewport-top-left-controls' }, { children: [_jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.structurePreset }, { children: "Structure" }), void 0) }), void 0), _jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.illustrativePreset }, { children: "Illustrative" }), void 0) }), void 0), _jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.surfacePreset }, { children: "Surface" }), void 0) }), void 0), _jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.interactionsPreset }, { children: "Interactions" }), void 0) }), void 0)] }), void 0), _jsx(VPControls, {}, void 0), _jsx(BackgroundTaskProgress, {}, void 0), _jsxs("div", __assign({ className: 'msp-highlight-toast-wrapper' }, { children: [_jsx(LociLabels, {}, void 0), _jsx(Toasts, {}, void 0)] }), void 0)] }, void 0);
+        return _jsxs(_Fragment, { children: [_jsx(Viewport, {}), this.showButtons && _jsxs("div", __assign({ className: 'msp-viewport-top-left-controls' }, { children: [_jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.structurePreset }, { children: "Structure" })) })), _jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.illustrativePreset }, { children: "Illustrative" })) })), _jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.surfacePreset }, { children: "Surface" })) })), _jsx("div", __assign({ style: { marginBottom: '4px' } }, { children: _jsx(Button, __assign({ onClick: this.interactionsPreset }, { children: "Interactions" })) }))] })), _jsx(VPControls, {}), _jsx(BackgroundTaskProgress, {}), _jsxs("div", __assign({ className: 'msp-highlight-toast-wrapper' }, { children: [_jsx(LociLabels, {}), _jsx(Toasts, {})] }))] });
     };
     return ViewportComponent;
 }(PluginUIComponent));

package/lib/apps/viewer/app.d.ts

@@ -7,7 +7,8 @@
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
 import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
@@ -21,7 +22,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -179,23 +180,23 @@ export interface LoadTrajectoryParams {
     } | {
         kind: 'topology-url';
         url: string;
-        format: BuildInStructureFormat;
+        format: BuiltInTopologyFormat;
         isBinary?: boolean;
     } | {
         kind: 'topology-data';
         data: string | number[] | ArrayBuffer | Uint8Array;
-        format: BuildInStructureFormat;
+        format: BuiltInTopologyFormat;
     };
     modelLabel?: string;
     coordinates: {
         kind: 'coordinates-url';
         url: string;
-        format: BuildInStructureFormat;
+        format: BuiltInCoordinatesFormat;
         isBinary?: boolean;
     } | {
         kind: 'coordinates-data';
         data: string | number[] | ArrayBuffer | Uint8Array;
-        format: BuildInStructureFormat;
+        format: BuiltInCoordinatesFormat;
     };
     coordinatesLabel?: string;
     preset?: keyof PresetTrajectoryHierarchy;

package/lib/apps/viewer/app.js

@@ -17,6 +17,7 @@ import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { ZenodoImport } from '../../extensions/zenodo';
 import { Volume } from '../../mol-model/volume';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
@@ -50,6 +51,7 @@ var Extensions = {
     'mp4-export': PluginSpec.Behavior(Mp4Export),
     'geo-export': PluginSpec.Behavior(GeometryExport),
     'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+    'zenodo-import': PluginSpec.Behavior(ZenodoImport),
 };
 var DefaultViewerOptions = {
     customFormats: CustomFormats,

package/lib/cli/chem-comp-dict/create-saccharides.d.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export {};

package/lib/cli/chem-comp-dict/create-saccharides.js

@@ -0,0 +1,67 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __awaiter, __generator } from "tslib";
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+var writeFile = util.promisify(fs.writeFile);
+import { ensureDataAvailable, readCCD } from './util';
+function extractSaccharideNames(ccd) {
+    var saccharideNames = [];
+    for (var k in ccd) {
+        var chem_comp = ccd[k].chem_comp;
+        var type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push('UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+    'SQD');
+    return saccharideNames;
+}
+function writeSaccharideNamesFile(filePath, ionNames) {
+    var output = "/**\n * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/cli/chem-comp-dict/create-saccharides\n */\n\nexport const SaccharideNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
+    writeFile(filePath, output);
+}
+function run(out, forceDownload) {
+    if (forceDownload === void 0) { forceDownload = false; }
+    return __awaiter(this, void 0, void 0, function () {
+        var ccd, saccharideNames;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, ensureDataAvailable(forceDownload)];
+                case 1:
+                    _a.sent();
+                    return [4 /*yield*/, readCCD()];
+                case 2:
+                    ccd = _a.sent();
+                    saccharideNames = extractSaccharideNames(ccd);
+                    if (!fs.existsSync(path.dirname(out))) {
+                        fs.mkdirSync(path.dirname(out));
+                    }
+                    writeSaccharideNamesFile(out, saccharideNames);
+                    return [2 /*return*/];
+            }
+        });
+    });
+}
+var parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
+    help: 'Force download of CCD and PVCD.'
+});
+var args = parser.parse_args();
+run(args.out, args.forceDownload);

package/lib/commonjs/apps/docking-viewer/index.js

@@ -58,12 +58,12 @@ var Viewer = /** @class */ (function () {
         var _a;
         if (colors === void 0) { colors = [(0, color_1.Color)(0x992211), (0, color_1.Color)(0xDDDDDD)]; }
         if (showButtons === void 0) { showButtons = true; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var o, defaultSpec, spec, element, plugin;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
-                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), {
+                        o = tslib_1.__assign(tslib_1.__assign({}, DefaultViewerOptions), {
                             layoutIsExpanded: false,
                             layoutShowControls: false,
                             layoutShowRemoteState: false,
@@ -96,7 +96,7 @@ var Viewer = /** @class */ (function () {
                                     controlsDisplay: o.layoutControlsDisplay,
                                 },
                             },
-                            components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none', viewport: {
+                            components: tslib_1.__assign(tslib_1.__assign({}, defaultSpec.components), { controls: tslib_1.__assign(tslib_1.__assign({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none', viewport: {
                                     view: viewport_1.ViewportComponent
                                 } }),
                             config: [
@@ -130,8 +130,8 @@ var Viewer = /** @class */ (function () {
                         plugin.behaviors.canvas3d.initialized.subscribe(function (v) {
                             if (v) {
                                 commands_1.PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-                                        renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, plugin.canvas3d.props.renderer), { backgroundColor: names_1.ColorNames.white }),
-                                        camera: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, plugin.canvas3d.props.camera), { helper: { axes: { name: 'off', params: {} } } })
+                                        renderer: tslib_1.__assign(tslib_1.__assign({}, plugin.canvas3d.props.renderer), { backgroundColor: names_1.ColorNames.white }),
+                                        camera: tslib_1.__assign(tslib_1.__assign({}, plugin.canvas3d.props.camera), { helper: { axes: { name: 'off', params: {} } } })
                                     } });
                             }
                         });
@@ -141,10 +141,10 @@ var Viewer = /** @class */ (function () {
         });
     };
     Viewer.prototype.loadStructuresFromUrlsAndMerge = function (sources) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structures, _i, sources_1, _a, url, format, isBinary, data_1, trajectory, model, modelProperties, structure_2, structureProperties_1, dependsOn, data, structure, structureProperties;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         structures = [];
@@ -192,8 +192,8 @@ var Viewer = /** @class */ (function () {
                         return [4 /*yield*/, this.plugin.builders.structure.insertStructureProperties(structure)];
                     case 11:
                         structureProperties = _b.sent();
-                        this.plugin.behaviors.canvas3d.initialized.subscribe(function (v) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                            return (0, tslib_1.__generator)(this, function (_a) {
+                        this.plugin.behaviors.canvas3d.initialized.subscribe(function (v) { 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*/, this.plugin.builders.structure.representation.applyPreset(structureProperties || structure, viewport_1.StructurePreset)];
                                     case 1:
@@ -227,9 +227,9 @@ var MergeStructures = objects_1.PluginStateTransform.BuiltIn({
     apply: function (_a) {
         var _this = this;
         var params = _a.params, dependencies = _a.dependencies;
-        return mol_task_1.Task.create('Merge Structures', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Merge Structures', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var first, builder, _i, _a, ref, s, _b, _c, unit, structure;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 if (params.structures.length === 0)
                     return [2 /*return*/, mol_state_1.StateObject.Null];
                 first = dependencies[params.structures[0].ref].data;

package/lib/commonjs/apps/docking-viewer/viewport.js

@@ -26,14 +26,14 @@ var color_1 = require("../../mol-util/color");
 var material_1 = require("../../mol-util/material");
 function shinyStyle(plugin) {
     return commands_1.PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-            renderer: (0, tslib_1.__assign)({}, plugin.canvas3d.props.renderer),
-            postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, plugin.canvas3d.props.postprocessing), { occlusion: { name: 'off', params: {} }, outline: { name: 'off', params: {} } })
+            renderer: tslib_1.__assign({}, plugin.canvas3d.props.renderer),
+            postprocessing: tslib_1.__assign(tslib_1.__assign({}, plugin.canvas3d.props.postprocessing), { occlusion: { name: 'off', params: {} }, outline: { name: 'off', params: {} } })
         } });
 }
 function occlusionStyle(plugin) {
     return commands_1.PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-            renderer: (0, tslib_1.__assign)({}, plugin.canvas3d.props.renderer),
-            postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, plugin.canvas3d.props.postprocessing), { occlusion: { name: 'on', params: {
+            renderer: tslib_1.__assign({}, plugin.canvas3d.props.renderer),
+            postprocessing: tslib_1.__assign(tslib_1.__assign({}, plugin.canvas3d.props.postprocessing), { occlusion: { name: 'on', params: {
                         bias: 0.8,
                         blurKernelSize: 15,
                         radius: 5,
@@ -59,17 +59,17 @@ var ligandSurroundings = (0, structure_selection_query_1.StructureSelectionQuery
         by: structure_selection_query_1.StructureSelectionQueries.ligand.expression
     })
 ]));
-var PresetParams = (0, tslib_1.__assign)({}, representation_preset_1.StructureRepresentationPresetProvider.CommonParams);
+var PresetParams = tslib_1.__assign({}, representation_preset_1.StructureRepresentationPresetProvider.CommonParams);
 var CustomMaterial = (0, material_1.Material)({ roughness: 0.2, metalness: 0 });
 exports.StructurePreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
     id: 'preset-structure',
     display: { name: 'Structure' },
     params: function () { return PresetParams; },
     apply: function (ref, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, _a, update, builder, typeParams, representations;
             var _b;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -85,8 +85,8 @@ exports.StructurePreset = (0, representation_preset_1.StructureRepresentationPre
                             _b);
                         _a = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _a.update, builder = _a.builder, typeParams = _a.typeParams;
                         representations = {
-                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, sizeFactor: 0.35 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial }), color: 'chain-id', colorParams: { palette: plugin.customState.colorPalette } }, { tag: 'polymer' }),
+                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, sizeFactor: 0.35 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial }), color: 'chain-id', colorParams: { palette: plugin.customState.colorPalette } }, { tag: 'polymer' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -106,10 +106,10 @@ exports.IllustrativePreset = (0, representation_preset_1.StructureRepresentation
     display: { name: 'Illustrative' },
     params: function () { return PresetParams; },
     apply: function (ref, params, plugin) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, components, _a, update, builder, typeParams, representations;
             var _b;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -125,8 +125,8 @@ exports.IllustrativePreset = (0, representation_preset_1.StructureRepresentation
                             _b);
                         _a = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _a.update, builder = _a.builder, typeParams = _a.typeParams;
                         representations = {
-                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { ignoreLight: true }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { ignoreLight: true }), color: 'illustrative', colorParams: { palette: plugin.customState.colorPalette } }, { tag: 'polymer' }),
+                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { ignoreLight: true }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { ignoreLight: true }), color: 'illustrative', colorParams: { palette: plugin.customState.colorPalette } }, { tag: 'polymer' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -147,10 +147,10 @@ var SurfacePreset = (0, representation_preset_1.StructureRepresentationPresetPro
     params: function () { return PresetParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, components, _b, update, builder, typeParams, representations;
             var _c;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -167,8 +167,8 @@ var SurfacePreset = (0, representation_preset_1.StructureRepresentationPresetPro
                             _c);
                         _b = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _b.update, builder = _b.builder, typeParams = _b.typeParams;
                         representations = {
-                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, sizeFactor: 0.26 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, quality: 'custom', resolution: 0.5, doubleSided: true }), color: 'partial-charge' }, { tag: 'polymer' }),
+                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, sizeFactor: 0.26 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, quality: 'custom', resolution: 0.5, doubleSided: true }), color: 'partial-charge' }, { tag: 'polymer' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -189,10 +189,10 @@ var PocketPreset = (0, representation_preset_1.StructureRepresentationPresetProv
     params: function () { return PresetParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, components, _b, update, builder, typeParams, representations;
             var _c;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -209,8 +209,8 @@ var PocketPreset = (0, representation_preset_1.StructureRepresentationPresetProv
                             _c);
                         _b = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _b.update, builder = _b.builder, typeParams = _b.typeParams;
                         representations = {
-                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, sizeFactor: 0.26 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-                            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }), color: 'partial-charge' }, { tag: 'surroundings' }),
+                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, sizeFactor: 0.26 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+                            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }), color: 'partial-charge' }, { tag: 'surroundings' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -231,10 +231,10 @@ var InteractionsPreset = (0, representation_preset_1.StructureRepresentationPres
     params: function () { return PresetParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure, components, _b, update, builder, typeParams, representations;
             var _c;
-            return (0, tslib_1.__generator)(this, function (_d) {
+            return tslib_1.__generator(this, function (_d) {
                 switch (_d.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
@@ -254,10 +254,10 @@ var InteractionsPreset = (0, representation_preset_1.StructureRepresentationPres
                             _c);
                         _b = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _b.update, builder = _b.builder, typeParams = _b.typeParams;
                         representations = {
-                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, sizeFactor: 0.3 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-                            ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, sizeFactor: 0.1, sizeAspectRatio: 1 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
-                            interactions: builder.buildRepresentation(update, components.interactions, { type: interactions_1.InteractionsRepresentationProvider, typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial }), color: interaction_type_1.InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
-                            label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), { material: CustomMaterial, background: false, borderWidth: 0.1 }), color: 'uniform', colorParams: { value: (0, color_1.Color)(0x000000) } }, { tag: 'label' }),
+                            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, sizeFactor: 0.3 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+                            ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, sizeFactor: 0.1, sizeAspectRatio: 1 }), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
+                            interactions: builder.buildRepresentation(update, components.interactions, { type: interactions_1.InteractionsRepresentationProvider, typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial }), color: interaction_type_1.InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+                            label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: tslib_1.__assign(tslib_1.__assign({}, typeParams), { material: CustomMaterial, background: false, borderWidth: 0.1 }), color: 'uniform', colorParams: { value: (0, color_1.Color)(0x000000) } }, { tag: 'label' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 4:
@@ -274,11 +274,11 @@ var InteractionsPreset = (0, representation_preset_1.StructureRepresentationPres
 });
 exports.ShowButtons = config_1.PluginConfig.item('showButtons', true);
 var ViewportComponent = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(ViewportComponent, _super);
+    tslib_1.__extends(ViewportComponent, _super);
     function ViewportComponent() {
         var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.set = function (preset) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        _this.set = function (preset) { 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*/, this._set(this.plugin.managers.structure.hierarchy.selection.structures, preset)];
                     case 1:
@@ -295,8 +295,8 @@ var ViewportComponent = /** @class */ (function (_super) {
         return _this;
     }
     ViewportComponent.prototype._set = function (structures, preset) {
-        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*/, this.plugin.managers.structure.component.clear(structures)];
                     case 1:
@@ -319,7 +319,7 @@ var ViewportComponent = /** @class */ (function (_super) {
     ViewportComponent.prototype.render = function () {
         var _a, _b;
         var VPControls = ((_b = (_a = this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.viewport) === null || _b === void 0 ? void 0 : _b.controls) || viewport_1.ViewportControls;
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(viewport_1.Viewport, {}, void 0), this.showButtons && (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-viewport-top-left-controls' }, { children: [(0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.structurePreset }, { children: "Structure" }), void 0) }), void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.illustrativePreset }, { children: "Illustrative" }), void 0) }), void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.surfacePreset }, { children: "Surface" }), void 0) }), void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.interactionsPreset }, { children: "Interactions" }), void 0) }), void 0)] }), void 0), (0, jsx_runtime_1.jsx)(VPControls, {}, void 0), (0, jsx_runtime_1.jsx)(task_1.BackgroundTaskProgress, {}, void 0), (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-highlight-toast-wrapper' }, { children: [(0, jsx_runtime_1.jsx)(controls_1.LociLabels, {}, void 0), (0, jsx_runtime_1.jsx)(toast_1.Toasts, {}, void 0)] }), void 0)] }, void 0);
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(viewport_1.Viewport, {}), this.showButtons && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-viewport-top-left-controls' }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.structurePreset }, { children: "Structure" })) })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.illustrativePreset }, { children: "Illustrative" })) })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.surfacePreset }, { children: "Surface" })) })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginBottom: '4px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.interactionsPreset }, { children: "Interactions" })) }))] })), (0, jsx_runtime_1.jsx)(VPControls, {}), (0, jsx_runtime_1.jsx)(task_1.BackgroundTaskProgress, {}), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-highlight-toast-wrapper' }, { children: [(0, jsx_runtime_1.jsx)(controls_1.LociLabels, {}), (0, jsx_runtime_1.jsx)(toast_1.Toasts, {})] }))] });
     };
     return ViewportComponent;
 }(base_1.PluginUIComponent));

package/lib/commonjs/apps/viewer/app.d.ts

@@ -7,7 +7,8 @@
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
 import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
@@ -21,7 +22,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -179,23 +180,23 @@ export interface LoadTrajectoryParams {
     } | {
         kind: 'topology-url';
         url: string;
-        format: BuildInStructureFormat;
+        format: BuiltInTopologyFormat;
         isBinary?: boolean;
     } | {
         kind: 'topology-data';
         data: string | number[] | ArrayBuffer | Uint8Array;
-        format: BuildInStructureFormat;
+        format: BuiltInTopologyFormat;
     };
     modelLabel?: string;
     coordinates: {
         kind: 'coordinates-url';
         url: string;
-        format: BuildInStructureFormat;
+        format: BuiltInCoordinatesFormat;
         isBinary?: boolean;
     } | {
         kind: 'coordinates-data';
         data: string | number[] | ArrayBuffer | Uint8Array;
-        format: BuildInStructureFormat;
+        format: BuiltInCoordinatesFormat;
     };
     coordinatesLabel?: string;
     preset?: keyof PresetTrajectoryHierarchy;