molstar 2.3.9 → 3.0.0-dev.10

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

@@ -51,82 +51,95 @@ var DefaultViewerOptions = {
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
 };
 var Viewer = /** @class */ (function () {
-    function Viewer(elementOrId, colors, showButtons) {
-        var _this = this;
+    function Viewer(plugin) {
+        this.plugin = plugin;
+    }
+    Viewer.create = function (elementOrId, colors, showButtons) {
+        var _a;
         if (colors === void 0) { colors = [(0, color_1.Color)(0x992211), (0, color_1.Color)(0xDDDDDD)]; }
         if (showButtons === void 0) { showButtons = true; }
-        var _a;
-        var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), {
-            layoutIsExpanded: false,
-            layoutShowControls: false,
-            layoutShowRemoteState: false,
-            layoutShowSequence: true,
-            layoutShowLog: false,
-            layoutShowLeftPanel: true,
-            viewportShowExpand: true,
-            viewportShowControls: false,
-            viewportShowSettings: false,
-            viewportShowSelectionMode: false,
-            viewportShowAnimation: false,
-        });
-        var defaultSpec = (0, spec_1.DefaultPluginUISpec)();
-        var spec = {
-            actions: defaultSpec.actions,
-            behaviors: [
-                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Representation.HighlightLoci, { mark: false }),
-                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Representation.DefaultLociLabelProvider),
-                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Camera.FocusLoci),
-                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.StructureInfo),
-                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.Interactions),
-                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.SecondaryStructure),
-            ],
-            animations: defaultSpec.animations,
-            customParamEditors: defaultSpec.customParamEditors,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    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: {
-                    view: viewport_1.ViewportComponent
-                } }),
-            config: [
-                [config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
-                [config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
-                [config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
-                [config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
-                [config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
-                [config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
-                [config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
-                [config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
-                [config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
-                [viewport_1.ShowButtons, showButtons]
-            ]
-        };
-        var element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element)
-            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
-        this.plugin = (0, mol_plugin_ui_1.createPlugin)(element, spec);
-        this.plugin.customState = {
-            colorPalette: {
-                name: 'colors',
-                params: { list: { colors: colors } }
-            }
-        };
-        this.plugin.behaviors.canvas3d.initialized.subscribe(function (v) {
-            if (v) {
-                commands_1.PluginCommands.Canvas3D.SetSettings(_this.plugin, { settings: {
-                        renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.canvas3d.props.renderer), { backgroundColor: names_1.ColorNames.white }),
-                        camera: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.canvas3d.props.camera), { helper: { axes: { name: 'off', params: {} } } })
-                    } });
-            }
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var o, defaultSpec, spec, element, plugin;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), {
+                            layoutIsExpanded: false,
+                            layoutShowControls: false,
+                            layoutShowRemoteState: false,
+                            layoutShowSequence: true,
+                            layoutShowLog: false,
+                            layoutShowLeftPanel: true,
+                            viewportShowExpand: true,
+                            viewportShowControls: false,
+                            viewportShowSettings: false,
+                            viewportShowSelectionMode: false,
+                            viewportShowAnimation: false,
+                        });
+                        defaultSpec = (0, spec_1.DefaultPluginUISpec)();
+                        spec = {
+                            actions: defaultSpec.actions,
+                            behaviors: [
+                                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Representation.HighlightLoci, { mark: false }),
+                                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Representation.DefaultLociLabelProvider),
+                                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Camera.FocusLoci),
+                                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.StructureInfo),
+                                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.Interactions),
+                                spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.SecondaryStructure),
+                            ],
+                            animations: defaultSpec.animations,
+                            customParamEditors: defaultSpec.customParamEditors,
+                            layout: {
+                                initial: {
+                                    isExpanded: o.layoutIsExpanded,
+                                    showControls: o.layoutShowControls,
+                                    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: {
+                                    view: viewport_1.ViewportComponent
+                                } }),
+                            config: [
+                                [config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                                [config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                                [config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                                [config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                                [config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                                [config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
+                                [config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
+                                [config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                                [config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                                [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                                [viewport_1.ShowButtons, showButtons]
+                            ]
+                        };
+                        element = typeof elementOrId === 'string'
+                            ? document.getElementById(elementOrId)
+                            : elementOrId;
+                        if (!element)
+                            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(element, spec)];
+                    case 1:
+                        plugin = _b.sent();
+                        plugin.customState = {
+                            colorPalette: {
+                                name: 'colors',
+                                params: { list: { colors: colors } }
+                            }
+                        };
+                        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: {} } } })
+                                    } });
+                            }
+                        });
+                        return [2 /*return*/, new Viewer(plugin)];
+                }
+            });
         });
-    }
+    };
     Viewer.prototype.loadStructuresFromUrlsAndMerge = function (sources) {
         return (0, 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;

package/lib/commonjs/apps/docking-viewer/viewport.d.ts

@@ -9,7 +9,7 @@ import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
 export declare const StructurePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;
         carbonColor: any;
@@ -31,7 +31,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;
         carbonColor: any;

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

@@ -23,15 +23,16 @@ var config_1 = require("../../mol-plugin/config");
 var builder_1 = require("../../mol-script/language/builder");
 var mol_state_1 = require("../../mol-state");
 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)((0, tslib_1.__assign)({}, plugin.canvas3d.props.renderer), { style: { name: 'plastic', params: {} } }),
+            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: {} } })
         } });
 }
 function occlusionStyle(plugin) {
     return commands_1.PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-            renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, plugin.canvas3d.props.renderer), { style: { name: 'flat', params: {} } }),
+            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: {
                         samples: 64,
                         radius: 8,
@@ -39,7 +40,8 @@ function occlusionStyle(plugin) {
                         blurKernelSize: 13
                     } }, outline: { name: 'on', params: {
                         scale: 1.0,
-                        threshold: 0.33
+                        threshold: 0.33,
+                        color: (0, color_1.Color)(0x0000),
                     } } })
         } });
 }
@@ -57,6 +59,7 @@ var ligandSurroundings = (0, structure_selection_query_1.StructureSelectionQuery
     })
 ]));
 var PresetParams = (0, 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' },
@@ -81,8 +84,8 @@ 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), { 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)({}, typeParams), color: 'chain-id', colorParams: { palette: plugin.customState.colorPalette } }, { tag: 'polymer' }),
+                            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' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -121,8 +124,8 @@ 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)({}, typeParams), color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-                            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: (0, tslib_1.__assign)({}, typeParams), color: 'illustrative', colorParams: { palette: plugin.customState.colorPalette } }, { tag: 'polymer' }),
+                            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' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -163,8 +166,8 @@ 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), { 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), { quality: 'custom', resolution: 0.5, doubleSided: true }), color: 'partial-charge' }, { tag: 'polymer' }),
+                            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' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -205,8 +208,8 @@ 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), { 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), { 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: (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' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 3:
@@ -250,10 +253,10 @@ 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), { 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), { 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)({}, typeParams), 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), { 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: (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' }),
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 4:

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

@@ -0,0 +1,230 @@
+/**
+ * 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>
+ */
+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 { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectSelector } from '../../mol-state';
+import { Color } from '../../mol-util/color';
+import '../../mol-util/polyfill';
+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" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    layoutIsExpanded: boolean;
+    layoutShowControls: boolean;
+    layoutShowRemoteState: boolean;
+    layoutControlsDisplay: PluginLayoutControlsDisplay;
+    layoutShowSequence: boolean;
+    layoutShowLog: boolean;
+    layoutShowLeftPanel: boolean;
+    collapseLeftPanel: boolean;
+    collapseRightPanel: boolean;
+    disableAntialiasing: boolean | undefined;
+    pixelScale: number | undefined;
+    pickScale: number | undefined;
+    pickPadding: number | undefined;
+    enableWboit: boolean | undefined;
+    preferWebgl1: boolean | undefined;
+    viewportShowExpand: boolean | undefined;
+    viewportShowControls: boolean | undefined;
+    viewportShowSettings: boolean | undefined;
+    viewportShowSelectionMode: boolean | undefined;
+    viewportShowAnimation: boolean | undefined;
+    pluginStateServer: string | undefined;
+    volumeStreamingServer: string | undefined;
+    volumeStreamingDisabled: boolean;
+    pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
+    emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
+};
+declare type ViewerOptions = typeof DefaultViewerOptions;
+export declare class Viewer {
+    plugin: PluginUIContext;
+    constructor(plugin: PluginUIContext);
+    static create(elementOrId: string | HTMLElement, options?: Partial<ViewerOptions>): Promise<Viewer>;
+    setRemoteSnapshot(id: string): Promise<void>;
+    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType): Promise<void>;
+    loadStructureFromUrl(url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, options?: LoadStructureOptions): Promise<void>;
+    loadAllModelsOrAssemblyFromUrl(url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, options?: LoadStructureOptions): Promise<void>;
+    loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: {
+        dataLabel?: string;
+    }): Promise<void>;
+    loadPdb(pdb: string, options?: LoadStructureOptions): Promise<void>;
+    loadPdbDev(pdbDev: string): Promise<void>;
+    loadEmdb(emdb: string, options?: {
+        detail?: number;
+    }): Promise<void>;
+    loadAlphaFoldDb(afdb: string): Promise<void>;
+    loadModelArchive(id: string): Promise<void>;
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    loadVolumeFromUrl({ url, format, isBinary }: {
+        url: string;
+        format: BuildInVolumeFormat;
+        isBinary: boolean;
+    }, isovalues: VolumeIsovalueInfo[], options?: {
+        entryId?: string | string[];
+        isLazy?: boolean;
+    }): Promise<void>;
+    /**
+     * @example
+     *  viewer.loadTrajectory({
+     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+     *      preset: 'all-models' // or 'default'
+     *  });
+     */
+    loadTrajectory(params: LoadTrajectoryParams): Promise<{
+        model: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, 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>>;
+        coords: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, 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>>;
+        preset: {
+            model: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
+            modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
+            unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, 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>> | undefined;
+            structure: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>;
+            structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>;
+            representation: any;
+        } | {
+            models?: undefined;
+            structures?: undefined;
+        } | {
+            models: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>[];
+            structures: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>[];
+        } | {
+            model: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
+            modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
+            unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, 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>> | undefined;
+            structure: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>;
+            structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>;
+            representation: any;
+        } | {
+            model: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
+            modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, 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>>;
+            unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, 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>> | undefined;
+            structure: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>;
+            structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>>;
+            representation: any;
+        } | undefined;
+    }>;
+    handleResize(): void;
+}
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams;
+}
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative';
+    value: number;
+    color: Color;
+    alpha?: number;
+    volumeIndex?: number;
+}
+export interface LoadTrajectoryParams {
+    model: {
+        kind: 'model-url';
+        url: string;
+        format?: BuiltInTrajectoryFormat;
+        isBinary?: boolean;
+    } | {
+        kind: 'model-data';
+        data: string | number[] | ArrayBuffer | Uint8Array;
+        format?: BuiltInTrajectoryFormat;
+    } | {
+        kind: 'topology-url';
+        url: string;
+        format: BuildInStructureFormat;
+        isBinary?: boolean;
+    } | {
+        kind: 'topology-data';
+        data: string | number[] | ArrayBuffer | Uint8Array;
+        format: BuildInStructureFormat;
+    };
+    modelLabel?: string;
+    coordinates: {
+        kind: 'coordinates-url';
+        url: string;
+        format: BuildInStructureFormat;
+        isBinary?: boolean;
+    } | {
+        kind: 'coordinates-data';
+        data: string | number[] | ArrayBuffer | Uint8Array;
+        format: BuildInStructureFormat;
+    };
+    coordinatesLabel?: string;
+    preset?: keyof PresetTrajectoryHierarchy;
+}
+export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
+    ignoreHydrogens: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+        globalName: any;
+        carbonColor: any;
+        symmetryColor: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>> | undefined;
+    };
+    representations: {
+        polymer: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, 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>>;
+    };
+} | {
+    components: {
+        all: StateObjectSelector<PluginStateObject.Molecule.Structure, 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>> | undefined;
+        branched: undefined;
+    };
+    representations: {
+        all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, 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>>;
+    };
+}>;