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+/**
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+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ *
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+ * @author David Sehnal <david.sehnal@gmail.com>
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+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
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+ */
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+
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+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
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+import { CellPack } from '../../extensions/cellpack';
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+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
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+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
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+import { Mp4Export } from '../../extensions/mp4-export';
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+import { GeometryExport } from '../../extensions/geo-export';
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+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
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+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
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+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
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+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
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+import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
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+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
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+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
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+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
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+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
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+import { PluginStateObject } from '../../mol-plugin-state/objects';
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+import { StateTransforms } from '../../mol-plugin-state/transforms';
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+import { createPlugin } from '../../mol-plugin-ui';
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+import { PluginUIContext } from '../../mol-plugin-ui/context';
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+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
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+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
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+import { PluginCommands } from '../../mol-plugin/commands';
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+import { PluginConfig } from '../../mol-plugin/config';
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+import { PluginSpec } from '../../mol-plugin/spec';
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+import { PluginState } from '../../mol-plugin/state';
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+import { StateObjectSelector } from '../../mol-state';
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+import { Asset } from '../../mol-util/assets';
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+import { Color } from '../../mol-util/color';
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+import '../../mol-util/polyfill';
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+import { ObjectKeys } from '../../mol-util/type-helpers';
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+import './embedded.html';
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+import './favicon.ico';
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+import './index.html';
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+
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+require('mol-plugin-ui/skin/light.scss');
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+
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+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
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+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
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+
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+const CustomFormats = [
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+ ['g3d', G3dProvider] as const
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+];
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+
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+const Extensions = {
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+ 'cellpack': PluginSpec.Behavior(CellPack),
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+ 'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
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+ 'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
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+ 'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
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+ 'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
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+ 'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
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+ 'g3d': PluginSpec.Behavior(G3DFormat),
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+ 'mp4-export': PluginSpec.Behavior(Mp4Export),
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+ 'geo-export': PluginSpec.Behavior(GeometryExport)
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+};
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+
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+const DefaultViewerOptions = {
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+ customFormats: CustomFormats as [string, DataFormatProvider][],
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+ extensions: ObjectKeys(Extensions),
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+ layoutIsExpanded: true,
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+ layoutShowControls: true,
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+ layoutShowRemoteState: true,
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+ layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
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+ layoutShowSequence: true,
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+ layoutShowLog: true,
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+ layoutShowLeftPanel: true,
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+ collapseLeftPanel: false,
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+ disableAntialiasing: false,
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+ pixelScale: 1,
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+ enableWboit: true,
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+
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+ viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
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+ viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
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+ viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
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+ viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
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+ viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
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+ pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
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+ volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
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+ volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
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+ pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
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+ emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
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+};
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+type ViewerOptions = typeof DefaultViewerOptions;
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+
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+export class Viewer {
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+ plugin: PluginUIContext
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+
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+ constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
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+ const o = { ...DefaultViewerOptions, ...options };
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+ const defaultSpec = DefaultPluginUISpec();
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+
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+ const spec: PluginUISpec = {
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+ actions: defaultSpec.actions,
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+ behaviors: [
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+ ...defaultSpec.behaviors,
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+ ...o.extensions.map(e => Extensions[e]),
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+ ],
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+ animations: [...defaultSpec.animations || []],
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+ customParamEditors: defaultSpec.customParamEditors,
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+ customFormats: o?.customFormats,
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+ layout: {
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+ initial: {
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+ isExpanded: o.layoutIsExpanded,
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+ showControls: o.layoutShowControls,
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+ controlsDisplay: o.layoutControlsDisplay,
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+ regionState: {
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+ bottom: 'full',
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+ left: o.collapseLeftPanel ? 'collapsed' : 'full',
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+ right: 'full',
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+ top: 'full',
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+ }
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+ },
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+ },
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+ components: {
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+ ...defaultSpec.components,
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+ controls: {
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+ ...defaultSpec.components?.controls,
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+ top: o.layoutShowSequence ? undefined : 'none',
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+ bottom: o.layoutShowLog ? undefined : 'none',
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+ left: o.layoutShowLeftPanel ? undefined : 'none',
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+ },
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+ remoteState: o.layoutShowRemoteState ? 'default' : 'none',
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+ },
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+ config: [
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+ [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
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+ [PluginConfig.General.PixelScale, o.pixelScale],
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+ [PluginConfig.General.EnableWboit, o.enableWboit],
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+ [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
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+ [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
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+ [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
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+ [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
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+ [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
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+ [PluginConfig.State.DefaultServer, o.pluginStateServer],
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+ [PluginConfig.State.CurrentServer, o.pluginStateServer],
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+ [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
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+ [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
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+ [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
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+ [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
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+ ]
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+ };
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+
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+ const element = typeof elementOrId === 'string'
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+ ? document.getElementById(elementOrId)
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+ : elementOrId;
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+ if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
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+ this.plugin = createPlugin(element, spec);
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+ }
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+
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+ setRemoteSnapshot(id: string) {
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+ const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
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+ return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
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+ }
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+
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+ loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
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+ return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
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+ }
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+
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+ loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
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+ const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
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+ return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
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+ source: {
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+ name: 'url',
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+ params: {
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+ url: Asset.Url(url),
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+ format: format as any,
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+ isBinary,
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+ options: { ...params.source.params.options, representationParams: options?.representationParams as any },
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+ }
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+ }
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+ }));
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+ }
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+
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+ async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
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+ const plugin = this.plugin;
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+
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+ const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
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+ const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
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+
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+ await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
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+ }
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+
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+ async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
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+ const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
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+ const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
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+ await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
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+ }
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+
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+ loadPdb(pdb: string, options?: LoadStructureOptions) {
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+ const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
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+ const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
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+ return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
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+ source: {
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+ name: 'pdb' as const,
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+ params: {
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+ provider: {
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+ id: pdb,
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+ server: {
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+ name: provider,
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+ params: PdbDownloadProvider[provider].defaultValue as any
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+ }
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+ },
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+ options: { ...params.source.params.options, representationParams: options?.representationParams as any },
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+ }
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+ }
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+ }));
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+ }
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+
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+ loadPdbDev(pdbDev: string) {
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+ const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
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+ return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
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+ source: {
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+ name: 'pdb-dev' as const,
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+ params: {
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+ provider: {
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+ id: pdbDev,
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+ encoding: 'bcif',
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+ },
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+ options: params.source.params.options,
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+ }
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+ }
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+ }));
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+ }
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+
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+ loadEmdb(emdb: string, options?: { detail?: number }) {
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+ const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
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+ return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
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+ source: {
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+ name: 'pdb-emd-ds' as const,
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+ params: {
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+ provider: {
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+ id: emdb,
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+ server: provider,
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+ },
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+ detail: options?.detail ?? 3,
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+ }
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+ }
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+ }));
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+ }
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+
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+ /**
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+ * @example Load X-ray density from volume server
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+ viewer.loadVolumeFromUrl({
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+ url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
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+ format: 'dscif',
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+ isBinary: true
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+ }, [{
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+ type: 'relative',
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+ value: 1.5,
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+ color: 0x3362B2
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+ }, {
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+ type: 'relative',
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+ value: 3,
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+ color: 0x33BB33,
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+ volumeIndex: 1
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+ }, {
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+ type: 'relative',
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+ value: -3,
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+ color: 0xBB3333,
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+ volumeIndex: 1
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+ }], {
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+ entryId: ['2FO-FC', 'FO-FC'],
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+ isLazy: true
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+ });
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+ * *********************
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+ * @example Load EM density from volume server
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+ viewer.loadVolumeFromUrl({
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+ url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
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+ format: 'dscif',
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+ isBinary: true
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+ }, [{
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+ type: 'relative',
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+ value: 1,
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+ color: 0x3377aa
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+ }], {
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+ entryId: 'EMD-30210',
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+ isLazy: true
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+ });
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+ */
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+ async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
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+ const plugin = this.plugin;
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+
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+ if (!plugin.dataFormats.get(format)) {
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+ throw new Error(`Unknown density format: ${format}`);
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+ }
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+
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+ if (options?.isLazy) {
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+ const update = this.plugin.build();
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+ update.toRoot().apply(StateTransforms.Data.LazyVolume, {
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+ url,
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+ format,
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+ entryId: options?.entryId,
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+ isBinary,
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+ isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
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+ });
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+ return update.commit();
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+ }
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+
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+ return plugin.dataTransaction(async () => {
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+ const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
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+
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+ const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
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+ const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
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+ if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
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+
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+ const repr = plugin.build();
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+ for (const iso of isovalues) {
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+ repr
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+ .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
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+ .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
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+ type: 'isosurface',
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+ typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
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+ color: 'uniform',
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+ colorParams: { value: iso.color }
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+ }));
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+ }
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+
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+ await repr.commit();
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+ });
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+ }
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+
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+ handleResize() {
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+ this.plugin.layout.events.updated.next();
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+ }
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+}
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+
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+export interface LoadStructureOptions {
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+ representationParams?: StructureRepresentationPresetProvider.CommonParams
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+}
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+
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+export interface VolumeIsovalueInfo {
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+ type: 'absolute' | 'relative',
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+ value: number,
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+ color: Color,
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+ alpha?: number,
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+ volumeIndex?: number
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+}
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