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@@ -1,484 +1,12 @@
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/**
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- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ * Copyright (c) 2018-2022 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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-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 { GeometryExport } from '../../extensions/geo-export';
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-import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
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-import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
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-import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
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-import { Mp4Export } from '../../extensions/mp4-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 { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
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-import { PresetStructureRepresentations, 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 { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
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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 { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
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-import { createPluginUI } from '../../mol-plugin-ui';
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-import { PluginUIContext } from '../../mol-plugin-ui/context';
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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 { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
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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 { StateObjectRef, 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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- 'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
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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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- collapseRightPanel: false,
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- disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
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- pixelScale: PluginConfig.General.PixelScale.defaultValue,
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- pickScale: PluginConfig.General.PickScale.defaultValue,
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- pickPadding: PluginConfig.General.PickPadding.defaultValue,
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- enableWboit: PluginConfig.General.EnableWboit.defaultValue,
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- preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
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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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- constructor(public plugin: PluginUIContext) {
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- }
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-
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- static async create(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: o.collapseRightPanel ? 'hidden' : '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.PickScale, o.pickScale],
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- [PluginConfig.General.PickPadding, o.pickPadding],
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- [PluginConfig.General.EnableWboit, o.enableWboit],
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- [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
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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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- [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
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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 '${elementOrId}'`);
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- const plugin = await createPluginUI(element, spec, {
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- onBeforeUIRender: plugin => {
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- // the preset needs to be added before the UI renders otherwise
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- // "Download Structure" wont be able to pick it up
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- plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
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- }
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- });
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- return new Viewer(plugin);
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- }
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-
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- setRemoteSnapshot(id: string) {
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- const url = `${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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- loadAlphaFoldDb(afdb: 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: 'alphafolddb' as const,
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- params: {
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- id: afdb,
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- options: {
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- ...params.source.params.options,
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- representation: 'preset-structure-representation-ma-quality-assessment-plddt'
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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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- loadModelArchive(id: 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: 'modelarchive' as const,
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- params: {
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- id,
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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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- /**
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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) {
|
|
|
- repr
|
|
|
- .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
|
|
|
- .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
|
|
|
- type: 'isosurface',
|
|
|
- typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
|
|
|
- color: 'uniform',
|
|
|
- colorParams: { value: iso.color }
|
|
|
- }));
|
|
|
- }
|
|
|
-
|
|
|
- await repr.commit();
|
|
|
- });
|
|
|
- }
|
|
|
-
|
|
|
- /**
|
|
|
- * @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'
|
|
|
- * });
|
|
|
- */
|
|
|
- async loadTrajectory(params: LoadTrajectoryParams) {
|
|
|
- const plugin = this.plugin;
|
|
|
-
|
|
|
- let model: StateObjectSelector, coords: StateObjectSelector;
|
|
|
-
|
|
|
- if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
|
|
|
- const data = params.model.kind === 'model-data'
|
|
|
- ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
|
|
|
- : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
|
|
|
-
|
|
|
- const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
|
|
|
- model = await plugin.builders.structure.createModel(trajectory);
|
|
|
- } else {
|
|
|
- const data = params.model.kind === 'topology-data'
|
|
|
- ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
|
|
|
- : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
|
|
|
-
|
|
|
- const provider = plugin.dataFormats.get(params.model.format);
|
|
|
- model = await provider!.parse(plugin, data);
|
|
|
- }
|
|
|
-
|
|
|
- {
|
|
|
- const data = params.coordinates.kind === 'coordinates-data'
|
|
|
- ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
|
|
|
- : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
|
|
|
-
|
|
|
- const provider = plugin.dataFormats.get(params.coordinates.format);
|
|
|
- coords = await provider!.parse(plugin, data);
|
|
|
- }
|
|
|
-
|
|
|
- const trajectory = await plugin.build().toRoot()
|
|
|
- .apply(TrajectoryFromModelAndCoordinates, {
|
|
|
- modelRef: model.ref,
|
|
|
- coordinatesRef: coords.ref
|
|
|
- }, { dependsOn: [model.ref, coords.ref] })
|
|
|
- .commit();
|
|
|
-
|
|
|
- const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
|
|
|
-
|
|
|
- return { model, coords, preset };
|
|
|
- }
|
|
|
-
|
|
|
- handleResize() {
|
|
|
- this.plugin.layout.events.updated.next(void 0);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-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 /* mmcif */, isBinary?: boolean }
|
|
|
- | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
|
|
|
- | { 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 const ViewerAutoPreset = StructureRepresentationPresetProvider({
|
|
|
- id: 'preset-structure-representation-viewer-auto',
|
|
|
- display: {
|
|
|
- name: 'Automatic (w/ Annotation)', group: 'Annotation',
|
|
|
- description: 'Show standard automatic representation but colored by quality assessment (if available in the model).'
|
|
|
- },
|
|
|
- isApplicable(a) {
|
|
|
- return (
|
|
|
- !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')) ||
|
|
|
- !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))
|
|
|
- );
|
|
|
- },
|
|
|
- params: () => StructureRepresentationPresetProvider.CommonParams,
|
|
|
- async apply(ref, params, plugin) {
|
|
|
- const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
|
|
|
- const structure = structureCell?.obj?.data;
|
|
|
- if (!structureCell || !structure) return {};
|
|
|
-
|
|
|
- if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT'))) {
|
|
|
- return await QualityAssessmentPLDDTPreset.apply(ref, params, plugin);
|
|
|
- } else if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))) {
|
|
|
- return await QualityAssessmentQmeanPreset.apply(ref, params, plugin);
|
|
|
- } else {
|
|
|
- return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
|
|
|
- }
|
|
|
- }
|
|
|
-});
|
|
|
+export * from './app';
|
Alexander Rose