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* Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * @author David Sehnal \n * @author Alexander Rose \n * @author Neli Fonseca \n * @author Adam Midlik \n */\n\nimport {\n // Extensions\n ANVILMembraneOrientation,\n AssemblySymmetry,\n AssemblySymmetryConfig,\n // Backgrounds,\n DnatcoNtCs,\n G3DFormat,\n G3dProvider,\n GeometryExport,\n MAQualityAssessment,\n MAQualityAssessmentConfig,\n ModelExport,\n Mp4Export,\n MolViewSpec,\n PDBeStructureQualityReport,\n QualityAssessment,\n QualityAssessmentPLDDTPreset,\n QualityAssessmentQmeanPreset,\n RCSBValidationReport,\n SbNcbrPartialCharges,\n SbNcbrPartialChargesPreset,\n SbNcbrPartialChargesPropertyProvider,\n SbNcbrTunnels,\n wwPDBChemicalComponentDictionary,\n wwPDBStructConnExtensionFunctions,\n ZenodoImport,\n // MVS\n loadMVS,\n loadMVSData,\n loadMVSX,\n type MolstarLoadingExtension,\n MVSData,\n // Types\n type SaccharideCompIdMapType,\n // Volume\n Volume,\n // Actions\n DownloadDensity,\n DownloadStructure,\n PdbDownloadProvider,\n // Hierarchy\n type PresetTrajectoryHierarchy,\n // Representation\n PresetStructureRepresentations,\n StructureRepresentationPresetProvider,\n // Formats\n type BuiltInCoordinatesFormat,\n type BuildInVolumeFormat,\n type BuiltInTopologyFormat,\n type BuiltInTrajectoryFormat,\n type DataFormatProvider,\n // Helpers\n createVolumeRepresentationParams,\n // Objects\n type PluginStateObject,\n // Transforms\n StateTransforms,\n TrajectoryFromModelAndCoordinates,\n // UI\n type PluginUIContext,\n createPluginUI,\n DefaultPluginUISpec,\n type PluginUISpec,\n renderReact18,\n // Plugin\n PluginCommands,\n PluginConfig,\n type PluginConfigItem,\n type PluginLayoutControlsDisplay,\n PluginSpec,\n type PluginState,\n // State\n StateObjectRef,\n type StateObjectSelector,\n // Task\n Task,\n // Util\n Asset,\n Color,\n ObjectKeys,\n OpenFiles,\n StringLike,\n // Debug exports\n consoleStats,\n isDebugMode,\n isProductionMode,\n isTimingMode,\n // PLUGIN_VERSION as version,\n setDebugMode,\n setProductionMode,\n setTimingMode,\n} from \"https://esm.sh/jsr/@zachcp/molstar@5.3.20\";\n\nexport {\n // version,\n consoleStats,\n isDebugMode,\n isProductionMode,\n isTimingMode,\n setDebugMode,\n setProductionMode,\n setTimingMode,\n};\n\nconst CustomFormats = [[\"g3d\", G3dProvider] as const];\n\nexport const ExtensionMap = {\n // backgrounds: PluginSpec.Behavior(Backgrounds),\n \"dnatco-ntcs\": PluginSpec.Behavior(DnatcoNtCs),\n \"pdbe-structure-quality-report\": PluginSpec.Behavior(\n PDBeStructureQualityReport,\n ),\n \"assembly-symmetry\": PluginSpec.Behavior(AssemblySymmetry),\n \"rcsb-validation-report\": PluginSpec.Behavior(RCSBValidationReport),\n \"anvil-membrane-orientation\": PluginSpec.Behavior(ANVILMembraneOrientation),\n g3d: PluginSpec.Behavior(G3DFormat),\n \"model-export\": PluginSpec.Behavior(ModelExport),\n \"mp4-export\": PluginSpec.Behavior(Mp4Export),\n \"geo-export\": PluginSpec.Behavior(GeometryExport),\n \"ma-quality-assessment\": PluginSpec.Behavior(MAQualityAssessment),\n \"zenodo-import\": PluginSpec.Behavior(ZenodoImport),\n \"sb-ncbr-partial-charges\": PluginSpec.Behavior(SbNcbrPartialCharges),\n \"wwpdb-chemical-component-dictionary\": PluginSpec.Behavior(\n wwPDBChemicalComponentDictionary,\n ),\n mvs: PluginSpec.Behavior(MolViewSpec),\n tunnels: PluginSpec.Behavior(SbNcbrTunnels),\n};\n\nconst DefaultViewerOptions = {\n customFormats: CustomFormats as [string, DataFormatProvider][],\n extensions: ObjectKeys(ExtensionMap),\n disabledExtensions: [] as string[],\n layoutIsExpanded: true,\n layoutShowControls: true,\n layoutShowRemoteState: true,\n layoutControlsDisplay: \"reactive\" as PluginLayoutControlsDisplay,\n layoutShowSequence: true,\n layoutShowLog: true,\n layoutShowLeftPanel: true,\n collapseLeftPanel: false,\n collapseRightPanel: false,\n disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,\n pixelScale: PluginConfig.General.PixelScale.defaultValue,\n pickScale: PluginConfig.General.PickScale.defaultValue,\n transparency: PluginConfig.General.Transparency.defaultValue,\n preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,\n allowMajorPerformanceCaveat:\n PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,\n powerPreference: PluginConfig.General.PowerPreference.defaultValue,\n resolutionMode: PluginConfig.General.ResolutionMode.defaultValue,\n illumination: false,\n\n viewportShowReset: PluginConfig.Viewport.ShowReset.defaultValue,\n viewportShowScreenshotControls:\n PluginConfig.Viewport.ShowScreenshotControls.defaultValue,\n viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,\n viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,\n viewportShowToggleFullscreen:\n PluginConfig.Viewport.ShowToggleFullscreen.defaultValue,\n viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,\n viewportShowSelectionMode:\n PluginConfig.Viewport.ShowSelectionMode.defaultValue,\n viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,\n viewportShowTrajectoryControls:\n PluginConfig.Viewport.ShowTrajectoryControls.defaultValue,\n pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,\n volumeStreamingServer:\n PluginConfig.VolumeStreaming.DefaultServer.defaultValue,\n volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,\n pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,\n emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,\n saccharideCompIdMapType: \"default\" as SaccharideCompIdMapType,\n rcsbAssemblySymmetryDefaultServerType:\n AssemblySymmetryConfig.DefaultServerType.defaultValue,\n rcsbAssemblySymmetryDefaultServerUrl:\n AssemblySymmetryConfig.DefaultServerUrl.defaultValue,\n rcsbAssemblySymmetryApplyColors:\n AssemblySymmetryConfig.ApplyColors.defaultValue,\n\n config: [] as [PluginConfigItem, any][],\n};\ntype ViewerOptions = typeof DefaultViewerOptions;\n\nexport class Viewer {\n constructor(public plugin: PluginUIContext) {}\n\n static async create(\n elementOrId: string | HTMLElement,\n options: Partial = {},\n ) {\n const definedOptions = {} as any;\n // filter for defined properies only so the default values\n // are property applied\n for (const p of Object.keys(options) as (keyof ViewerOptions)[]) {\n if (options[p] !== void 0) definedOptions[p] = options[p];\n }\n\n const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };\n const defaultSpec = DefaultPluginUISpec();\n\n const disabledExtension = new Set(o.disabledExtensions ?? []);\n\n const spec: PluginUISpec = {\n actions: defaultSpec.actions,\n behaviors: [\n ...defaultSpec.behaviors,\n ...o.extensions\n .filter((e) => !disabledExtension.has(e))\n .map((e) => ExtensionMap[e]),\n ],\n animations: [...(defaultSpec.animations || [])],\n customParamEditors: defaultSpec.customParamEditors,\n customFormats: o?.customFormats,\n layout: {\n initial: {\n isExpanded: o.layoutIsExpanded,\n showControls: o.layoutShowControls,\n controlsDisplay: o.layoutControlsDisplay,\n regionState: {\n bottom: \"full\",\n left: o.collapseLeftPanel ? \"collapsed\" : \"full\",\n right: o.collapseRightPanel ? \"hidden\" : \"full\",\n top: \"full\",\n },\n },\n },\n components: {\n ...defaultSpec.components,\n controls: {\n ...defaultSpec.components?.controls,\n top: o.layoutShowSequence ? undefined : \"none\",\n bottom: o.layoutShowLog ? undefined : \"none\",\n left: o.layoutShowLeftPanel ? undefined : \"none\",\n },\n remoteState: o.layoutShowRemoteState ? \"default\" : \"none\",\n },\n\n config: [\n [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],\n [PluginConfig.General.PixelScale, o.pixelScale],\n [PluginConfig.General.PickScale, o.pickScale],\n [PluginConfig.General.Transparency, o.transparency],\n [PluginConfig.General.PreferWebGl1, o.preferWebgl1],\n [\n PluginConfig.General.AllowMajorPerformanceCaveat,\n o.allowMajorPerformanceCaveat,\n ],\n [PluginConfig.General.PowerPreference, o.powerPreference],\n [PluginConfig.General.ResolutionMode, o.resolutionMode],\n [PluginConfig.Viewport.ShowReset, o.viewportShowReset],\n [\n PluginConfig.Viewport.ShowScreenshotControls,\n o.viewportShowScreenshotControls,\n ],\n [PluginConfig.Viewport.ShowControls, o.viewportShowControls],\n [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],\n [\n PluginConfig.Viewport.ShowToggleFullscreen,\n o.viewportShowToggleFullscreen,\n ],\n [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],\n [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],\n [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],\n [\n PluginConfig.Viewport.ShowTrajectoryControls,\n o.viewportShowTrajectoryControls,\n ],\n [PluginConfig.State.DefaultServer, o.pluginStateServer],\n [PluginConfig.State.CurrentServer, o.pluginStateServer],\n [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],\n [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],\n [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],\n [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],\n [\n PluginConfig.Structure.DefaultRepresentationPreset,\n ViewerAutoPreset.id,\n ],\n [\n PluginConfig.Structure.SaccharideCompIdMapType,\n o.saccharideCompIdMapType,\n ],\n [\n AssemblySymmetryConfig.DefaultServerType,\n o.rcsbAssemblySymmetryDefaultServerType,\n ],\n [\n AssemblySymmetryConfig.DefaultServerUrl,\n o.rcsbAssemblySymmetryDefaultServerUrl,\n ],\n [AssemblySymmetryConfig.ApplyColors, o.rcsbAssemblySymmetryApplyColors],\n ...(o.config ?? []),\n ],\n };\n\n const element =\n typeof elementOrId === \"string\"\n ? document.getElementById(elementOrId)\n : elementOrId;\n if (!element)\n throw new Error(`Could not get element with id '${elementOrId}'`);\n const plugin = await createPluginUI({\n target: element,\n spec,\n render: renderReact18,\n onBeforeUIRender: (plugin) => {\n // the preset needs to be added before the UI renders otherwise\n // \"Download Structure\" wont be able to pick it up\n plugin.builders.structure.representation.registerPreset(\n ViewerAutoPreset,\n );\n },\n });\n plugin.canvas3d?.setProps({ illumination: { enabled: o.illumination } });\n return new Viewer(plugin);\n }\n\n setRemoteSnapshot(id: string) {\n const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;\n return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });\n }\n\n loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {\n return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });\n }\n\n loadStructureFromUrl(\n url: string,\n format: BuiltInTrajectoryFormat = \"mmcif\",\n isBinary = false,\n options?: LoadStructureOptions & { label?: string },\n ) {\n const params = DownloadStructure.createDefaultParams(\n this.plugin.state.data.root.obj!,\n this.plugin,\n );\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(DownloadStructure, {\n source: {\n name: \"url\",\n params: {\n url: Asset.Url(url),\n format: format as any,\n isBinary,\n label: options?.label,\n options: {\n ...params.source.params.options,\n representationParams: options?.representationParams as any,\n },\n },\n },\n }),\n );\n }\n\n async loadAllModelsOrAssemblyFromUrl(\n url: string,\n format: BuiltInTrajectoryFormat = \"mmcif\",\n isBinary = false,\n options?: LoadStructureOptions,\n ) {\n const plugin = this.plugin;\n\n const data = await plugin.builders.data.download(\n { url, isBinary },\n { state: { isGhost: true } },\n );\n const trajectory = await plugin.builders.structure.parseTrajectory(\n data,\n format,\n );\n\n await this.plugin.builders.structure.hierarchy.applyPreset(\n trajectory,\n \"all-models\",\n {\n useDefaultIfSingleModel: true,\n representationPresetParams: options?.representationParams,\n },\n );\n }\n\n async loadStructureFromData(\n data: string | number[],\n format: BuiltInTrajectoryFormat,\n options?: { dataLabel?: string },\n ) {\n const _data = await this.plugin.builders.data.rawData({\n data,\n label: options?.dataLabel,\n });\n const trajectory = await this.plugin.builders.structure.parseTrajectory(\n _data,\n format,\n );\n await this.plugin.builders.structure.hierarchy.applyPreset(\n trajectory,\n \"default\",\n );\n }\n\n loadPdb(pdb: string, options?: LoadStructureOptions) {\n const params = DownloadStructure.createDefaultParams(\n this.plugin.state.data.root.obj!,\n this.plugin,\n );\n const provider = this.plugin.config.get(\n PluginConfig.Download.DefaultPdbProvider,\n )!;\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(DownloadStructure, {\n source: {\n name: \"pdb\" as const,\n params: {\n provider: {\n id: pdb,\n server: {\n name: provider,\n params: PdbDownloadProvider[provider].defaultValue as any,\n },\n },\n options: {\n ...params.source.params.options,\n representationParams: options?.representationParams as any,\n },\n },\n },\n }),\n );\n }\n\n /**\n * @deprecated Scheduled for removal in v5. Use {@link loadPdbIhm | loadPdbIhm(pdbIhm: string)} instead.\n */\n loadPdbDev(pdbDev: string) {\n return this.loadPdbIhm(pdbDev);\n }\n\n loadPdbIhm(pdbIhm: string) {\n const params = DownloadStructure.createDefaultParams(\n this.plugin.state.data.root.obj!,\n this.plugin,\n );\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(DownloadStructure, {\n source: {\n name: \"pdb-ihm\" as const,\n params: {\n provider: {\n id: pdbIhm,\n encoding: \"bcif\",\n },\n options: params.source.params.options,\n },\n },\n }),\n );\n }\n\n loadEmdb(emdb: string, options?: { detail?: number }) {\n const provider = this.plugin.config.get(\n PluginConfig.Download.DefaultEmdbProvider,\n )!;\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(DownloadDensity, {\n source: {\n name: \"pdb-emd-ds\" as const,\n params: {\n provider: {\n id: emdb,\n server: provider,\n },\n detail: options?.detail ?? 3,\n },\n },\n }),\n );\n }\n\n loadAlphaFoldDb(afdb: string) {\n const params = DownloadStructure.createDefaultParams(\n this.plugin.state.data.root.obj!,\n this.plugin,\n );\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(DownloadStructure, {\n source: {\n name: \"alphafolddb\" as const,\n params: {\n provider: {\n id: afdb,\n encoding: \"bcif\",\n },\n options: {\n ...params.source.params.options,\n representation:\n \"preset-structure-representation-ma-quality-assessment-plddt\",\n },\n },\n },\n }),\n );\n }\n\n loadModelArchive(id: string) {\n const params = DownloadStructure.createDefaultParams(\n this.plugin.state.data.root.obj!,\n this.plugin,\n );\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(DownloadStructure, {\n source: {\n name: \"modelarchive\" as const,\n params: {\n id,\n options: params.source.params.options,\n },\n },\n }),\n );\n }\n\n /**\n * @example Load X-ray density from volume server\n viewer.loadVolumeFromUrl({\n url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',\n format: 'dscif',\n isBinary: true\n }, [{\n type: 'relative',\n value: 1.5,\n color: 0x3362B2\n }, {\n type: 'relative',\n value: 3,\n color: 0x33BB33,\n volumeIndex: 1\n }, {\n type: 'relative',\n value: -3,\n color: 0xBB3333,\n volumeIndex: 1\n }], {\n entryId: ['2FO-FC', 'FO-FC'],\n isLazy: true\n });\n * *********************\n * @example Load EM density from volume server\n viewer.loadVolumeFromUrl({\n url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',\n format: 'dscif',\n isBinary: true\n }, [{\n type: 'relative',\n value: 1,\n color: 0x3377aa\n }], {\n entryId: 'EMD-30210',\n isLazy: true\n });\n */\n async loadVolumeFromUrl(\n {\n url,\n format,\n isBinary,\n }: { url: string; format: BuildInVolumeFormat; isBinary: boolean },\n isovalues: VolumeIsovalueInfo[],\n options?: { entryId?: string | string[]; isLazy?: boolean },\n ) {\n const plugin = this.plugin;\n\n if (!plugin.dataFormats.get(format)) {\n throw new Error(`Unknown density format: ${format}`);\n }\n\n if (options?.isLazy) {\n const update = this.plugin.build();\n update.toRoot().apply(StateTransforms.Data.LazyVolume, {\n url,\n format,\n entryId: options?.entryId,\n isBinary,\n isovalues: isovalues.map((v) => ({ alpha: 1, volumeIndex: 0, ...v })),\n });\n return update.commit();\n }\n\n return plugin.dataTransaction(async () => {\n const data = await plugin.builders.data.download(\n { url, isBinary },\n { state: { isGhost: true } },\n );\n\n const parsed = await plugin.dataFormats\n .get(format)!\n .parse(plugin, data, { entryId: options?.entryId });\n const firstVolume = (parsed.volume ||\n parsed\n .volumes[0]) as StateObjectSelector;\n if (!firstVolume?.isOk) throw new Error(\"Failed to parse any volume.\");\n\n const repr = plugin.build();\n for (const iso of isovalues) {\n const volume: StateObjectSelector =\n parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume;\n const volumeData = volume.cell!.obj!.data;\n repr.to(volume).apply(\n StateTransforms.Representation.VolumeRepresentation3D,\n createVolumeRepresentationParams(this.plugin, firstVolume.data!, {\n type: \"isosurface\",\n typeParams: {\n alpha: iso.alpha ?? 1,\n isoValue: Volume.adjustedIsoValue(\n volumeData,\n iso.value,\n iso.type,\n ),\n },\n color: \"uniform\",\n colorParams: { value: iso.color },\n }),\n );\n }\n\n await repr.commit();\n });\n }\n\n loadFullResolutionEMDBMap(\n emdbId: string,\n options: { isoValue: Volume.IsoValue; color?: Color },\n ) {\n const plugin = this.plugin;\n const numericId = parseInt(emdbId.toUpperCase().replace(\"EMD-\", \"\"));\n const url = `https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-${numericId}/map/emd_${numericId}.map.gz`;\n\n return plugin.dataTransaction(async () => {\n const data = await plugin\n .build()\n .toRoot()\n .apply(\n StateTransforms.Data.Download,\n { url, isBinary: true, label: emdbId },\n {\n state: { isGhost: true },\n },\n )\n .apply(StateTransforms.Data.DeflateData)\n .commit();\n\n const parsed = await plugin.dataFormats\n .get(\"ccp4\")!\n .parse(plugin, data, { entryId: emdbId });\n const firstVolume = (parsed.volume ||\n parsed\n .volumes[0]) as StateObjectSelector;\n if (!firstVolume?.isOk) throw new Error(\"Failed to parse any volume.\");\n\n const volume: StateObjectSelector =\n parsed.volumes?.[0] ?? parsed.volume;\n await plugin\n .build()\n .to(volume)\n .apply(\n StateTransforms.Representation.VolumeRepresentation3D,\n createVolumeRepresentationParams(this.plugin, firstVolume.data!, {\n type: \"isosurface\",\n typeParams: { alpha: 1, isoValue: options.isoValue },\n color: \"uniform\",\n colorParams: { value: options.color ?? Color(0x33bb33) },\n }),\n )\n .commit();\n });\n }\n\n /**\n * @example\n * viewer.loadTrajectory({\n * model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },\n * coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },\n * preset: 'all-models' // or 'default'\n * });\n */\n async loadTrajectory(params: LoadTrajectoryParams) {\n const plugin = this.plugin;\n\n let model: StateObjectSelector;\n\n if (\n params.model.kind === \"model-data\" ||\n params.model.kind === \"model-url\"\n ) {\n const data =\n params.model.kind === \"model-data\"\n ? await plugin.builders.data.rawData({\n data: params.model.data,\n label: params.modelLabel,\n })\n : await plugin.builders.data.download({\n url: params.model.url,\n isBinary: params.model.isBinary,\n label: params.modelLabel,\n });\n\n const trajectory = await plugin.builders.structure.parseTrajectory(\n data,\n params.model.format ?? \"mmcif\",\n );\n model = await plugin.builders.structure.createModel(trajectory);\n } else {\n const data =\n params.model.kind === \"topology-data\"\n ? await plugin.builders.data.rawData({\n data: params.model.data,\n label: params.modelLabel,\n })\n : await plugin.builders.data.download({\n url: params.model.url,\n isBinary: params.model.isBinary,\n label: params.modelLabel,\n });\n\n const provider = plugin.dataFormats.get(params.model.format);\n const parsed = await provider!.parse(plugin, data);\n model = parsed.topology;\n }\n\n const data =\n params.coordinates.kind === \"coordinates-data\"\n ? await plugin.builders.data.rawData({\n data: params.coordinates.data,\n label: params.coordinatesLabel,\n })\n : await plugin.builders.data.download({\n url: params.coordinates.url,\n isBinary: params.coordinates.isBinary,\n label: params.coordinatesLabel,\n });\n\n const provider = plugin.dataFormats.get(params.coordinates.format);\n const coords = await provider!.parse(plugin, data);\n\n const trajectory = await plugin\n .build()\n .toRoot()\n .apply(\n TrajectoryFromModelAndCoordinates,\n {\n modelRef: model.ref,\n coordinatesRef: coords.ref,\n },\n { dependsOn: [model.ref, coords.ref] },\n )\n .commit();\n\n const preset = await plugin.builders.structure.hierarchy.applyPreset(\n trajectory,\n params.preset ?? \"default\",\n );\n\n return { model, coords, preset };\n }\n\n async loadMvsFromUrl(\n url: string,\n format: \"mvsj\" | \"mvsx\",\n options?: {\n appendSnapshots?: boolean;\n keepCamera?: boolean;\n extensions?: MolstarLoadingExtension[];\n },\n ) {\n if (format === \"mvsj\") {\n const data = await this.plugin.runTask(\n this.plugin.fetch({ url, type: \"string\" }),\n );\n const mvsData = MVSData.fromMVSJ(StringLike.toString(data));\n await loadMVS(this.plugin, mvsData, {\n sanityChecks: true,\n sourceUrl: url,\n ...options,\n });\n } else if (format === \"mvsx\") {\n const data = await this.plugin.runTask(\n this.plugin.fetch({ url, type: \"binary\" }),\n );\n await this.plugin.runTask(\n Task.create(\"Load MVSX file\", async (ctx) => {\n const parsed = await loadMVSX(this.plugin, ctx, data);\n await loadMVS(this.plugin, parsed.mvsData, {\n sanityChecks: true,\n sourceUrl: parsed.sourceUrl,\n ...options,\n });\n }),\n );\n } else {\n throw new Error(`Unknown MolViewSpec format: ${format}`);\n }\n }\n\n /** Load MolViewSpec from `data`.\n * If `format` is 'mvsj', `data` must be a string or a Uint8Array containing a UTF8-encoded string.\n * If `format` is 'mvsx', `data` must be a Uint8Array or a string containing base64-encoded binary data prefixed with 'base64,'. */\n loadMvsData(\n data: string | Uint8Array,\n format: \"mvsj\" | \"mvsx\",\n options?: {\n appendSnapshots?: boolean;\n keepCamera?: boolean;\n extensions?: MolstarLoadingExtension[];\n },\n ) {\n return loadMVSData(this.plugin, data, format, options);\n }\n\n loadFiles(files: File[]) {\n const sessions = files.filter((f) => {\n const fn = f.name.toLowerCase();\n return fn.endsWith(\".molx\") || fn.endsWith(\".molj\");\n });\n\n if (sessions.length > 0) {\n return PluginCommands.State.Snapshots.OpenFile(this.plugin, {\n file: sessions[0],\n });\n } else {\n return this.plugin.runTask(\n this.plugin.state.data.applyAction(OpenFiles, {\n files: files.map((f) => Asset.File(f)),\n format: { name: \"auto\", params: {} },\n visuals: true,\n }),\n );\n }\n }\n\n handleResize() {\n this.plugin.layout.events.updated.next(void 0);\n }\n\n dispose() {\n this.plugin.dispose();\n }\n}\n\nexport interface LoadStructureOptions {\n representationParams?: StructureRepresentationPresetProvider.CommonParams;\n}\n\nexport interface VolumeIsovalueInfo {\n type: \"absolute\" | \"relative\";\n value: number;\n color: Color;\n alpha?: number;\n volumeIndex?: number;\n}\n\nexport interface LoadTrajectoryParams {\n model:\n | {\n kind: \"model-url\";\n url: string;\n format?: BuiltInTrajectoryFormat /* mmcif */;\n isBinary?: boolean;\n }\n | {\n kind: \"model-data\";\n data: string | number[] | ArrayBuffer | Uint8Array;\n format?: BuiltInTrajectoryFormat /* mmcif */;\n }\n | {\n kind: \"topology-url\";\n url: string;\n format: BuiltInTopologyFormat;\n isBinary?: boolean;\n }\n | {\n kind: \"topology-data\";\n data: string | number[] | ArrayBuffer | Uint8Array;\n format: BuiltInTopologyFormat;\n };\n modelLabel?: string;\n coordinates:\n | {\n kind: \"coordinates-url\";\n url: string;\n format: BuiltInCoordinatesFormat;\n isBinary?: boolean;\n }\n | {\n kind: \"coordinates-data\";\n data: string | number[] | ArrayBuffer | Uint8Array;\n format: BuiltInCoordinatesFormat;\n };\n coordinatesLabel?: string;\n preset?: keyof PresetTrajectoryHierarchy;\n}\n\nexport const ViewerAutoPreset = StructureRepresentationPresetProvider({\n id: \"preset-structure-representation-viewer-auto\",\n display: {\n name: \"Automatic (w/ Annotation)\",\n group: \"Annotation\",\n description:\n \"Show standard automatic representation but colored by quality assessment (if available in the model).\",\n },\n isApplicable(a): boolean {\n return (\n !!a.data.models.some((m) => QualityAssessment.isApplicable(m, \"pLDDT\")) ||\n !!a.data.models.some((m) => QualityAssessment.isApplicable(m, \"qmean\"))\n );\n },\n params: () => StructureRepresentationPresetProvider.CommonParams,\n async apply(ref, params, plugin) {\n const structureCell = StateObjectRef.resolveAndCheck(\n plugin.state.data,\n ref,\n );\n const structure = structureCell?.obj?.data;\n if (!structureCell || !structure) return {};\n\n if (\n !!structure.models.some((m) => QualityAssessment.isApplicable(m, \"pLDDT\"))\n ) {\n return await QualityAssessmentPLDDTPreset.apply(ref, params, plugin);\n } else if (\n !!structure.models.some((m) => QualityAssessment.isApplicable(m, \"qmean\"))\n ) {\n return await QualityAssessmentQmeanPreset.apply(ref, params, plugin);\n } else if (\n !!structure.models.some((m) =>\n SbNcbrPartialChargesPropertyProvider.isApplicable(m),\n )\n ) {\n return await SbNcbrPartialChargesPreset.apply(ref, params, plugin);\n } else {\n return await PresetStructureRepresentations.auto.apply(\n ref,\n params,\n plugin,\n );\n }\n },\n});\n\nexport const PluginExtensions = {\n wwPDBStructConn: wwPDBStructConnExtensionFunctions,\n mvs: { MVSData, loadMVS, loadMVSData },\n modelArchive: {\n qualityAssessment: {\n config: MAQualityAssessmentConfig,\n },\n },\n};\n","deleted","label",[167,168,149],"frontend","viewer","permalink","https://www.val.town/x/zcpbx/MolstarViewer/code/frontend/viewer/app.ts","extension","actionData","errors"]