molstar 3.0.0-dev.6 → 3.0.0

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

@@ -0,0 +1,230 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
+import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectSelector } from '../../mol-state';
+import { Color } from '../../mol-util/color';
+import '../../mol-util/polyfill';
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+declare const DefaultViewerOptions: {
+    customFormats: [string, DataFormatProvider<any, any, any>][];
+    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    layoutIsExpanded: boolean;
+    layoutShowControls: boolean;
+    layoutShowRemoteState: boolean;
+    layoutControlsDisplay: PluginLayoutControlsDisplay;
+    layoutShowSequence: boolean;
+    layoutShowLog: boolean;
+    layoutShowLeftPanel: boolean;
+    collapseLeftPanel: boolean;
+    collapseRightPanel: boolean;
+    disableAntialiasing: boolean | undefined;
+    pixelScale: number | undefined;
+    pickScale: number | undefined;
+    pickPadding: number | undefined;
+    enableWboit: boolean | undefined;
+    preferWebgl1: boolean | undefined;
+    viewportShowExpand: boolean | undefined;
+    viewportShowControls: boolean | undefined;
+    viewportShowSettings: boolean | undefined;
+    viewportShowSelectionMode: boolean | undefined;
+    viewportShowAnimation: boolean | undefined;
+    pluginStateServer: string | undefined;
+    volumeStreamingServer: string | undefined;
+    volumeStreamingDisabled: boolean;
+    pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
+    emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
+};
+declare type ViewerOptions = typeof DefaultViewerOptions;
+export declare class Viewer {
+    plugin: PluginUIContext;
+    constructor(plugin: PluginUIContext);
+    static create(elementOrId: string | HTMLElement, options?: Partial<ViewerOptions>): Promise<Viewer>;
+    setRemoteSnapshot(id: string): Promise<void>;
+    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType): Promise<void>;
+    loadStructureFromUrl(url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, options?: LoadStructureOptions): Promise<void>;
+    loadAllModelsOrAssemblyFromUrl(url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, options?: LoadStructureOptions): Promise<void>;
+    loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: {
+        dataLabel?: string;
+    }): Promise<void>;
+    loadPdb(pdb: string, options?: LoadStructureOptions): Promise<void>;
+    loadPdbDev(pdbDev: string): Promise<void>;
+    loadEmdb(emdb: string, options?: {
+        detail?: number;
+    }): Promise<void>;
+    loadAlphaFoldDb(afdb: string): Promise<void>;
+    loadModelArchive(id: string): Promise<void>;
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    loadVolumeFromUrl({ url, format, isBinary }: {
+        url: string;
+        format: BuildInVolumeFormat;
+        isBinary: boolean;
+    }, isovalues: VolumeIsovalueInfo[], options?: {
+        entryId?: string | string[];
+        isLazy?: boolean;
+    }): Promise<void>;
+    /**
+     * @example
+     *  viewer.loadTrajectory({
+     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+     *      preset: 'all-models' // or 'default'
+     *  });
+     */
+    loadTrajectory(params: LoadTrajectoryParams): Promise<{
+        model: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        coords: StateObjectSelector<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        preset: {
+            model: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+            structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            representation: any;
+        } | {
+            models?: undefined;
+            structures?: undefined;
+        } | {
+            models: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[];
+            structures: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[];
+        } | {
+            model: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+            structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            representation: any;
+        } | {
+            model: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            modelProperties: StateObjectSelector<PluginStateObject.Molecule.Model, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+            structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+            representation: any;
+        } | undefined;
+    }>;
+    handleResize(): void;
+}
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams;
+}
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative';
+    value: number;
+    color: Color;
+    alpha?: number;
+    volumeIndex?: number;
+}
+export interface LoadTrajectoryParams {
+    model: {
+        kind: 'model-url';
+        url: string;
+        format?: BuiltInTrajectoryFormat;
+        isBinary?: boolean;
+    } | {
+        kind: 'model-data';
+        data: string | number[] | ArrayBuffer | Uint8Array;
+        format?: BuiltInTrajectoryFormat;
+    } | {
+        kind: 'topology-url';
+        url: string;
+        format: BuildInStructureFormat;
+        isBinary?: boolean;
+    } | {
+        kind: 'topology-data';
+        data: string | number[] | ArrayBuffer | Uint8Array;
+        format: BuildInStructureFormat;
+    };
+    modelLabel?: string;
+    coordinates: {
+        kind: 'coordinates-url';
+        url: string;
+        format: BuildInStructureFormat;
+        isBinary?: boolean;
+    } | {
+        kind: 'coordinates-data';
+        data: string | number[] | ArrayBuffer | Uint8Array;
+        format: BuildInStructureFormat;
+    };
+    coordinatesLabel?: string;
+    preset?: keyof PresetTrajectoryHierarchy;
+}
+export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
+    ignoreHydrogens: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+        globalName: any;
+        carbonColor: any;
+        symmetryColor: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+    };
+    representations: {
+        polymer: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+} | {
+    components: {
+        all: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        branched: undefined;
+    };
+    representations: {
+        all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+}>;