pdbe-molstar 3.2.1-beta.1 → 3.2.1-beta.3

package/lib/index.d.ts

@@ -1,179 +1,4 @@
-import { Canvas3DProps } from 'Molstar/mol-canvas3d/canvas3d';
-import { EmptyLoci } from 'Molstar/mol-model/loci';
-import { StructureElement } from 'Molstar/mol-model/structure';
-import { StructureRef } from 'Molstar/mol-plugin-state/manager/structure/hierarchy-state';
-import { PluginContext } from 'Molstar/mol-plugin/context';
-import { Color } from 'Molstar/mol-util/color/color';
-import * as Foldseek from './extensions/foldseek';
-import { LoadParams, QueryParam } from './helpers';
-import { ColorParams, InitParams } from './spec';
-import 'Molstar/mol-plugin-ui/skin/dark.scss';
-import './overlay.scss';
-export declare class PDBeMolstarPlugin {
-    private _ev;
-    readonly events: {
-        loadComplete: import("rxjs").Subject<boolean>;
-    };
-    plugin: PluginContext;
-    initParams: InitParams;
-    targetElement: HTMLElement;
-    assemblyRef: string;
-    defaultRendererProps: Canvas3DProps['renderer'];
-    defaultMarkingProps: Canvas3DProps['marking'];
-    isHighlightColorUpdated: boolean;
-    isSelectedColorUpdated: boolean;
-    /** Keeps track of representations added by `.visual.select` for each structure. */
-    private addedReprs;
-    /** Maps structure IDs (assigned when loading) to cell refs. */
-    private structureRefMap;
-    /** Extract InitParams from attributes of an HTML element */
-    static initParamsFromHtmlAttributes(element: HTMLElement): Partial<InitParams>;
-    render(target: string | HTMLElement, options: Partial<InitParams>): Promise<void>;
-    getMoleculeSrcUrl(): {
-        url: string;
-        format: string;
-        isBinary: boolean;
-    };
-    get state(): import("molstar/lib/mol-state/state").State;
-    createLigandStructure(isBranched: boolean): Promise<void>;
-    load({ url, format, isBinary, assemblyId, progressMessage, id }: LoadParams, fullLoad?: boolean): Promise<void>;
-    /** Remove loaded structure(s).
-     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
-     * If `structureNumberOrId` is undefined, remove all structures.
-     * You will likely need to call `await this.visual.reset({ camera: true })` afterwards. */
-    deleteStructure(structureNumberOrId?: number): Promise<void>;
-    applyVisualParams: () => void;
-    /** Get loci corresponding to a selection within a structure.
-     * If `params` contains more items, return loci for the union of the selections.
-     * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
-    getLociForParams(params: QueryParam[], structureNumber?: number): StructureElement.Loci | EmptyLoci;
-    getLociByPLDDT(score: number, structureNumber?: number): StructureElement.Loci | {
-        kind: "empty-loci";
-    };
-    /** For each item in params, get loci and bundle */
-    private getSelections;
-    private getBundle;
-    normalizeColor(colorVal: AnyColor | null | undefined, defaultColor?: Color): Color;
-    /** Get structure ref for a structure with given `structureNumberOrId`.
-     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
-     * If `structureNumberOrId` is undefined, return refs for all loaded structures. */
-    private getStructures;
-    /** Get StructureRef for a structure with given `structureNumberOrId`.
-     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure. */
-    getStructure(structureNumberOrId: number | string): StructureRef | undefined;
-    /** Helper methods related to canvas and layout */
-    canvas: {
-        /** Set canvas background color. */
-        setBgColor: (color?: {
-            r: number;
-            g: number;
-            b: number;
-        }) => Promise<void>;
-        /** Set controls panel visibility. Without `isVisible` parameter, toggle controls panel visibility. */
-        toggleControls: (isVisible?: boolean) => void;
-        /** Set full-screen mode on or off. Without `isExpanded` parameter, toggle full-screen mode. */
-        toggleExpanded: (isExpanded?: boolean) => void;
-        applySettings: (settings?: {
-            color?: {
-                r: number;
-                g: number;
-                b: number;
-            };
-            lighting?: string;
-        }) => Promise<void>;
-    };
-    /** Helper methods related to 3D visuals */
-    visual: {
-        /** Change the visibility of individual entity visuals */
-        visibility: (data: {
-            polymer?: boolean;
-            het?: boolean;
-            water?: boolean;
-            carbs?: boolean;
-            nonStandard?: boolean;
-            maps?: boolean;
-        }) => Promise<void>;
-        /** Change the visibility of a structure.
-         * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
-         * If `visibility` is undefined, toggle current visibility state. */
-        structureVisibility: (structureNumberOrId: string | number, visibility?: boolean) => Promise<void>;
-        /** With `isSpinning` parameter, switch visual rotation on or off. Without `isSpinning` parameter, toggle rotation. If `resetCamera`, also reset the camera zoom. */
-        toggleSpin: (isSpinning?: boolean, resetCamera?: boolean) => Promise<void>;
-        /** Focus (zoom) on the part of the structure defined by `selection`.
-         * If `selection` contains more items, focus on the union of those.
-         * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
-        focus: (selection: QueryParam[], structureNumber?: number) => Promise<void>;
-        /** Trigger highlight on the part of the structure defined by `data`
-         * (this will look the same as when the user hovers over a part of the structure).
-         * If `focus`, also zoom on the highlighted part.
-         * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
-        highlight: (params: {
-            data: QueryParam[];
-            color?: ColorParams;
-            focus?: boolean;
-            structureNumber?: number;
-        }) => Promise<void>;
-        /** Remove any current highlight and reset the highlight color to its default value. */
-        clearHighlight: () => Promise<void>;
-        /** Color the parts of the structure defined by `data`. Color the rest of the structure in `nonSelectedColor` if provided.
-         * If any items in `data` contain `focus`, zoom to the union of these items.
-         * If any items in `data` contain `sideChain` or `representation`, add extra representations to them (colored in `representationColor` if provided).
-         * If `structureNumber` is provided, apply to the specified structure (numbered from 1!); otherwise apply to all loaded structures.
-         * Remove any previously added coloring and extra representations, unless `keepColors` and/or `keepRepresentations` is set. */
-        select: (params: {
-            data: QueryParam[];
-            nonSelectedColor?: any;
-            structureId?: string;
-            structureNumber?: number;
-            keepColors?: boolean;
-            keepRepresentations?: boolean;
-        }) => Promise<void>;
-        /** Remove any coloring and extra representations previously added by the `select` method.
-         * If `structureNumber` is provided, apply to the specified structure (numbered from 1!); otherwise apply to all loaded structures.
-         * If `keepColors`, current residue coloring is preserved. If `keepRepresentations`, current added representations are preserved. */
-        clearSelection: (structureNumberOrId?: number | string, options?: {
-            keepColors?: boolean;
-            keepRepresentations?: boolean;
-        }) => Promise<void>;
-        /** Add interactive tooltips to parts of the structure. The added tooltips will be shown on a separate line in the tooltip box.
-         * Repeated call to this function removes any previously added tooltips.
-         * `structureNumber` counts from 1; if not provided, tooltips will be applied to all loaded structures.
-         * Example: `await this.visual.tooltips({ data: [{ struct_asym_id: 'A', tooltip: 'Chain A' }, { struct_asym_id: 'B', tooltip: 'Chain B' }] });`. */
-        tooltips: (params: {
-            data: QueryParam[];
-            structureId?: string;
-            structureNumber?: number;
-        }) => Promise<void>;
-        /** Remove any custom tooltips added by the `tooltips` method. */
-        clearTooltips: (structureNumberOrId?: number) => Promise<void>;
-        /** Set highlight and/or selection color.
-         * Highlight color is used when the user hovers over a part of the structure or when applying the `highlight` method.
-         * Selection color is used when creating selections with Selection Mode (the mouse cursor icon) and is not related to the color used by the `select` method. */
-        setColor: (params: {
-            highlight?: ColorParams;
-            select?: ColorParams;
-        }) => Promise<void>;
-        /** Reset various settings to defaults:
-         * `camera` resets camera position (i.e. zooms on the whole scene).
-         * `theme` resets color theme for visual representations.
-         * `highlightColor` and `selectColor` reset colors previously set by the `setColor` method. */
-        reset: (params: {
-            camera?: boolean;
-            theme?: boolean;
-            highlightColor?: boolean;
-            selectColor?: boolean;
-        }) => Promise<void>;
-        /** Change parameters of the plugin instance.
-         * Can be used to load a different structure.
-         * If `fullLoad`, remove currently loaded structure before loading the new one;
-         * otherwise add the new structure to existing structures. */
-        update: (options: Partial<InitParams>, fullLoad?: boolean) => Promise<boolean>;
-    };
-    clear(): Promise<void>;
-    /** Helper functions related to specific views or use cases */
-    static extensions: {
-        foldseek: typeof Foldseek;
-    };
-}
-type AnyColor = ColorParams | string | number;
-export {};
+/** Entrypoint for the bundler. If you want to import PDBeMolstarPlugin without CSS, import from ./viewer instead. */
+export * from './viewer';
+import 'molstar/lib/mol-plugin-ui/skin/dark.scss';
+import './styles/index.scss';