molstar
Version:
A comprehensive macromolecular library.
242 lines (241 loc) • 16.7 kB
TypeScript
/**
* 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 { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
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';
import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
export { setDebugMode, setProductionMode, setTimingMode } 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" | "zenodo-import" | "backgrounds" | "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;
enableDpoit: boolean | undefined;
preferWebgl1: boolean | undefined;
allowMajorPerformanceCaveat: boolean | undefined;
viewportShowExpand: boolean | undefined;
viewportShowControls: boolean | undefined;
viewportShowSettings: boolean | undefined;
viewportShowSelectionMode: boolean | undefined;
viewportShowAnimation: boolean | undefined;
viewportShowTrajectoryControls: boolean | undefined;
pluginStateServer: string | undefined;
volumeStreamingServer: string | undefined;
volumeStreamingDisabled: boolean;
pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
saccharideCompIdMapType: SaccharideCompIdMapType;
};
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 & {
label?: string;
}): 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: 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: BuiltInTopologyFormat;
isBinary?: boolean;
} | {
kind: 'topology-data';
data: string | number[] | ArrayBuffer | Uint8Array;
format: BuiltInTopologyFormat;
};
modelLabel?: string;
coordinates: {
kind: 'coordinates-url';
url: string;
format: BuiltInCoordinatesFormat;
isBinary?: boolean;
} | {
kind: 'coordinates-data';
data: string | number[] | ArrayBuffer | Uint8Array;
format: BuiltInCoordinatesFormat;
};
coordinatesLabel?: string;
preset?: keyof PresetTrajectoryHierarchy;
}
export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
ignoreHydrogens: boolean | undefined;
ignoreLight: boolean | undefined;
quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
globalName: any;
globalColorParams: any;
carbonColor: any;
symmetryColor: any;
symmetryColorParams: 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>>;
};
}>;