molstar 3.0.0-dev.3 → 3.0.0-dev.7

package/lib/commonjs/apps/viewer/index.d.ts

@@ -24,7 +24,7 @@ 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" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation")[];
+    extensions: ("cellpack" | "g3d" | "geo-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;
@@ -53,7 +53,8 @@ declare const DefaultViewerOptions: {
 declare type ViewerOptions = typeof DefaultViewerOptions;
 export declare class Viewer {
     plugin: PluginUIContext;
-    constructor(elementOrId: string | HTMLElement, options?: Partial<ViewerOptions>);
+    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>;
@@ -66,6 +67,8 @@ export declare class Viewer {
     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({
@@ -130,77 +133,7 @@ export declare class Viewer {
             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: {} | {
-                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;
-                    lipid: 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>>;
-                    lipid: 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?: 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?: 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;
-                    ligand: 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;
-                    nonStandard: 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: 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;
-                    water: 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;
-                    ion: 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;
-                    lipid: 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;
-                    coarse: 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>>;
-                    ligand: 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>>;
-                    nonStandard: 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>>;
-                    branchedBallAndStick: 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>>;
-                    branchedSnfg3d: 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>>;
-                    water: 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>>;
-                    ion: 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>>;
-                    lipid: 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>>;
-                    coarse: 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?: undefined;
-                representations?: undefined;
-            } | {
-                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>>;
-                };
-            } | {
-                components?: undefined;
-                representations?: undefined;
-            } | {
-                components: {
-                    protein: 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;
-                    nucleic: 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: {
-                    protein: 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>>;
-                    nucleic: 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>>;
-                };
-            } | undefined;
+            representation: any;
         } | {
             models?: undefined;
             structures?: undefined;
@@ -213,154 +146,14 @@ export declare class Viewer {
             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: {} | {
-                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;
-                    lipid: 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>>;
-                    lipid: 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?: 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?: 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;
-                    ligand: 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;
-                    nonStandard: 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: 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;
-                    water: 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;
-                    ion: 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;
-                    lipid: 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;
-                    coarse: 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>>;
-                    ligand: 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>>;
-                    nonStandard: 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>>;
-                    branchedBallAndStick: 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>>;
-                    branchedSnfg3d: 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>>;
-                    water: 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>>;
-                    ion: 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>>;
-                    lipid: 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>>;
-                    coarse: 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?: undefined;
-                representations?: undefined;
-            } | {
-                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>>;
-                };
-            } | {
-                components?: undefined;
-                representations?: undefined;
-            } | {
-                components: {
-                    protein: 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;
-                    nucleic: 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: {
-                    protein: 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>>;
-                    nucleic: 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>>;
-                };
-            } | undefined;
+            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: {} | {
-                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;
-                    lipid: 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>>;
-                    lipid: 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?: 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?: 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;
-                    ligand: 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;
-                    nonStandard: 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: 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;
-                    water: 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;
-                    ion: 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;
-                    lipid: 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;
-                    coarse: 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>>;
-                    ligand: 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>>;
-                    nonStandard: 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>>;
-                    branchedBallAndStick: 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>>;
-                    branchedSnfg3d: 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>>;
-                    water: 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>>;
-                    ion: 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>>;
-                    lipid: 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>>;
-                    coarse: 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?: undefined;
-                representations?: undefined;
-            } | {
-                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>>;
-                };
-            } | {
-                components?: undefined;
-                representations?: undefined;
-            } | {
-                components: {
-                    protein: 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;
-                    nucleic: 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: {
-                    protein: 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>>;
-                    nucleic: 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>>;
-                };
-            } | undefined;
+            representation: any;
         } | undefined;
     }>;
     handleResize(): void;
@@ -409,3 +202,31 @@ export interface LoadTrajectoryParams {
     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>>;
+    };
+}>;

package/lib/commonjs/apps/viewer/index.js

@@ -6,18 +6,22 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Viewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
+exports.ViewerAutoPreset = exports.Viewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
 var tslib_1 = require("tslib");
 var behavior_1 = require("../../extensions/anvil/behavior");
 var cellpack_1 = require("../../extensions/cellpack");
 var dnatco_1 = require("../../extensions/dnatco");
 var format_1 = require("../../extensions/g3d/format");
 var geo_export_1 = require("../../extensions/geo-export");
+var behavior_2 = require("../../extensions/model-archive/quality-assessment/behavior");
+var behavior_3 = require("../../extensions/model-archive/quality-assessment/behavior");
+var prop_1 = require("../../extensions/model-archive/quality-assessment/prop");
 var mp4_export_1 = require("../../extensions/mp4-export");
 var pdbe_1 = require("../../extensions/pdbe");
 var rcsb_1 = require("../../extensions/rcsb");
 var structure_1 = require("../../mol-plugin-state/actions/structure");
 var volume_1 = require("../../mol-plugin-state/actions/volume");
+var representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
 var volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
 var model_1 = require("../../mol-plugin-state/transforms/model");
@@ -26,6 +30,7 @@ var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var config_1 = require("../../mol-plugin/config");
 var spec_2 = require("../../mol-plugin/spec");
+var mol_state_1 = require("../../mol-state");
 var assets_1 = require("../../mol-util/assets");
 require("../../mol-util/polyfill");
 var type_helpers_1 = require("../../mol-util/type-helpers");
@@ -50,7 +55,8 @@ var Extensions = {
     'anvil-membrane-orientation': spec_2.PluginSpec.Behavior(behavior_1.ANVILMembraneOrientation),
     'g3d': spec_2.PluginSpec.Behavior(format_1.G3DFormat),
     'mp4-export': spec_2.PluginSpec.Behavior(mp4_export_1.Mp4Export),
-    'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport)
+    'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport),
+    'ma-quality-assessment': spec_2.PluginSpec.Behavior(behavior_2.MAQualityAssessment),
 };
 var DefaultViewerOptions = {
     customFormats: CustomFormats,
@@ -81,57 +87,78 @@ var DefaultViewerOptions = {
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
 };
 var Viewer = /** @class */ (function () {
-    function Viewer(elementOrId, options) {
-        if (options === void 0) { options = {}; }
-        var _a;
-        var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), options);
-        var defaultSpec = (0, spec_1.DefaultPluginUISpec)();
-        var spec = {
-            actions: defaultSpec.actions,
-            behaviors: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
-            animations: (0, tslib_1.__spreadArray)([], defaultSpec.animations || [], true),
-            customParamEditors: defaultSpec.customParamEditors,
-            customFormats: o === null || o === void 0 ? void 0 : o.customFormats,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    controlsDisplay: o.layoutControlsDisplay,
-                    regionState: {
-                        bottom: 'full',
-                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
-                        right: o.collapseRightPanel ? 'hidden' : 'full',
-                        top: 'full',
-                    }
-                },
-            },
-            components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none' }),
-            config: [
-                [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
-                [config_1.PluginConfig.General.PixelScale, o.pixelScale],
-                [config_1.PluginConfig.General.PickScale, o.pickScale],
-                [config_1.PluginConfig.General.PickPadding, o.pickPadding],
-                [config_1.PluginConfig.General.EnableWboit, o.enableWboit],
-                [config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
-                [config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
-                [config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
-                [config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
-                [config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
-                [config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
-                [config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
-                [config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
-                [config_1.PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
-                [config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
-            ]
-        };
-        var element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element)
-            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
-        this.plugin = (0, mol_plugin_ui_1.createPlugin)(element, spec);
+    function Viewer(plugin) {
+        this.plugin = plugin;
     }
+    Viewer.create = function (elementOrId, options) {
+        var _a;
+        if (options === void 0) { options = {}; }
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var o, defaultSpec, spec, element, plugin;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), options);
+                        defaultSpec = (0, spec_1.DefaultPluginUISpec)();
+                        spec = {
+                            actions: defaultSpec.actions,
+                            behaviors: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
+                            animations: (0, tslib_1.__spreadArray)([], defaultSpec.animations || [], true),
+                            customParamEditors: defaultSpec.customParamEditors,
+                            customFormats: o === null || o === void 0 ? void 0 : o.customFormats,
+                            layout: {
+                                initial: {
+                                    isExpanded: o.layoutIsExpanded,
+                                    showControls: o.layoutShowControls,
+                                    controlsDisplay: o.layoutControlsDisplay,
+                                    regionState: {
+                                        bottom: 'full',
+                                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                                        right: o.collapseRightPanel ? 'hidden' : 'full',
+                                        top: 'full',
+                                    }
+                                },
+                            },
+                            components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none' }),
+                            config: [
+                                [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                                [config_1.PluginConfig.General.PixelScale, o.pixelScale],
+                                [config_1.PluginConfig.General.PickScale, o.pickScale],
+                                [config_1.PluginConfig.General.PickPadding, o.pickPadding],
+                                [config_1.PluginConfig.General.EnableWboit, o.enableWboit],
+                                [config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                                [config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                                [config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                                [config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                                [config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                                [config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
+                                [config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
+                                [config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                                [config_1.PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
+                                [config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                                [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                                [config_1.PluginConfig.Structure.DefaultRepresentationPreset, exports.ViewerAutoPreset.id],
+                            ]
+                        };
+                        element = typeof elementOrId === 'string'
+                            ? document.getElementById(elementOrId)
+                            : elementOrId;
+                        if (!element)
+                            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(element, spec, {
+                                onBeforeUIRender: function (plugin) {
+                                    // the preset needs to be added before the UI renders otherwise
+                                    // "Download Structure" wont be able to pick it up
+                                    plugin.builders.structure.representation.registerPreset(exports.ViewerAutoPreset);
+                                }
+                            })];
+                    case 1:
+                        plugin = _b.sent();
+                        return [2 /*return*/, new Viewer(plugin)];
+                }
+            });
+        });
+    };
     Viewer.prototype.setRemoteSnapshot = function (id) {
         var url = "".concat(this.plugin.config.get(config_1.PluginConfig.State.CurrentServer), "/get/").concat(id);
         return commands_1.PluginCommands.State.Snapshots.Fetch(this.plugin, { url: url });
@@ -247,6 +274,30 @@ var Viewer = /** @class */ (function () {
             }
         }));
     };
+    Viewer.prototype.loadAlphaFoldDb = function (afdb) {
+        var params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
+            source: {
+                name: 'alphafolddb',
+                params: {
+                    id: afdb,
+                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadModelArchive = function (id) {
+        var params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
+            source: {
+                name: 'modelarchive',
+                params: {
+                    id: id,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    };
     /**
      * @example Load X-ray density from volume server
         viewer.loadVolumeFromUrl({
@@ -433,4 +484,40 @@ var Viewer = /** @class */ (function () {
     return Viewer;
 }());
 exports.Viewer = Viewer;
+exports.ViewerAutoPreset = (0, representation_preset_1.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: function (a) {
+        return (!!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); }) ||
+            !!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); }));
+    },
+    params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
+    apply: function (ref, params, plugin) {
+        var _a;
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var structureCell, structure;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+                        structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
+                        if (!structureCell || !structure)
+                            return [2 /*return*/, {}];
+                        if (!!!structure.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); })) return [3 /*break*/, 2];
+                        return [4 /*yield*/, behavior_3.QualityAssessmentPLDDTPreset.apply(ref, params, plugin)];
+                    case 1: return [2 /*return*/, _b.sent()];
+                    case 2:
+                        if (!!!structure.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); })) return [3 /*break*/, 4];
+                        return [4 /*yield*/, behavior_3.QualityAssessmentQmeanPreset.apply(ref, params, plugin)];
+                    case 3: return [2 /*return*/, _b.sent()];
+                    case 4: return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, params, plugin)];
+                    case 5: return [2 /*return*/, _b.sent()];
+                }
+            });
+        });
+    }
+});
 //# sourceMappingURL=index.js.map

package/lib/commonjs/cli/cifschema/index.d.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */