molstar 4.2.0 → 4.4.0

package/lib/mol-model/structure/query/queries/generators.js

@@ -107,7 +107,7 @@ function atomGroupsSegmented({ unitTest, entityTest, chainTest, residueTest, ato
                 }
             }
             else {
-                const { chainElementSegments } = 1 /* Unit.Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
+                const { chainElementSegments } = unit.kind === 1 /* Unit.Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
                 const chainsIt = Segmentation.transientSegments(chainElementSegments, elements);
                 while (chainsIt.hasNext) {
                     const chainSegment = chainsIt.move();
@@ -174,7 +174,7 @@ function atomGroupsGrouped({ unitTest, entityTest, chainTest, residueTest, atomT
                 }
             }
             else {
-                const { chainElementSegments } = 1 /* Unit.Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
+                const { chainElementSegments } = unit.kind === 1 /* Unit.Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
                 const chainsIt = Segmentation.transientSegments(chainElementSegments, elements);
                 while (chainsIt.hasNext) {
                     const chainSegment = chainsIt.move();

package/lib/mol-model/structure/structure/properties.d.ts

@@ -61,6 +61,7 @@ declare const StructureProperties: {
         pdbx_mutation: StructureElement.Property<string>;
         pdbx_fragment: StructureElement.Property<string>;
         pdbx_ec: StructureElement.Property<string[]>;
+        pdbx_parent_entity_id: StructureElement.Property<string>;
         subtype: StructureElement.Property<import("../model/properties/common").EntitySubtype>;
         prd_id: StructureElement.Property<string>;
     };

package/lib/mol-model/structure/structure/properties.js

@@ -141,6 +141,7 @@ const entity = {
     pdbx_mutation: p(l => l.unit.model.entities.data.pdbx_mutation.value(eK(l))),
     pdbx_fragment: p(l => l.unit.model.entities.data.pdbx_fragment.value(eK(l))),
     pdbx_ec: p(l => l.unit.model.entities.data.pdbx_ec.value(eK(l))),
+    pdbx_parent_entity_id: p(l => l.unit.model.entities.data.pdbx_parent_entity_id.value(eK(l))),
     subtype: p(l => l.unit.model.entities.subtype.value(eK(l))),
     prd_id: p(l => { var _a, _b; return (_b = (_a = l.unit.model.entities.prd_id) === null || _a === void 0 ? void 0 : _a.value(eK(l))) !== null && _b !== void 0 ? _b : ''; }),
 };

package/lib/mol-model/volume/volume.d.ts

@@ -78,24 +78,24 @@ export declare namespace Volume {
         }>, number>;
     }>;
     const IsoValueParam: PD.Conditioned<Readonly<{
-        kind: 'absolute';
+        kind: "absolute";
         absoluteValue: number;
     }> | Readonly<{
-        kind: 'relative';
+        kind: "relative";
         relativeValue: number;
     }>, PD.Base<Readonly<{
-        kind: 'absolute';
+        kind: "absolute";
         absoluteValue: number;
     }> | Readonly<{
-        kind: 'relative';
+        kind: "relative";
         relativeValue: number;
     }>>, {
         absolute: PD.Converted<Readonly<{
-            kind: 'absolute';
+            kind: "absolute";
             absoluteValue: number;
         }>, number>;
         relative: PD.Converted<Readonly<{
-            kind: 'relative';
+            kind: "relative";
             relativeValue: number;
         }>, number>;
     }>;

package/lib/mol-model-formats/shape/ply.d.ts

@@ -36,6 +36,7 @@ export declare const PlyShapeParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -87,6 +88,7 @@ export declare function shapeFromPly(source: PlyFile, params?: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/mol-model-formats/structure/basic/schema.d.ts

@@ -63,6 +63,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db").Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: import("../../../mol-data/db").Column.Schema.List<string>;
         pdbx_number_of_molecules: import("../../../mol-data/db").Column.Schema.Int;
+        pdbx_parent_entity_id: import("../../../mol-data/db").Column.Schema.Str;
         pdbx_mutation: import("../../../mol-data/db").Column.Schema.Str;
         pdbx_fragment: import("../../../mol-data/db").Column.Schema.Str;
         pdbx_ec: import("../../../mol-data/db").Column.Schema.List<string>;

package/lib/mol-model-formats/structure/common/entity.d.ts

@@ -31,6 +31,7 @@ export declare class EntityBuilder {
         type: Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: Column.Schema.List<string>;
         pdbx_number_of_molecules: Column.Schema.Int;
+        pdbx_parent_entity_id: Column.Schema.Str;
         pdbx_mutation: Column.Schema.Str;
         pdbx_fragment: Column.Schema.Str;
         pdbx_ec: Column.Schema.List<string>;

package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts

@@ -28,6 +28,7 @@ export declare const InteractionsInterUnitParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts

@@ -28,6 +28,7 @@ export declare const InteractionsIntraUnitParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/mol-model-props/computed/representations/interactions.d.ts

@@ -32,6 +32,7 @@ export declare const InteractionsParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -84,6 +85,7 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -137,6 +139,7 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -30,6 +30,7 @@ export declare const CrossLinkRestraintCylinderParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -79,6 +80,7 @@ export declare const CrossLinkRestraintParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -127,6 +129,7 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -176,6 +179,7 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/mol-model-props/sequence/themes/sifts-mapping.d.ts

@@ -18,7 +18,7 @@ export declare const SIFTSMappingColorThemeParams: {
         sampleCountFactor: number;
     }>, "generate"> | PD.NamedParams<PD.Normalize<{
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "colors">>;
@@ -36,7 +36,7 @@ export declare function getSIFTSMappingColorThemeParams(ctx: ThemeDataContext):
         sampleCountFactor: number;
     }>, "generate"> | PD.NamedParams<PD.Normalize<{
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "colors">>;

package/lib/mol-plugin/animation-loop.d.ts

@@ -15,6 +15,7 @@ export declare class PluginAnimationLoop {
         isSynchronous?: boolean;
         manualDraw?: boolean;
         animation?: PluginAnimationManager.AnimationInfo;
+        updateControls?: boolean;
     }): Promise<void>;
     private frame;
     resetTime(t?: number): void;

package/lib/mol-plugin/behavior/behavior.d.ts

@@ -22,48 +22,48 @@ declare namespace PluginBehavior {
     const Root_base: {
         new (data: {}, props?: {
             label: string;
-            description?: string | undefined;
+            description?: string;
         } | undefined): {
             id: import("../../mol-util").UUID;
             type: PluginStateObject.TypeInfo;
             label: string;
-            description?: string | undefined;
+            description?: string;
             data: {};
         };
         type: PluginStateObject.TypeInfo;
-        is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<{}, PluginStateObject.TypeInfo>;
+        is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<{}, PluginStateObject.TypeInfo>;
     };
     export class Root extends Root_base {
     }
     const Category_base: {
         new (data: {}, props?: {
             label: string;
-            description?: string | undefined;
+            description?: string;
         } | undefined): {
             id: import("../../mol-util").UUID;
             type: PluginStateObject.TypeInfo;
             label: string;
-            description?: string | undefined;
+            description?: string;
             data: {};
         };
         type: PluginStateObject.TypeInfo;
-        is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<{}, PluginStateObject.TypeInfo>;
+        is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<{}, PluginStateObject.TypeInfo>;
     };
     export class Category extends Category_base {
     }
     const Behavior_base: {
         new (data: PluginBehavior<unknown>, props?: {
             label: string;
-            description?: string | undefined;
+            description?: string;
         } | undefined): {
             id: import("../../mol-util").UUID;
             type: PluginStateObject.TypeInfo;
             label: string;
-            description?: string | undefined;
+            description?: string;
             data: PluginBehavior<unknown>;
         };
         type: PluginStateObject.TypeInfo;
-        is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<PluginBehavior<unknown>, PluginStateObject.TypeInfo>;
+        is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<PluginBehavior<unknown>, PluginStateObject.TypeInfo>;
     };
     export class Behavior extends Behavior_base {
     }

package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts

@@ -17,16 +17,16 @@ import { PluginContext } from '../../../context';
 declare const VolumeStreaming_base: {
     new (data: VolumeStreaming.Behavior, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: VolumeStreaming.Behavior;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../../mol-state").StateObject<any, import("../../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../../mol-state").StateObject<VolumeStreaming.Behavior, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../../../mol-state").StateObject): obj is import("../../../../mol-state").StateObject<VolumeStreaming.Behavior, PluginStateObject.TypeInfo>;
 };
 export declare class VolumeStreaming extends VolumeStreaming_base {
 }
@@ -55,14 +55,14 @@ export declare namespace VolumeStreaming {
                 topRight: Vec3;
             }>, "box"> | PD.NamedParams<PD.Normalize<{
                 radius: number;
+                dynamicDetailLevel: number;
                 bottomLeft: Vec3;
                 topRight: Vec3;
-            }>, "selection-box"> | PD.NamedParams<PD.Normalize<{
+            }>, "camera-target"> | PD.NamedParams<PD.Normalize<{
                 radius: number;
-                dynamicDetailLevel: number;
                 bottomLeft: Vec3;
                 topRight: Vec3;
-            }>, "camera-target">>;
+            }>, "selection-box">>;
             detailLevel: PD.Select<number>;
             channels: PD.Group<PD.Normalize<{
                 em: PD.Normalize<ChannelParams>;
@@ -92,14 +92,14 @@ export declare namespace VolumeStreaming {
             topRight: Vec3;
         }>, "box"> | PD.NamedParams<PD.Normalize<{
             radius: number;
+            dynamicDetailLevel: number;
             bottomLeft: Vec3;
             topRight: Vec3;
-        }>, "selection-box"> | PD.NamedParams<PD.Normalize<{
+        }>, "camera-target"> | PD.NamedParams<PD.Normalize<{
             radius: number;
-            dynamicDetailLevel: number;
             bottomLeft: Vec3;
             topRight: Vec3;
-        }>, "camera-target">>;
+        }>, "selection-box">>;
         detailLevel: PD.Select<number>;
         channels: PD.Group<PD.Normalize<{
             em: PD.Normalize<ChannelParams>;

package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -10,16 +10,16 @@ import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: VolumeServerInfo.Data;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../../mol-state").StateObject<any, import("../../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../../mol-state").StateObject<VolumeServerInfo.Data, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../../../mol-state").StateObject): obj is import("../../../../mol-state").StateObject<VolumeServerInfo.Data, PluginStateObject.TypeInfo>;
 };
 export declare class VolumeServerInfo extends VolumeServerInfo_base {
 }

package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts

@@ -50,14 +50,14 @@ declare const CreateVolumeStreamingBehavior: StateTransformer<VolumeServerInfo,
             topRight: any;
         }>, "box"> | PD.NamedParams<PD.Normalize<{
             radius: any;
+            dynamicDetailLevel: any;
             bottomLeft: any;
             topRight: any;
-        }>, "selection-box"> | PD.NamedParams<PD.Normalize<{
+        }>, "camera-target"> | PD.NamedParams<PD.Normalize<{
             radius: any;
-            dynamicDetailLevel: any;
             bottomLeft: any;
             topRight: any;
-        }>, "camera-target">>;
+        }>, "selection-box">>;
         detailLevel: PD.Select<number>;
         channels: PD.Group<PD.Normalize<{
             em: any;

package/lib/mol-plugin/commands.d.ts

@@ -23,17 +23,17 @@ export declare const PluginCommands: {
         ApplyAction: PluginCommand<{
             state: State;
             action: StateAction.Instance;
-            ref?: string | undefined;
+            ref?: StateTransform.Ref;
         }>;
         Update: PluginCommand<{
             state: State;
             tree: State.Tree | State.Builder;
-            options?: Partial<State.UpdateOptions> | undefined;
+            options?: Partial<State.UpdateOptions>;
         }>;
         RemoveObject: PluginCommand<{
             state: State;
             ref: StateTransform.Ref;
-            removeParentGhosts?: boolean | undefined;
+            removeParentGhosts?: boolean;
         }>;
         ToggleExpanded: PluginCommand<{
             state: State;
@@ -45,46 +45,14 @@ export declare const PluginCommands: {
         }>;
         Snapshots: {
             Add: PluginCommand<{
-                key?: string | undefined;
-                name?: string | undefined;
-                description?: string | undefined;
-                params?: Partial<import("../mol-util/param-definition").ParamDefinition.Values<{
-                    durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
-                    data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    structureSelection: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3dContext: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    interactivity: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    camera: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    cameraTransition: import("../mol-util/param-definition").ParamDefinition.Mapped<import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        durationInMs: number;
-                    }>, "animate"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "instant">>;
-                    image: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                }>> | undefined;
+                key?: string;
+                name?: string;
+                description?: string;
+                params?: PluginState.SnapshotParams;
             }>;
             Replace: PluginCommand<{
                 id: string;
-                params?: Partial<import("../mol-util/param-definition").ParamDefinition.Values<{
-                    durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
-                    data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    structureSelection: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3dContext: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    interactivity: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    camera: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    cameraTransition: import("../mol-util/param-definition").ParamDefinition.Mapped<import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        durationInMs: number;
-                    }>, "animate"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "instant">>;
-                    image: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                }>> | undefined;
+                params?: PluginState.SnapshotParams;
             }>;
             Move: PluginCommand<{
                 id: string;
@@ -98,51 +66,19 @@ export declare const PluginCommands: {
             }>;
             Clear: PluginCommand<{}>;
             Upload: PluginCommand<{
-                name?: string | undefined;
-                description?: string | undefined;
-                playOnLoad?: boolean | undefined;
+                name?: string;
+                description?: string;
+                playOnLoad?: boolean;
                 serverUrl: string;
-                params?: Partial<import("../mol-util/param-definition").ParamDefinition.Values<{
-                    durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
-                    data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    structureSelection: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3dContext: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    interactivity: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    camera: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    cameraTransition: import("../mol-util/param-definition").ParamDefinition.Mapped<import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        durationInMs: number;
-                    }>, "animate"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "instant">>;
-                    image: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                }>> | undefined;
+                params?: PluginState.SnapshotParams;
             }>;
             Fetch: PluginCommand<{
                 url: string;
             }>;
             DownloadToFile: PluginCommand<{
-                name?: string | undefined;
+                name?: string;
                 type: PluginState.SnapshotType;
-                params?: Partial<import("../mol-util/param-definition").ParamDefinition.Values<{
-                    durationInMs: import("../mol-util/param-definition").ParamDefinition.Numeric;
-                    data: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    behavior: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    structureSelection: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    componentManager: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    animation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    startAnimation: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3d: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    canvas3dContext: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    interactivity: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    camera: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                    cameraTransition: import("../mol-util/param-definition").ParamDefinition.Mapped<import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        durationInMs: number;
-                    }>, "animate"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "instant">>;
-                    image: import("../mol-util/param-definition").ParamDefinition.BooleanParam;
-                }>> | undefined;
+                params?: PluginState.SnapshotParams;
             }>;
             OpenFile: PluginCommand<{
                 file: File;
@@ -163,11 +99,11 @@ export declare const PluginCommands: {
         Structure: {
             Highlight: PluginCommand<{
                 loci: StructureElement.Loci;
-                isOff?: boolean | undefined;
+                isOff?: boolean;
             }>;
             Select: PluginCommand<{
                 loci: StructureElement.Loci;
-                isOff?: boolean | undefined;
+                isOff?: boolean;
             }>;
         };
         ClearHighlights: PluginCommand<{}>;
@@ -185,24 +121,24 @@ export declare const PluginCommands: {
     };
     Camera: {
         Reset: PluginCommand<{
-            durationMs?: number | undefined;
-            snapshot?: Partial<Camera.Snapshot> | undefined;
+            durationMs?: number;
+            snapshot?: Partial<Camera.Snapshot>;
         }>;
         SetSnapshot: PluginCommand<{
             snapshot: Partial<Camera.Snapshot>;
-            durationMs?: number | undefined;
+            durationMs?: number;
         }>;
         Focus: PluginCommand<{
             center: Vec3;
             radius: number;
-            durationMs?: number | undefined;
+            durationMs?: number;
         }>;
         OrientAxes: PluginCommand<{
-            structures?: Structure[] | undefined;
-            durationMs?: number | undefined;
+            structures?: Structure[];
+            durationMs?: number;
         }>;
         ResetAxes: PluginCommand<{
-            durationMs?: number | undefined;
+            durationMs?: number;
         }>;
     };
     Canvas3D: {

package/lib/mol-plugin/context.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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>
@@ -164,7 +164,7 @@ export declare class PluginContext {
     readonly customStructureProperties: CustomProperty.Registry<Structure>;
     readonly customStructureControls: Map<string, new () => any>;
     readonly customImportControls: Map<string, new () => any>;
-    readonly genericRepresentationControls: Map<string, (selection: StructureHierarchyManager['selection']) => [StructureHierarchyRef[], string]>;
+    readonly genericRepresentationControls: Map<string, (selection: StructureHierarchyManager["selection"]) => [StructureHierarchyRef[], string]>;
     /**
      * Used to store application specific custom state which is then available
      * to State Actions and similar constructs via the PluginContext.
@@ -209,6 +209,7 @@ export declare class PluginContext {
     clear(resetViewportSettings?: boolean): Promise<void>;
     dispose(options?: {
         doNotForceWebGLContextLoss?: boolean;
+        doNotDisposeCanvas3DContext?: boolean;
     }): void;
     private initBehaviorEvents;
     private initBuiltInBehavior;

package/lib/mol-plugin/context.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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>
@@ -209,7 +209,9 @@ export class PluginContext {
         this.animationLoop.stop();
         this.commands.dispose();
         (_a = this.canvas3d) === null || _a === void 0 ? void 0 : _a.dispose();
-        (_b = this.canvas3dContext) === null || _b === void 0 ? void 0 : _b.dispose(options);
+        if (!(options === null || options === void 0 ? void 0 : options.doNotDisposeCanvas3DContext)) {
+            (_b = this.canvas3dContext) === null || _b === void 0 ? void 0 : _b.dispose(options);
+        }
         this.ev.dispose();
         this.state.dispose();
         this.helpers.substructureParent.dispose();

package/lib/mol-plugin/state.d.ts

@@ -25,26 +25,26 @@ declare class PluginState extends PluginComponent {
     readonly events: {
         readonly cell: {
             readonly stateUpdated: import("rxjs").Observable<State.ObjectEvent & {
-                cell: import("../mol-state").StateObjectCell<import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>, StateTransform<StateTransformer<import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>, import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>, any>>>;
+                cell: import("../mol-state").StateObjectCell;
             }>;
             readonly created: import("rxjs").Observable<State.ObjectEvent & {
-                cell: import("../mol-state").StateObjectCell<import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>, StateTransform<StateTransformer<import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>, import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>, any>>>;
+                cell: import("../mol-state").StateObjectCell;
             }>;
             readonly removed: import("rxjs").Observable<State.ObjectEvent & {
-                parent: string;
+                parent: StateTransform.Ref;
             }>;
         };
         readonly object: {
             readonly created: import("rxjs").Observable<State.ObjectEvent & {
-                obj: import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>;
+                obj: import("../mol-state").StateObject;
             }>;
             readonly removed: import("rxjs").Observable<State.ObjectEvent & {
-                obj?: import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>> | undefined;
+                obj?: import("../mol-state").StateObject;
             }>;
             readonly updated: import("rxjs").Observable<State.ObjectEvent & {
                 action: "in-place" | "recreate";
-                obj: import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>>;
-                oldObj?: import("../mol-state").StateObject<any, import("../mol-state").StateObject.Type<any>> | undefined;
+                obj: import("../mol-state").StateObject;
+                oldObj?: import("../mol-state").StateObject;
                 oldData?: any;
             }>;
         };

package/lib/mol-plugin/util/headless-screenshot.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Jesse Liang <jesse.liang@rcsb.org>