molstar 4.3.0 → 4.4.1

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>

package/lib/mol-plugin/util/headless-screenshot.js

@@ -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>
@@ -181,6 +181,7 @@ export function defaultImagePassParams() {
             ...DefaultCanvas3DParams.multiSample,
             mode: 'on',
             sampleLevel: 4,
+            reuseOcclusion: false,
         }
     };
 }
@@ -192,6 +193,7 @@ export const STYLIZED_POSTPROCESSING = {
             radius: 5,
             bias: 0.8,
             blurKernelSize: 15,
+            blurDepthBias: 0.5,
             resolutionScale: 1,
             color: ColorNames.black,
         }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-plugin/util/viewport-screenshot.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -84,6 +84,7 @@ class ViewportScreenshotHelper extends PluginComponent {
                 ...c.props.multiSample,
                 mode: multisample ? 'on' : 'off',
                 sampleLevel: colorBufferFloat && textureFloat ? 4 : 2,
+                reuseOcclusion: false,
             },
             postprocessing: {
                 ...c.props.postprocessing,

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '4.3.0';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1716707835175);
+export var PLUGIN_VERSION = '4.4.1';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1719787970602);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 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>

package/lib/mol-plugin-state/actions/volume.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 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>
@@ -23,7 +23,7 @@ const DownloadDensity = StateAction.build({
                 'pdb-xray': PD.Group({
                     provider: PD.Group({
                         id: PD.Text('1tqn', { label: 'Id' }),
-                        server: PD.Select('rcsb', [['pdbe', 'PDBe'], ['rcsb', 'RCSB PDB']]),
+                        server: PD.Select('pdbe', [['pdbe', 'PDBe']]),
                     }, { pivot: 'id' }),
                     type: PD.Select('2fofc', [['2fofc', '2Fo-Fc'], ['fofc', 'Fo-Fc']]),
                 }, { isFlat: true }),
@@ -66,18 +66,12 @@ const DownloadDensity = StateAction.build({
             downloadParams = src.params;
             break;
         case 'pdb-xray':
-            downloadParams = src.params.provider.server === 'pdbe' ? {
+            downloadParams = {
                 url: Asset.Url(src.params.type === '2fofc'
                     ? `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}.ccp4`
                     : `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}_diff.ccp4`),
                 isBinary: true,
                 label: `PDBe X-ray map: ${src.params.provider.id}`
-            } : {
-                url: Asset.Url(src.params.type === '2fofc'
-                    ? `https://edmaps.rcsb.org/maps/${src.params.provider.id.toLowerCase()}_2fofc.dsn6`
-                    : `https://edmaps.rcsb.org/maps/${src.params.provider.id.toLowerCase()}_fofc.dsn6`),
-                isBinary: true,
-                label: `RCSB X-ray map: ${src.params.provider.id}`
             };
             break;
         case 'pdb-emd-ds':
@@ -113,9 +107,7 @@ const DownloadDensity = StateAction.build({
             break;
         case 'pdb-xray':
             entryId = src.params.provider.id;
-            provider = src.params.provider.server === 'pdbe'
-                ? plugin.dataFormats.get('ccp4')
-                : plugin.dataFormats.get('dsn6');
+            provider = plugin.dataFormats.get('ccp4');
             break;
         case 'pdb-emd-ds':
         case 'pdb-xray-ds':

package/lib/mol-plugin-state/animation/built-in/model-index.d.ts

@@ -20,6 +20,6 @@ export declare const AnimateModelIndex: PluginStateAnimation<{
     }>, "computed">;
 }, {
     palindromeDirections?: {
-        [id: string]: 1 | -1 | undefined;
-    } | undefined;
+        [id: string]: -1 | 1 | undefined;
+    };
 }>;

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

@@ -25,6 +25,6 @@ export declare class DataFormatRegistry {
     get(name: string): DataFormatProvider | undefined;
     get list(): {
         name: string;
-        provider: DataFormatProvider<any, any, any>;
+        provider: DataFormatProvider;
     }[];
 }

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

@@ -28,39 +28,39 @@ export declare const MolProvider: TrajectoryFormatProvider;
 export declare const SdfProvider: TrajectoryFormatProvider;
 export declare const Mol2Provider: TrajectoryFormatProvider;
 export declare const BuiltInTrajectoryFormats: readonly [readonly ["mmcif", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["cifCore", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["pdb", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["pdbqt", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["gro", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["xyz", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["mol", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["sdf", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["mol2", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>]];

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

@@ -8,7 +8,6 @@
 import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
 import { PluginStateObject } from '../objects';
-import { Volume } from '../../mol-model/volume';
 export declare const VolumeFormatCategory = "Volume";
 type Params = {
     entryId?: string;

package/lib/mol-plugin-state/manager/structure/hierarchy.d.ts

@@ -27,9 +27,9 @@ export declare class StructureHierarchyManager extends PluginComponent {
     get seletionSet(): Set<string>;
     get current(): StructureHierarchy;
     get selection(): {
-        trajectories: readonly TrajectoryRef[];
-        models: readonly ModelRef[];
-        structures: readonly StructureRef[];
+        trajectories: ReadonlyArray<TrajectoryRef>;
+        models: ReadonlyArray<ModelRef>;
+        structures: ReadonlyArray<StructureRef>;
     };
     getStructuresWithSelection(): StructureRef[];
     findStructure(structure: Structure | undefined): StructureRef | undefined;

package/lib/mol-plugin-state/manager/structure/measurement.d.ts

@@ -168,6 +168,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             doubleSided: boolean;
             flipSided: boolean;
             flatShaded: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;
@@ -237,6 +238,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             doubleSided: boolean;
             flipSided: boolean;
             flatShaded: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;
@@ -324,6 +326,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             flipSided: boolean;
             flatShaded: boolean;
             ignoreLight: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;
@@ -365,6 +368,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             flipSided: boolean;
             flatShaded: boolean;
             ignoreLight: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;