molstar 4.2.0 → 4.4.0

package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts

@@ -70,7 +70,7 @@ export declare abstract class MeshExporter<D extends RenderObjectExportData> imp
         vertices: Float32Array;
         normals: Float32Array | undefined;
         indices: Uint32Array | undefined;
-        groups: Uint8Array | Float32Array;
+        groups: Float32Array | Uint8Array;
         vertexCount: number;
         drawCount: number;
     };
@@ -88,7 +88,7 @@ export declare abstract class MeshExporter<D extends RenderObjectExportData> imp
         includeHidden: boolean;
         linesAsTriangles: boolean;
         pointsAsTriangles: boolean;
-        primitivesQuality: "auto" | "medium" | "high" | "low";
+        primitivesQuality: "auto" | "high" | "medium" | "low";
     };
     abstract getData(ctx: RuntimeContext): Promise<D>;
     abstract getBlob(ctx: RuntimeContext): Promise<Blob>;

package/lib/commonjs/extensions/geo-export/ui.d.ts

@@ -3,7 +3,6 @@
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  */
-/// <reference types="react" />
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
 import { GeometryControls } from './controls';
 interface State {

package/lib/commonjs/extensions/meshes/examples.js

@@ -5,7 +5,15 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.runCifMeshExample = exports.runIsosurfaceExample = exports.runMolsurfaceExample = exports.runMeshStreamingExample = exports.runMultimeshExample = exports.runMeshExample2 = exports.runMeshExample = exports.runMeshExtensionExamples = exports.DB_URL = void 0;
+exports.DB_URL = void 0;
+exports.runMeshExtensionExamples = runMeshExtensionExamples;
+exports.runMeshExample = runMeshExample;
+exports.runMeshExample2 = runMeshExample2;
+exports.runMultimeshExample = runMultimeshExample;
+exports.runMeshStreamingExample = runMeshStreamingExample;
+exports.runMolsurfaceExample = runMolsurfaceExample;
+exports.runIsosurfaceExample = runIsosurfaceExample;
+exports.runCifMeshExample = runCifMeshExample;
 const tslib_1 = require("tslib");
 /** Testing examples for using mesh-extension.ts. */
 const cif_1 = require("../../mol-io/reader/cif");
@@ -34,7 +42,6 @@ async function runMeshExtensionExamples(plugin, db_url = exports.DB_URL) {
     await runMeshStreamingExample(plugin);
     console.timeEnd('TIME MESH EXAMPLES');
 }
-exports.runMeshExtensionExamples = runMeshExtensionExamples;
 /** Example for downloading multiple separate segments, each containing 1 mesh. */
 async function runMeshExample(plugin, segments, db_url = exports.DB_URL) {
     const detail = 2;
@@ -45,7 +52,6 @@ async function runMeshExample(plugin, segments, db_url = exports.DB_URL) {
         await (0, mesh_extension_1.createMeshFromUrl)(plugin, `${db_url}/empiar-10070-mesh-rounded/segment-${segmentId}/detail-${detail}`, segmentId, detail, true, undefined);
     }
 }
-exports.runMeshExample = runMeshExample;
 /** Example for downloading multiple separate segments, each containing 1 mesh. */
 async function runMeshExample2(plugin, segments) {
     const detail = 1;
@@ -57,14 +63,12 @@ async function runMeshExample2(plugin, segments) {
         await (0, mesh_extension_1.createMeshFromUrl)(plugin, `http://localhost:9000/v2/empiar/empiar-10070/mesh_bcif/${segmentId}/${detail}`, segmentId, detail, false, undefined);
     }
 }
-exports.runMeshExample2 = runMeshExample2;
 /** Example for downloading a single segment containing multiple meshes. */
 async function runMultimeshExample(plugin, segments, detailChoice, db_url = exports.DB_URL) {
     const urlDetail = (detailChoice === 'best') ? '2' : 'worst';
     const numDetail = (detailChoice === 'best') ? 2 : 1000;
     await (0, mesh_extension_1.createMeshFromUrl)(plugin, `${db_url}/empiar-10070-multimesh-rounded/segments-${segments}/detail-${urlDetail}`, 0, numDetail, false, undefined);
 }
-exports.runMultimeshExample = runMultimeshExample;
 async function runMeshStreamingExample(plugin, source = 'empiar', entryId = 'empiar-10070', serverUrl, parent) {
     const params = param_definition_1.ParamDefinition.getDefaultValues(server_info_1.MeshServerInfo.Params);
     if (serverUrl)
@@ -73,7 +77,6 @@ async function runMeshStreamingExample(plugin, source = 'empiar', entryId = 'emp
     params.entryId = entryId;
     await plugin.runTask(plugin.state.data.applyAction(transformers_1.InitMeshStreaming, params, parent === null || parent === void 0 ? void 0 : parent.ref), { useOverlay: false });
 }
-exports.runMeshStreamingExample = runMeshStreamingExample;
 /** Example for downloading a protein structure and visualizing molecular surface. */
 async function runMolsurfaceExample(plugin) {
     const entryId = 'pdb-7etq';
@@ -97,7 +100,6 @@ async function runMolsurfaceExample(plugin) {
     const repr = await plugin.build().to(structure).apply(transforms_1.StateTransforms.Representation.StructureRepresentation3D, reprParams).commit();
     console.log('repr:', repr);
 }
-exports.runMolsurfaceExample = runMolsurfaceExample;
 /** Example for downloading an EMDB density data and visualizing isosurface. */
 async function runIsosurfaceExample(plugin, db_url = exports.DB_URL) {
     var _a, _b;
@@ -143,12 +145,10 @@ async function runIsosurfaceExample(plugin, db_url = exports.DB_URL) {
     root.to(volume).apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, volumeParams);
     await root.commit();
 }
-exports.runIsosurfaceExample = runIsosurfaceExample;
 async function runCifMeshExample(plugin, api = 'http://localhost:9000/v2', source = 'empiar', entryId = 'empiar-10070', segmentId = 1, detail = 10) {
     const url = `${api}/${source}/${entryId}/mesh_bcif/${segmentId}/${detail}`;
     getMeshFromBcif(plugin, url);
 }
-exports.runCifMeshExample = runCifMeshExample;
 async function getMeshFromBcif(plugin, url) {
     const urlAsset = assets_1.Asset.getUrlAsset(plugin.managers.asset, url);
     const asset = await plugin.runTask(plugin.managers.asset.resolve(urlAsset, 'binary'));

package/lib/commonjs/extensions/meshes/mesh-extension.d.ts

@@ -37,18 +37,16 @@ export declare namespace MeshlistData {
 declare const MeshlistStateObject_base: {
     new (data: MeshlistData, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../mol-util").UUID;
-        /** Data type for `MeshlistStateObject` - list of meshes */
         type: PluginStateObject.TypeInfo;
-        /** Data type for `MeshlistStateObject` - list of meshes */
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: MeshlistData;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<MeshlistData, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<MeshlistData, PluginStateObject.TypeInfo>;
 };
 export declare class MeshlistStateObject extends MeshlistStateObject_base {
 }

package/lib/commonjs/extensions/meshes/mesh-extension.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createMeshFromUrl = exports.MeshShapeTransformer = exports.ParseMeshlistTransformer = exports.MeshlistStateObject = exports.MeshlistData = exports.VolsegTransform = exports.FOREROUND_OPACITY = exports.BACKGROUND_OPACITY = void 0;
+exports.MeshShapeTransformer = exports.ParseMeshlistTransformer = exports.MeshlistStateObject = exports.MeshlistData = exports.VolsegTransform = exports.FOREROUND_OPACITY = exports.BACKGROUND_OPACITY = void 0;
+exports.createMeshFromUrl = createMeshFromUrl;
 const tslib_1 = require("tslib");
 /** Defines new types of State tree transformers for dealing with mesh data. */
 const base_1 = require("../../mol-geo/geometry/base");
@@ -176,4 +177,3 @@ async function createMeshFromUrl(plugin, meshDataUrl, segmentId, detail, collaps
         .commit();
     return rawDataNodeRef;
 }
-exports.createMeshFromUrl = createMeshFromUrl;

package/lib/commonjs/extensions/meshes/mesh-streaming/behavior.d.ts

@@ -18,16 +18,16 @@ export declare const BACKGROUND_SEGMENT_VOLUME_THRESHOLD = 0.5;
 declare const MeshStreaming_base: {
     new (data: MeshStreaming.Behavior, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: MeshStreaming.Behavior;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<MeshStreaming.Behavior, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<MeshStreaming.Behavior, PluginStateObject.TypeInfo>;
 };
 export declare class MeshStreaming extends MeshStreaming_base {
 }

package/lib/commonjs/extensions/meshes/mesh-streaming/server-info.d.ts

@@ -14,12 +14,12 @@ declare const MeshServerInfo_base: {
         entryId: PD.Text<string>;
     }>, 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: PD.Values<{
             serverUrl: PD.Text<string>;
             source: PD.Select<"emdb" | "empiar">;
@@ -27,7 +27,7 @@ declare const MeshServerInfo_base: {
         }>;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<PD.Values<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<PD.Values<{
         serverUrl: PD.Text<string>;
         source: PD.Select<"emdb" | "empiar">;
         entryId: PD.Text<string>;

package/lib/commonjs/extensions/meshes/mesh-utils.js

@@ -5,7 +5,15 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ColorGenerator = exports.meshFromBox = exports.fakeMesh4 = exports.fakeFakeMesh1 = exports.bbox = exports.meshFromCif = exports.concat = exports.copy = exports.modify = void 0;
+exports.ColorGenerator = void 0;
+exports.modify = modify;
+exports.copy = copy;
+exports.concat = concat;
+exports.meshFromCif = meshFromCif;
+exports.bbox = bbox;
+exports.fakeFakeMesh1 = fakeFakeMesh1;
+exports.fakeMesh4 = fakeMesh4;
+exports.meshFromBox = meshFromBox;
 /** Helper functions for manipulation with mesh data. */
 const mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
 const cif_1 = require("../../mol-io/reader/cif");
@@ -63,7 +71,6 @@ function modify(m, params) {
         }
     }
 }
-exports.modify = modify;
 /** Create a copy a mesh, possibly modified */
 function copy(m, modification) {
     const nVertices = m.vertexCount;
@@ -78,7 +85,6 @@ function copy(m, modification) {
     }
     return result;
 }
-exports.copy = copy;
 /** Join more meshes into one */
 function concat(...meshes) {
     const nVertices = sum(meshes.map(m => m.vertexCount));
@@ -95,7 +101,6 @@ function concat(...meshes) {
     const indices = concatArrays(Uint32Array, newIndices);
     return mesh_1.Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
 }
-exports.concat = concat;
 /** Return Mesh from CIF data and mesh IDs (group IDs).
  * Assume the CIF contains coords in grid space,
  * transform the output mesh to `space` */
@@ -151,7 +156,6 @@ async function meshFromCif(data, invertSides = undefined, outSpace = 'cartesian'
     // mesh = concat(mesh, boxMesh);  // debug
     return { mesh: mesh, meshIds: Array.from(mesh_id) };
 }
-exports.meshFromCif = meshFromCif;
 function isInverted(mesh) {
     const vertices = mesh.vertexBuffer.ref.value;
     const indices = mesh.indexBuffer.ref.value;
@@ -232,7 +236,6 @@ function bbox(mesh) {
     }
     return geometry_1.Box3D.create(linear_algebra_1.Vec3.create(minX, minY, minZ), linear_algebra_1.Vec3.create(maxX, maxY, maxZ));
 }
-exports.bbox = bbox;
 /** Example mesh - 1 triangle */
 function fakeFakeMesh1() {
     const nVertices = 3;
@@ -243,7 +246,6 @@ function fakeFakeMesh1() {
     const groups = new Float32Array([0]);
     return mesh_1.Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
 }
-exports.fakeFakeMesh1 = fakeFakeMesh1;
 /** Example mesh - irregular tetrahedron */
 function fakeMesh4() {
     const nVertices = 4;
@@ -254,7 +256,6 @@ function fakeMesh4() {
     const groups = new Float32Array([0, 1, 2, 3]);
     return mesh_1.Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
 }
-exports.fakeMesh4 = fakeMesh4;
 /** Return a box-shaped mesh */
 function meshFromBox(box, group = 0) {
     const [[x0, y0, z0], [x1, y1, z1]] = box;
@@ -282,7 +283,6 @@ function meshFromBox(box, group = 0) {
     mesh_1.Mesh.computeNormals(mesh); // normals only necessary if flatShaded==false
     return mesh;
 }
-exports.meshFromBox = meshFromBox;
 function sum(array) {
     return array.reduce((a, b) => a + b, 0);
 }

package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Mandar Deshpande <mandar@ebi.ac.uk>
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>

package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js

@@ -1,13 +1,15 @@
 "use strict";
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Mandar Deshpande <mandar@ebi.ac.uk>
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PLDDTConfidenceColorThemeProvider = exports.PLDDTConfidenceColorTheme = exports.getPLDDTConfidenceColorThemeParams = void 0;
+exports.PLDDTConfidenceColorThemeProvider = void 0;
+exports.getPLDDTConfidenceColorThemeParams = getPLDDTConfidenceColorThemeParams;
+exports.PLDDTConfidenceColorTheme = PLDDTConfidenceColorTheme;
 const prop_1 = require("../prop");
 const structure_1 = require("../../../../mol-model/structure");
 const color_1 = require("../../../../mol-theme/color");
@@ -26,18 +28,20 @@ const ConfidenceColorLegend = (0, legend_1.TableLegend)(Object.entries(Confidenc
 function getPLDDTConfidenceColorThemeParams(ctx) {
     return {};
 }
-exports.getPLDDTConfidenceColorThemeParams = getPLDDTConfidenceColorThemeParams;
 function PLDDTConfidenceColorTheme(ctx, props) {
     let color = () => DefaultColor;
     if (ctx.structure) {
         const l = structure_1.StructureElement.Location.create(ctx.structure.root);
         const getColor = (location) => {
-            var _a, _b;
+            var _a;
             const { unit, element } = location;
             if (!structure_1.Unit.isAtomic(unit))
                 return DefaultColor;
             const qualityAssessment = prop_1.QualityAssessmentProvider.get(unit.model).value;
-            const score = (_b = (_a = qualityAssessment === null || qualityAssessment === void 0 ? void 0 : qualityAssessment.pLDDT) === null || _a === void 0 ? void 0 : _a.get(unit.model.atomicHierarchy.residueAtomSegments.index[element])) !== null && _b !== void 0 ? _b : -1;
+            let score = (_a = qualityAssessment === null || qualityAssessment === void 0 ? void 0 : qualityAssessment.pLDDT) === null || _a === void 0 ? void 0 : _a.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]);
+            if (typeof score !== 'number') {
+                score = unit.model.atomicConformation.B_iso_or_equiv.value(element);
+            }
             if (score < 0) {
                 return DefaultColor;
             }
@@ -72,11 +76,10 @@ function PLDDTConfidenceColorTheme(ctx, props) {
         preferSmoothing: true,
         color,
         props,
-        description: 'Assigns residue colors according to the pLDDT Confidence score.',
+        description: 'Assigns residue colors according to the pLDDT Confidence score. If no Model Archive quality assessment score is available, the B-factor value is used instead.',
         legend: ConfidenceColorLegend
     };
 }
-exports.PLDDTConfidenceColorTheme = PLDDTConfidenceColorTheme;
 exports.PLDDTConfidenceColorThemeProvider = {
     name: 'plddt-confidence',
     label: 'pLDDT Confidence',
@@ -84,7 +87,7 @@ exports.PLDDTConfidenceColorThemeProvider = {
     factory: PLDDTConfidenceColorTheme,
     getParams: getPLDDTConfidenceColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
-    isApplicable: (ctx) => { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'pLDDT'))); },
+    isApplicable: (ctx) => { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'pLDDT') || m.atomicConformation.B_iso_or_equiv.isDefined)); },
     ensureCustomProperties: {
         attach: async (ctx, data) => {
             if (data.structure) {

package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js

@@ -5,7 +5,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.QmeanScoreColorThemeProvider = exports.QmeanScoreColorTheme = exports.getQmeanScoreColorThemeParams = void 0;
+exports.QmeanScoreColorThemeProvider = void 0;
+exports.getQmeanScoreColorThemeParams = getQmeanScoreColorThemeParams;
+exports.QmeanScoreColorTheme = QmeanScoreColorTheme;
 const prop_1 = require("../prop");
 const structure_1 = require("../../../../mol-model/structure");
 const color_1 = require("../../../../mol-theme/color");
@@ -15,7 +17,6 @@ const DefaultColor = (0, color_2.Color)(0xaaaaaa);
 function getQmeanScoreColorThemeParams(ctx) {
     return {};
 }
-exports.getQmeanScoreColorThemeParams = getQmeanScoreColorThemeParams;
 function QmeanScoreColorTheme(ctx, props) {
     let color = () => DefaultColor;
     const scale = color_2.ColorScale.create({
@@ -62,7 +63,6 @@ function QmeanScoreColorTheme(ctx, props) {
         legend: scale.legend
     };
 }
-exports.QmeanScoreColorTheme = QmeanScoreColorTheme;
 exports.QmeanScoreColorThemeProvider = {
     name: 'qmean-score',
     label: 'QMEAN Score',

package/lib/commonjs/extensions/model-export/export.js

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.exportHierarchy = exports.ModelExport = void 0;
+exports.ModelExport = void 0;
+exports.exportHierarchy = exportHierarchy;
 const utf8_1 = require("../../mol-io/common/utf8");
 const structure_1 = require("../../mol-model/structure");
 const mol_task_1 = require("../../mol-task");
@@ -31,7 +32,6 @@ async function exportHierarchy(plugin, options) {
         plugin.log.error(`Model export failed. See console for details.`);
     }
 }
-exports.exportHierarchy = exportHierarchy;
 function _exportHierarchy(plugin, options) {
     return mol_task_1.Task.create('Export', async (ctx) => {
         var _a, _b, _c, _d, _e, _f, _g, _h;

package/lib/commonjs/extensions/model-export/ui.d.ts

@@ -3,7 +3,6 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-/// <reference types="react" />
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
 export declare class ModelExportUI extends CollapsableControls<{}, {}> {
     protected defaultState(): CollapsableState;

package/lib/commonjs/extensions/mp4-export/controls.d.ts

@@ -34,7 +34,7 @@ export declare class Mp4Controls extends PluginComponent {
     setCurrent(name?: string): void;
     setCurrentParams(values: any): void;
     get current(): {
-        anim: PluginStateAnimation<any, any>;
+        anim: PluginStateAnimation;
         params: PD.Params;
         values: any;
     } | undefined;

package/lib/commonjs/extensions/mp4-export/encoder.js

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.encodeMp4Animation = void 0;
+exports.encodeMp4Animation = encodeMp4Animation;
 const tslib_1 = require("tslib");
 const HME = tslib_1.__importStar(require("h264-mp4-encoder"));
 const model_1 = require("../../mol-plugin-state/animation/model");
@@ -51,7 +51,7 @@ async function encodeMp4Animation(plugin, ctx, params) {
         await plugin.managers.animation.play(params.animation.definition, params.animation.params);
         stoppedAnimation = false;
         for (let i = 0; i <= N; i++) {
-            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true });
+            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true, updateControls: true });
             const image = params.pass.getImageData(width, height, normalizedViewport);
             encoder.addFrameRgba(image.data);
             if (ctx.shouldUpdate) {
@@ -77,7 +77,6 @@ async function encodeMp4Animation(plugin, ctx, params) {
             loop.start();
     }
 }
-exports.encodeMp4Animation = encodeMp4Animation;
 function validateViewport(params) {
     if (params.viewport.x + params.viewport.width > params.width || params.viewport.y + params.viewport.height > params.height) {
         throw new Error('Viewport exceeds the canvas dimensions.');

package/lib/commonjs/extensions/mp4-export/ui.d.ts

@@ -3,7 +3,6 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-/// <reference types="react" />
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
 import { Mp4Controls } from './controls';
 interface State {

package/lib/commonjs/extensions/mvs/camera.js

@@ -5,7 +5,10 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.setCanvas = exports.setFocus = exports.setCamera = exports.suppressCameraAutoreset = void 0;
+exports.suppressCameraAutoreset = suppressCameraAutoreset;
+exports.setCamera = setCamera;
+exports.setFocus = setFocus;
+exports.setCanvas = setCanvas;
 const canvas3d_1 = require("../../mol-canvas3d/canvas3d");
 const boundary_helper_1 = require("../../mol-math/geometry/boundary-helper");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
@@ -30,7 +33,6 @@ async function suppressCameraAutoreset(plugin) {
     adjustSceneRadiusFactor(plugin, snapshot.target);
     await commands_1.PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
 }
-exports.suppressCameraAutoreset = suppressCameraAutoreset;
 /** Set the camera based on a camera node params. */
 async function setCamera(plugin, params) {
     const target = linear_algebra_1.Vec3.create(...params.target);
@@ -43,7 +45,6 @@ async function setCamera(plugin, params) {
     adjustSceneRadiusFactor(plugin, snapshot.target);
     await commands_1.PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
 }
-exports.setCamera = setCamera;
 /** Focus the camera on the bounding sphere of a (sub)structure (or on the whole scene if `structureNodeSelector` is null).
  * Orient the camera based on a focus node params. */
 async function setFocus(plugin, structureNodeSelector, params = mvs_defaults_1.MVSDefaults.focus) {
@@ -75,7 +76,6 @@ async function setFocus(plugin, structureNodeSelector, params = mvs_defaults_1.M
         await commands_1.PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
     }
 }
-exports.setFocus = setFocus;
 /** Adjust `sceneRadiusFactor` property so that the current scene is not cropped */
 function adjustSceneRadiusFactor(plugin, cameraTarget) {
     var _a;
@@ -160,4 +160,3 @@ function setCanvas(plugin, params) {
         }));
     }
 }
-exports.setCanvas = setCanvas;

package/lib/commonjs/extensions/mvs/components/annotation-color-theme.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MVSAnnotationColorThemeProvider = exports.MVSAnnotationColorTheme = exports.MVSAnnotationColorThemeParams = void 0;
+exports.MVSAnnotationColorThemeProvider = exports.MVSAnnotationColorThemeParams = void 0;
+exports.MVSAnnotationColorTheme = MVSAnnotationColorTheme;
 const structure_1 = require("../../../mol-model/structure");
 const color_1 = require("../../../mol-theme/color");
 const names_1 = require("../../../mol-util/color/names");
@@ -59,7 +60,6 @@ function MVSAnnotationColorTheme(ctx, props) {
         description: 'Assigns colors based on custom MolViewSpec annotation data.',
     };
 }
-exports.MVSAnnotationColorTheme = MVSAnnotationColorTheme;
 /** A thingy that is needed to register color theme "MVS Annotation" */
 exports.MVSAnnotationColorThemeProvider = {
     name: 'mvs-annotation',

package/lib/commonjs/extensions/mvs/components/annotation-label/representation.d.ts

@@ -14,24 +14,24 @@ export declare const MVSAnnotationLabelParams: {
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;
@@ -77,7 +77,6 @@ export declare const MVSAnnotationLabelParams: {
     ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    /** Parameter values for representation type "MVS Annotation Label" */
     annotationId: PD.Text<string>;
     fieldName: PD.Text<string>;
 };
@@ -92,24 +91,24 @@ export declare const MVSAnnotationLabelRepresentationProvider: StructureRepresen
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;
@@ -155,7 +154,6 @@ export declare const MVSAnnotationLabelRepresentationProvider: StructureRepresen
     ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    /** Parameter values for representation type "MVS Annotation Label" */
     annotationId: PD.Text<string>;
     fieldName: PD.Text<string>;
 }, "mvs-annotation-label">;

package/lib/commonjs/extensions/mvs/components/annotation-label/representation.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MVSAnnotationLabelRepresentationProvider = exports.MVSAnnotationLabelRepresentation = exports.MVSAnnotationLabelParams = void 0;
+exports.MVSAnnotationLabelRepresentationProvider = exports.MVSAnnotationLabelParams = void 0;
+exports.MVSAnnotationLabelRepresentation = MVSAnnotationLabelRepresentation;
 const representation_1 = require("../../../../mol-repr/representation");
 const representation_2 = require("../../../../mol-repr/structure/representation");
 const marker_action_1 = require("../../../../mol-util/marker-action");
@@ -25,7 +26,6 @@ function MVSAnnotationLabelRepresentation(ctx, getParams) {
     repr.setState({ pickable: false, markerActions: marker_action_1.MarkerAction.None });
     return repr;
 }
-exports.MVSAnnotationLabelRepresentation = MVSAnnotationLabelRepresentation;
 /** A thingy that is needed to register representation type "MVS Annotation Label", allowing showing labels based on "MVS Annotations" custom props */
 exports.MVSAnnotationLabelRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
     name: 'mvs-annotation-label',