molstar 4.3.0 → 4.4.1

package/lib/commonjs/examples/alpha-orbitals/example-data.js

@@ -1,166 +1,166 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DemoOrbitals = exports.DemoMoleculeSDF = void 0;
-exports.DemoMoleculeSDF = `60823
-  -OEChem-10232017443D
-
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-    3.3901   -2.4373    3.0602 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.8234   -0.9362   -0.1694 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.0484   -0.0236    1.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.9513   -3.8220   -3.4785 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.7344   -1.5960   -3.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.3212    0.0758    1.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.4511   -1.1575   -0.3628 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.8535   -0.6250    1.5997 C   0  0  0  0  0  0  0  0  0  0  0  0
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-M  END
+exports.DemoMoleculeSDF = `60823
+  -OEChem-10232017443D
+
+ 76 79  0     1  0  0  0  0  0999 V2000
+    4.2325    4.8495   -0.2414 F   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3901   -2.4373    3.0602 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.8234   -0.9362   -0.1694 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0484   -0.0236    1.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.9513   -3.8220   -3.4785 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.7344   -1.5960   -3.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3212    0.0758    1.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4511   -1.1575   -0.3628 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8535   -0.6250    1.5997 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5803   -0.3344    2.1283 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1278    1.2100    0.7719 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9533   -1.9004    2.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4473   -1.2165    1.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8115    0.0728    0.8978 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1907    1.2338    0.3742 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7416   -1.7120    1.8781 C   0  0  2  0  0  0  0  0  0  0  0  0
+    4.5791   -2.6487    0.9881 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1949    2.1553    0.5088 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -8.0344   -3.3656   -1.8250 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1 33  1  0  0  0  0
+  2 16  1  0  0  0  0
+  2 61  1  0  0  0  0
+  3 22  1  0  0  0  0
+  3 67  1  0  0  0  0
+  4 23  2  0  0  0  0
+  5 35  1  0  0  0  0
+  5 73  1  0  0  0  0
+  6 35  2  0  0  0  0
+  7  9  1  0  0  0  0
+  7 10  1  0  0  0  0
+  7 11  1  0  0  0  0
+  8 23  1  0  0  0  0
+  8 34  1  0  0  0  0
+  8 64  1  0  0  0  0
+  9 12  1  0  0  0  0
+  9 14  2  0  0  0  0
+ 10 13  1  0  0  0  0
+ 10 42  1  0  0  0  0
+ 10 43  1  0  0  0  0
+ 11 15  2  0  0  0  0
+ 11 18  1  0  0  0  0
+ 12 19  1  0  0  0  0
+ 12 20  1  0  0  0  0
+ 12 44  1  0  0  0  0
+ 13 16  1  0  0  0  0
+ 13 45  1  0  0  0  0
+ 13 46  1  0  0  0  0
+ 14 15  1  0  0  0  0
+ 14 23  1  0  0  0  0
+ 15 21  1  0  0  0  0
+ 16 17  1  0  0  0  0
+ 16 47  1  0  0  0  0
+ 17 22  1  0  0  0  0
+ 17 48  1  0  0  0  0
+ 17 49  1  0  0  0  0
+ 18 25  2  0  0  0  0
+ 18 26  1  0  0  0  0
+ 19 50  1  0  0  0  0
+ 19 51  1  0  0  0  0
+ 19 52  1  0  0  0  0
+ 20 53  1  0  0  0  0
+ 20 54  1  0  0  0  0
+ 20 55  1  0  0  0  0
+ 21 27  2  0  0  0  0
+ 21 28  1  0  0  0  0
+ 22 24  1  0  0  0  0
+ 22 56  1  0  0  0  0
+ 24 35  1  0  0  0  0
+ 24 57  1  0  0  0  0
+ 24 58  1  0  0  0  0
+ 25 29  1  0  0  0  0
+ 25 59  1  0  0  0  0
+ 26 30  2  0  0  0  0
+ 26 60  1  0  0  0  0
+ 27 31  1  0  0  0  0
+ 27 62  1  0  0  0  0
+ 28 32  2  0  0  0  0
+ 28 63  1  0  0  0  0
+ 29 33  2  0  0  0  0
+ 29 65  1  0  0  0  0
+ 30 33  1  0  0  0  0
+ 30 66  1  0  0  0  0
+ 31 36  2  0  0  0  0
+ 31 68  1  0  0  0  0
+ 32 36  1  0  0  0  0
+ 32 69  1  0  0  0  0
+ 34 37  2  0  0  0  0
+ 34 38  1  0  0  0  0
+ 36 70  1  0  0  0  0
+ 37 39  1  0  0  0  0
+ 37 71  1  0  0  0  0
+ 38 40  2  0  0  0  0
+ 38 72  1  0  0  0  0
+ 39 41  2  0  0  0  0
+ 39 74  1  0  0  0  0
+ 40 41  1  0  0  0  0
+ 40 75  1  0  0  0  0
+ 41 76  1  0  0  0  0
+M  END
 `;
 exports.DemoOrbitals = {
     order: 'cca-reverse',

package/lib/commonjs/examples/basic-wrapper/custom-theme.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CustomColorThemeProvider = exports.CustomColorTheme = void 0;
+exports.CustomColorThemeProvider = void 0;
+exports.CustomColorTheme = CustomColorTheme;
 const location_iterator_1 = require("../../mol-geo/util/location-iterator");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const color_1 = require("../../mol-theme/color");
@@ -36,7 +37,6 @@ function CustomColorTheme(ctx, props) {
         description: '',
     };
 }
-exports.CustomColorTheme = CustomColorTheme;
 exports.CustomColorThemeProvider = {
     name: 'basic-wrapper-custom-color-theme',
     label: 'Custom Color Theme',

package/lib/commonjs/examples/basic-wrapper/superposition.js

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.dynamicSuperpositionTest = exports.StaticSuperpositionTestData = exports.buildStaticSuperposition = void 0;
+exports.StaticSuperpositionTestData = void 0;
+exports.buildStaticSuperposition = buildStaticSuperposition;
+exports.dynamicSuperpositionTest = dynamicSuperpositionTest;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const structure_1 = require("../../mol-model/structure");
 const superposition_1 = require("../../mol-model/structure/structure/util/superposition");
@@ -24,7 +26,6 @@ function buildStaticSuperposition(plugin, src) {
         }
     });
 }
-exports.buildStaticSuperposition = buildStaticSuperposition;
 exports.StaticSuperpositionTestData = [
     {
         pdbId: '1aj5', auth_asym_id: 'A', matrix: linear_algebra_1.Mat4.identity()
@@ -75,7 +76,6 @@ function dynamicSuperpositionTest(plugin, src, comp_id) {
         }
     });
 }
-exports.dynamicSuperpositionTest = dynamicSuperpositionTest;
 async function siteVisual(plugin, s, pivot, rest) {
     const center = await plugin.builders.structure.tryCreateComponentFromExpression(s, pivot, 'pivot');
     if (center)

package/lib/commonjs/examples/domain-annotation-server/mapping.js

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createMapping = void 0;
+exports.createMapping = createMapping;
 const tslib_1 = require("tslib");
 const db_1 = require("../../mol-data/db");
 const cif_1 = require("../../mol-io/writer/cif");
@@ -27,7 +27,6 @@ function createMapping(allData) {
     }
     return enc.getData();
 }
-exports.createMapping = createMapping;
 function writeDomain(enc, domain) {
     if (!domain)
         return;

package/lib/commonjs/examples/lighting/index.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>
  */

package/lib/commonjs/examples/lighting/index.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -25,6 +25,7 @@ const Canvas3DPresets = {
                         radius: 5,
                         bias: 0.8,
                         blurKernelSize: 15,
+                        blurDepthBias: 0.5,
                         resolutionScale: 1,
                         color: (0, color_1.Color)(0x000000),
                     }

package/lib/commonjs/examples/proteopedia-wrapper/coloring.d.ts

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Color } from '../../mol-util/color';
-import { ColorTheme, LocationColor } from '../../mol-theme/color';
+import { ColorTheme } from '../../mol-theme/color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../../mol-theme/theme';
 export declare function createProteopediaCustomTheme(colors: number[]): {
@@ -16,26 +16,11 @@ export declare function createProteopediaCustomTheme(colors: number[]): {
         colors: PD.ObjectList<PD.Normalize<{
             color: Color;
         }>>;
-    }>) => {
-        readonly granularity: import("../../mol-geo/geometry/color-data").ColorTypeLocation;
-        readonly color: LocationColor;
-    } & {
-        readonly factory: ColorTheme.Factory<{
-            colors: PD.ObjectList<PD.Normalize<{
-                color: Color;
-            }>>;
-        }, import("../../mol-geo/geometry/color-data").ColorTypeLocation>;
-        readonly props: Readonly<PD.Values<{
-            colors: PD.ObjectList<PD.Normalize<{
-                color: Color;
-            }>>;
+    }>) => ColorTheme<{
+        colors: PD.ObjectList<PD.Normalize<{
+            color: Color;
         }>>;
-        readonly palette?: Readonly<ColorTheme.Palette> | undefined;
-        readonly preferSmoothing?: boolean | undefined;
-        readonly contextHash?: number | undefined;
-        readonly description?: string | undefined;
-        readonly legend?: Readonly<import("../../mol-util/legend").TableLegend | import("../../mol-util/legend").ScaleLegend> | undefined;
-    };
+    }>;
     getParams: (ctx: ThemeDataContext) => {
         colors: PD.ObjectList<PD.Normalize<{
             color: Color;

package/lib/commonjs/examples/proteopedia-wrapper/coloring.js

@@ -6,7 +6,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createProteopediaCustomTheme = void 0;
+exports.createProteopediaCustomTheme = createProteopediaCustomTheme;
 const structure_1 = require("../../mol-model/structure");
 const color_1 = require("../../mol-util/color");
 const param_definition_1 = require("../../mol-util/param-definition");
@@ -90,4 +90,3 @@ function createProteopediaCustomTheme(colors) {
         isApplicable: (ctx) => !!ctx.structure
     };
 }
-exports.createProteopediaCustomTheme = createProteopediaCustomTheme;

package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.volumeStreamingControls = void 0;
+exports.volumeStreamingControls = volumeStreamingControls;
 const tslib_1 = require("tslib");
 const jsx_runtime_1 = require("react/jsx-runtime");
 /**
@@ -15,4 +15,3 @@ const helpers_1 = require("../helpers");
 function volumeStreamingControls(plugin, parent) {
     ReactDOM.render((0, jsx_runtime_1.jsx)(plugin_1.PluginContextContainer, { plugin: plugin, children: (0, jsx_runtime_1.jsx)(update_transform_1.TransformUpdaterControl, { nodeRef: helpers_1.StateElements.VolumeStreaming }) }), parent);
 }
-exports.volumeStreamingControls = volumeStreamingControls;

package/lib/commonjs/examples/task.js

@@ -5,7 +5,12 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.logP = exports.abortingObserver = exports.ms = exports.testTree = exports.abortAfter = exports.test1 = void 0;
+exports.ms = void 0;
+exports.test1 = test1;
+exports.abortAfter = abortAfter;
+exports.testTree = testTree;
+exports.abortingObserver = abortingObserver;
+exports.logP = logP;
 const mol_task_1 = require("../mol-task");
 const now_1 = require("../mol-util/now");
 async function test1() {
@@ -13,7 +18,6 @@ async function test1() {
     const r = await t.run();
     console.log(r);
 }
-exports.test1 = test1;
 function messageTree(root, prefix = '') {
     const p = root.progress;
     if (!root.children.length) {
@@ -44,7 +48,6 @@ function abortAfter(delay) {
         // return r;
     });
 }
-exports.abortAfter = abortAfter;
 function testTree() {
     return mol_task_1.Task.create('test o', async (ctx) => {
         await mol_task_1.Scheduler.delay(250);
@@ -67,7 +70,6 @@ function testTree() {
         return r + 1;
     }, () => console.log('On abort O'));
 }
-exports.testTree = testTree;
 function processChunk(n, state) {
     const toProcess = Math.min(state.current + n, state.total);
     const start = state.current;
@@ -101,9 +103,7 @@ function abortingObserver(p) {
         p.requestAbort('test');
     }
 }
-exports.abortingObserver = abortingObserver;
 function logP(p) { console.log(messageTree(p.root)); }
-exports.logP = logP;
 async function test() {
     try {
         // const r = await Run(testTree(), p => console.log(messageTree(p.root)), 250);

package/lib/commonjs/extensions/alpha-orbitals/collocation.js

@@ -7,7 +7,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.sphericalCollocation = void 0;
+exports.sphericalCollocation = sphericalCollocation;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const array_1 = require("../../mol-util/array");
 const spherical_functions_1 = require("./spherical-functions");
@@ -47,7 +47,6 @@ async function sphericalCollocation(grid, orbital, taskCtx) {
     }
     return matrix;
 }
-exports.sphericalCollocation = sphericalCollocation;
 function collocationBasis(matrix, grid, L, coefficients, exponents, center, cutoffThreshold, alpha) {
     const ncoeff = exponents.length;
     const sphericalFunc = spherical_functions_1.SphericalFunctions[L];

package/lib/commonjs/extensions/alpha-orbitals/data-model.js

@@ -5,7 +5,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createGrid = exports.initCubeGrid = exports.isCubeGridData = exports.CubeGridFormat = void 0;
+exports.CubeGridFormat = CubeGridFormat;
+exports.isCubeGridData = isCubeGridData;
+exports.initCubeGrid = initCubeGrid;
+exports.createGrid = createGrid;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const geometry_1 = require("../../mol-math/geometry");
 const array_1 = require("../../mol-util/array");
@@ -13,11 +16,9 @@ const array_1 = require("../../mol-util/array");
 function CubeGridFormat(grid) {
     return { name: 'custom grid', kind: 'cube-grid', data: grid };
 }
-exports.CubeGridFormat = CubeGridFormat;
 function isCubeGridData(f) {
     return f.kind === 'cube-grid';
 }
-exports.isCubeGridData = isCubeGridData;
 function initCubeGrid(params) {
     const geometry = params.basis.atoms.map(a => a.center);
     const { gridSpacing: spacing, boxExpand: expand } = params;
@@ -42,7 +43,6 @@ function initCubeGrid(params) {
         delta: linear_algebra_1.Vec3.div((0, linear_algebra_1.Vec3)(), size, linear_algebra_1.Vec3.subScalar((0, linear_algebra_1.Vec3)(), dimensions, 1)),
     };
 }
-exports.initCubeGrid = initCubeGrid;
 const BohrToAngstromFactor = 0.529177210859;
 function createGrid(gridInfo, values, axisOrder) {
     const boxSize = geometry_1.Box3D.size((0, linear_algebra_1.Vec3)(), gridInfo.box);
@@ -64,4 +64,3 @@ function createGrid(gridInfo, values, axisOrder) {
     };
     return grid;
 }
-exports.createGrid = createGrid;

package/lib/commonjs/extensions/alpha-orbitals/density.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeDensityIsocontourValues = exports.createSphericalCollocationDensityGrid = void 0;
+exports.createSphericalCollocationDensityGrid = createSphericalCollocationDensityGrid;
+exports.computeDensityIsocontourValues = computeDensityIsocontourValues;
 const util_1 = require("../../mol-data/util");
 const grid3d_1 = require("../../mol-gl/compute/grid3d");
 const mol_task_1 = require("../../mol-task");
@@ -34,7 +35,6 @@ function createSphericalCollocationDensityGrid(params, orbitals, webgl) {
         return { grid, isovalues };
     });
 }
-exports.createSphericalCollocationDensityGrid = createSphericalCollocationDensityGrid;
 function computeDensityIsocontourValues(input, cumulativeThreshold) {
     let weightSum = 0;
     for (let i = 0, _i = input.length; i < _i; i++) {
@@ -106,4 +106,3 @@ function computeDensityIsocontourValues(input, cumulativeThreshold) {
         positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
     };
 }
-exports.computeDensityIsocontourValues = computeDensityIsocontourValues;

package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.gpuComputeAlphaOrbitalsDensityGridValues = exports.gpuComputeAlphaOrbitalsGridValues = void 0;
+exports.gpuComputeAlphaOrbitalsGridValues = gpuComputeAlphaOrbitalsGridValues;
+exports.gpuComputeAlphaOrbitalsDensityGridValues = gpuComputeAlphaOrbitalsDensityGridValues;
 const grid3d_1 = require("../../../mol-gl/compute/grid3d");
 const schema_1 = require("../../../mol-gl/renderable/schema");
 const mol_util_1 = require("../../../mol-util");
@@ -61,11 +62,9 @@ const Density = (0, grid3d_1.createGrid3dComputeRenderable)({
 function gpuComputeAlphaOrbitalsGridValues(ctx, webgl, grid, orbital) {
     return Orbitals(ctx, webgl, grid, { grid, orbital });
 }
-exports.gpuComputeAlphaOrbitalsGridValues = gpuComputeAlphaOrbitalsGridValues;
 function gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl, grid, orbitals) {
     return Density(ctx, webgl, grid, { grid, orbitals });
 }
-exports.gpuComputeAlphaOrbitalsDensityGridValues = gpuComputeAlphaOrbitalsDensityGridValues;
 function getNormalizedAlpha(basis, alphaOrbitals, sphericalOrder) {
     const alpha = new Float32Array(alphaOrbitals.length);
     let aO = 0;