molstar 2.3.9 → 3.0.0-dev.2

package/lib/extensions/geo-export/ui.js

@@ -17,37 +17,38 @@ var GeometryExporterUI = /** @class */ (function (_super) {
     function GeometryExporterUI() {
         var _this = _super !== null && _super.apply(this, arguments) || this;
         _this.save = function () { return __awaiter(_this, void 0, void 0, function () {
-            var data, _a;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
+            var data, e_1;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
                     case 0:
-                        _b.trys.push([0, 2, , 3]);
+                        _a.trys.push([0, 2, 3, 4]);
                         this.setState({ busy: true });
                         return [4 /*yield*/, this.controls.exportGeometry()];
                     case 1:
-                        data = _b.sent();
-                        this.setState({ busy: false });
+                        data = _a.sent();
                         download(data.blob, data.filename);
-                        return [3 /*break*/, 3];
+                        return [3 /*break*/, 4];
                     case 2:
-                        _a = _b.sent();
+                        e_1 = _a.sent();
+                        console.error(e_1);
+                        return [3 /*break*/, 4];
+                    case 3:
                         this.setState({ busy: false });
-                        return [3 /*break*/, 3];
-                    case 3: return [2 /*return*/];
+                        return [7 /*endfinally*/];
+                    case 4: return [2 /*return*/];
                 }
             });
         }); };
         _this.viewInAR = function () { return __awaiter(_this, void 0, void 0, function () {
-            var data, a_1, _a;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
+            var data, a_1, e_2;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
                     case 0:
-                        _b.trys.push([0, 2, , 3]);
+                        _a.trys.push([0, 2, 3, 4]);
                         this.setState({ busy: true });
                         return [4 /*yield*/, this.controls.exportGeometry()];
                     case 1:
-                        data = _b.sent();
-                        this.setState({ busy: false });
+                        data = _a.sent();
                         a_1 = document.createElement('a');
                         a_1.rel = 'ar';
                         a_1.href = URL.createObjectURL(data.blob);
@@ -56,12 +57,15 @@ var GeometryExporterUI = /** @class */ (function (_super) {
                         a_1.appendChild(document.createElement('img'));
                         setTimeout(function () { return URL.revokeObjectURL(a_1.href); }, 4E4); // 40s
                         setTimeout(function () { return a_1.dispatchEvent(new MouseEvent('click')); });
-                        return [3 /*break*/, 3];
+                        return [3 /*break*/, 4];
                     case 2:
-                        _a = _b.sent();
+                        e_2 = _a.sent();
+                        console.error(e_2);
+                        return [3 /*break*/, 4];
+                    case 3:
                         this.setState({ busy: false });
-                        return [3 /*break*/, 3];
-                    case 3: return [2 /*return*/];
+                        return [7 /*endfinally*/];
+                    case 4: return [2 /*return*/];
                 }
             });
         }); };

package/lib/extensions/geo-export/usdz-exporter.d.ts

@@ -2,8 +2,8 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { Style } from '../../mol-gl/renderer';
 import { Box3D } from '../../mol-math/geometry';
 import { RuntimeContext } from '../../mol-task';
 import { MeshExporter, AddMeshInput } from './mesh-exporter';
@@ -11,18 +11,16 @@ export declare type UsdzData = {
     usdz: ArrayBuffer;
 };
 export declare class UsdzExporter extends MeshExporter<UsdzData> {
-    private style;
     readonly fileExtension = "usdz";
     private meshes;
     private materials;
-    private materialSet;
+    private materialMap;
     private centerTransform;
-    private static getMaterialKey;
     private addMaterial;
     protected addMeshWithColors(input: AddMeshInput): Promise<void>;
     getData(ctx: RuntimeContext): Promise<{
         usdz: ArrayBufferLike;
     }>;
     getBlob(ctx: RuntimeContext): Promise<Blob>;
-    constructor(style: Style, boundingBox: Box3D, radius: number);
+    constructor(boundingBox: Box3D, radius: number);
 }

package/lib/extensions/geo-export/usdz-exporter.js

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { __awaiter, __extends, __generator, __spreadArray } from "tslib";
 import { asciiWrite } from '../../mol-io/common/ascii';
@@ -18,13 +19,12 @@ var v3transformMat3 = Vec3.transformMat3;
 var mat3directionTransform = Mat3.directionTransform;
 var UsdzExporter = /** @class */ (function (_super) {
     __extends(UsdzExporter, _super);
-    function UsdzExporter(style, boundingBox, radius) {
+    function UsdzExporter(boundingBox, radius) {
         var _this = _super.call(this) || this;
-        _this.style = style;
         _this.fileExtension = 'usdz';
         _this.meshes = [];
         _this.materials = [];
-        _this.materialSet = new Set();
+        _this.materialMap = new Map();
         var t = Mat4();
         // scale the model so that it fits within 1 meter
         Mat4.fromUniformScaling(t, Math.min(1 / (radius * 2), 1));
@@ -33,20 +33,19 @@ var UsdzExporter = /** @class */ (function (_super) {
         _this.centerTransform = t;
         return _this;
     }
-    UsdzExporter.getMaterialKey = function (color, alpha) {
-        return color * 256 + Math.round(alpha * 255);
-    };
-    UsdzExporter.prototype.addMaterial = function (color, alpha) {
-        var materialKey = UsdzExporter.getMaterialKey(color, alpha);
-        if (this.materialSet.has(materialKey))
-            return;
-        this.materialSet.add(materialKey);
-        var _a = Color.toRgbNormalized(color), r = _a[0], g = _a[1], b = _a[2];
-        this.materials.push("\ndef Material \"material".concat(materialKey, "\"\n{\n    token outputs:surface.connect = </material").concat(materialKey, "/shader.outputs:surface>\n    def Shader \"shader\"\n    {\n        uniform token info:id = \"UsdPreviewSurface\"\n        color3f inputs:diffuseColor = (").concat(r, ",").concat(g, ",").concat(b, ")\n        float inputs:opacity = ").concat(alpha, "\n        float inputs:metallic = ").concat(this.style.metalness, "\n        float inputs:roughness = ").concat(this.style.roughness, "\n        token outputs:surface\n    }\n}\n"));
+    UsdzExporter.prototype.addMaterial = function (color, alpha, metalness, roughness) {
+        var hash = "".concat(color, "|").concat(alpha, "|").concat(metalness, "|").concat(roughness);
+        if (this.materialMap.has(hash))
+            return this.materialMap.get(hash);
+        var materialKey = this.materialMap.size;
+        this.materialMap.set(hash, materialKey);
+        var _a = Color.toRgbNormalized(color).map(function (v) { return Math.round(v * 1000) / 1000; }), r = _a[0], g = _a[1], b = _a[2];
+        this.materials.push("\ndef Material \"material".concat(materialKey, "\"\n{\n    token outputs:surface.connect = </material").concat(materialKey, "/shader.outputs:surface>\n    def Shader \"shader\"\n    {\n        uniform token info:id = \"UsdPreviewSurface\"\n        color3f inputs:diffuseColor = (").concat(r, ",").concat(g, ",").concat(b, ")\n        float inputs:opacity = ").concat(alpha, "\n        float inputs:metallic = ").concat(metalness, "\n        float inputs:roughness = ").concat(roughness, "\n        token outputs:surface\n    }\n}\n"));
+        return materialKey;
     };
     UsdzExporter.prototype.addMeshWithColors = function (input) {
         return __awaiter(this, void 0, void 0, function () {
-            var mesh, values, isGeoTexture, webgl, ctx, t, n, tmpV, stride, groupCount, colorType, uAlpha, dTransparency, tTransparency, aTransform, instanceCount, interpolatedColors, _loop_1, this_1, instanceIndex;
+            var mesh, values, isGeoTexture, webgl, ctx, t, n, tmpV, stride, colorType, overpaintType, transparencyType, uAlpha, aTransform, instanceCount, metalness, roughness, interpolatedColors, interpolatedOverpaint, stride_1, interpolatedTransparency, stride_2, _loop_1, this_1, instanceIndex;
             return __generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
@@ -55,22 +54,30 @@ var UsdzExporter = /** @class */ (function (_super) {
                         n = Mat3();
                         tmpV = Vec3();
                         stride = isGeoTexture ? 4 : 3;
-                        groupCount = values.uGroupCount.ref.value;
                         colorType = values.dColorType.ref.value;
+                        overpaintType = values.dOverpaintType.ref.value;
+                        transparencyType = values.dTransparencyType.ref.value;
                         uAlpha = values.uAlpha.ref.value;
-                        dTransparency = values.dTransparency.ref.value;
-                        tTransparency = values.tTransparency.ref.value;
                         aTransform = values.aTransform.ref.value;
                         instanceCount = values.uInstanceCount.ref.value;
+                        metalness = values.uMetalness.ref.value;
+                        roughness = values.uRoughness.ref.value;
                         if (colorType === 'volume' || colorType === 'volumeInstance') {
-                            interpolatedColors = UsdzExporter.getInterpolatedColors(mesh.vertices, mesh.vertexCount, values, stride, colorType, webgl);
-                            UsdzExporter.quantizeColors(interpolatedColors, mesh.vertexCount);
+                            interpolatedColors = UsdzExporter.getInterpolatedColors(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: colorType });
+                        }
+                        if (overpaintType === 'volumeInstance') {
+                            stride_1 = isGeoTexture ? 4 : 3;
+                            interpolatedOverpaint = UsdzExporter.getInterpolatedOverpaint(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride_1, colorType: overpaintType });
+                        }
+                        if (transparencyType === 'volumeInstance') {
+                            stride_2 = isGeoTexture ? 4 : 3;
+                            interpolatedTransparency = UsdzExporter.getInterpolatedTransparency(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride_2, colorType: transparencyType });
                         }
                         return [4 /*yield*/, ctx.update({ isIndeterminate: false, current: 0, max: instanceCount })];
                     case 1:
                         _a.sent();
                         _loop_1 = function (instanceIndex) {
-                            var _b, vertices, normals, indices, groups, vertexCount, drawCount, vertexBuilder, normalBuilder, indexBuilder, i, i, i, v, faceIndicesByMaterial, i, v, color, alpha, group, transparency, materialKey, faceIndices, materialBinding, materialKey, geomSubsets_1;
+                            var _b, vertices, normals, indices, groups, vertexCount, drawCount, vertexBuilder, normalBuilder, indexBuilder, i, i, geoData, i, v, quantizedColors, i, v, color, faceIndicesByMaterial, i, color, transparency, alpha, materialKey, faceIndices, materialBinding, materialKey, geomSubsets_1;
                             return __generator(this, function (_c) {
                                 switch (_c.label) {
                                     case 0:
@@ -109,6 +116,7 @@ var UsdzExporter = /** @class */ (function (_super) {
                                             StringBuilder.writeFloat(normalBuilder, tmpV[2], 100);
                                             StringBuilder.writeSafe(normalBuilder, ')');
                                         }
+                                        geoData = { values: values, groups: groups, vertexCount: vertexCount, instanceIndex: instanceIndex, isGeoTexture: isGeoTexture };
                                         // face
                                         for (i = 0; i < drawCount; ++i) {
                                             v = isGeoTexture ? i : indices[i];
@@ -116,18 +124,19 @@ var UsdzExporter = /** @class */ (function (_super) {
                                                 StringBuilder.writeSafe(indexBuilder, ',');
                                             StringBuilder.writeInteger(indexBuilder, v);
                                         }
-                                        faceIndicesByMaterial = new Map();
+                                        quantizedColors = new Uint8Array(drawCount * 3);
                                         for (i = 0; i < drawCount; i += 3) {
                                             v = isGeoTexture ? i : indices[i];
-                                            color = UsdzExporter.getColor(values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors, v);
-                                            alpha = uAlpha;
-                                            if (dTransparency) {
-                                                group = isGeoTexture ? UsdzExporter.getGroup(groups, i) : groups[indices[i]];
-                                                transparency = tTransparency.array[instanceIndex * groupCount + group] / 255;
-                                                alpha *= 1 - transparency;
-                                            }
-                                            this_1.addMaterial(color, alpha);
-                                            materialKey = UsdzExporter.getMaterialKey(color, alpha);
+                                            color = UsdzExporter.getColor(v, geoData, interpolatedColors, interpolatedOverpaint);
+                                            Color.toArray(color, quantizedColors, i);
+                                        }
+                                        UsdzExporter.quantizeColors(quantizedColors, mesh.vertexCount);
+                                        faceIndicesByMaterial = new Map();
+                                        for (i = 0; i < drawCount; i += 3) {
+                                            color = Color.fromArray(quantizedColors, i);
+                                            transparency = UsdzExporter.getTransparency(i, geoData, interpolatedTransparency);
+                                            alpha = Math.round(uAlpha * (1 - transparency) * 10) / 10;
+                                            materialKey = this_1.addMaterial(color, alpha, metalness, roughness);
                                             faceIndices = faceIndicesByMaterial.get(materialKey);
                                             if (faceIndices === undefined) {
                                                 faceIndices = [];

package/lib/extensions/mp4-export/controls.js

@@ -72,7 +72,7 @@ var Mp4Controls = /** @class */ (function (_super) {
                         return [2 /*return*/, { movie: movie, filename: "".concat((_c = this.plugin.helpers.viewportScreenshot) === null || _c === void 0 ? void 0 : _c.getFilename(''), "_").concat(filename, ".mp4") }];
                     case 2:
                         e_1 = _d.sent();
-                        this.plugin.log.error('' + e_1);
+                        this.plugin.log.error('Error during animation export');
                         throw e_1;
                     case 3: return [2 /*return*/];
                 }

package/lib/extensions/mp4-export/ui.js

@@ -21,19 +21,20 @@ var Mp4EncoderUI = /** @class */ (function (_super) {
             download(new Blob([_this.state.data.movie]), _this.state.data.filename);
         };
         _this.generate = function () { return __awaiter(_this, void 0, void 0, function () {
-            var data, _a;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
+            var data, e_1;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
                     case 0:
-                        _b.trys.push([0, 2, , 3]);
+                        _a.trys.push([0, 2, , 3]);
                         this.setState({ busy: true });
                         return [4 /*yield*/, this.controls.render()];
                     case 1:
-                        data = _b.sent();
+                        data = _a.sent();
                         this.setState({ busy: false, data: data });
                         return [3 /*break*/, 3];
                     case 2:
-                        _a = _b.sent();
+                        e_1 = _a.sent();
+                        console.error(e_1);
                         this.setState({ busy: false });
                         return [3 /*break*/, 3];
                     case 3: return [2 /*return*/];

package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts

@@ -25,18 +25,22 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     ignoreLight: boolean;
     xrayShaded: boolean;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
     axesColor: PD.NamedParams<PD.Normalize<{
         colorValue: any;
     }>, "uniform"> | PD.NamedParams<PD.Normalize<unknown>, "byOrder">;
 }>>;
 export declare const AssemblySymmetryPresetParams: {
     ignoreHydrogens: PD.Base<boolean | undefined>;
-    quality: PD.Base<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined>;
+    quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
     theme: PD.Base<PD.Normalize<{
-        globalName: "uniform" | "occupancy" | "element-symbol" | "element-index" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "unit-index" | "uncertainty" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+        globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
         carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
-        symmetryColor: "uniform" | "occupancy" | "element-symbol" | "element-index" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "unit-index" | "uncertainty" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
         focus: PD.Normalize<{
             name: any;
             params: any;
@@ -45,7 +49,7 @@ export declare const AssemblySymmetryPresetParams: {
 };
 export declare const AssemblySymmetryPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;

package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts

@@ -17,7 +17,11 @@ export declare const AssemblySymmetryParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
     axesColor: PD.Mapped<PD.NamedParams<PD.Normalize<{
         colorValue: Color;
     }>, "uniform"> | PD.NamedParams<PD.Normalize<unknown>, "byOrder">>;

package/lib/extensions/rcsb/graphql/types.d.ts

@@ -1,4 +1,5 @@
 export declare type Maybe<T> = T | null;
+export declare type InputMaybe<T> = Maybe<T>;
 export declare type Exact<T extends {
     [key: string]: unknown;
 }> = {
@@ -6653,7 +6654,7 @@ export declare type Query = {
 };
 /** Query root */
 export declare type QueryAssembliesArgs = {
-    assembly_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    assembly_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryAssemblyArgs = {
@@ -6676,7 +6677,7 @@ export declare type QueryBranched_Entity_InstanceArgs = {
 };
 /** Query root */
 export declare type QueryBranched_Entity_InstancesArgs = {
-    instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    instance_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryChem_CompArgs = {
@@ -6684,7 +6685,7 @@ export declare type QueryChem_CompArgs = {
 };
 /** Query root */
 export declare type QueryChem_CompsArgs = {
-    comp_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    comp_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryEntriesArgs = {
@@ -6710,7 +6711,7 @@ export declare type QueryNonpolymer_Entity_InstanceArgs = {
 };
 /** Query root */
 export declare type QueryNonpolymer_Entity_InstancesArgs = {
-    instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    instance_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryPolymer_EntitiesArgs = {
@@ -6728,7 +6729,7 @@ export declare type QueryPolymer_Entity_InstanceArgs = {
 };
 /** Query root */
 export declare type QueryPolymer_Entity_InstancesArgs = {
-    instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    instance_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryPubmedArgs = {
@@ -12849,25 +12850,25 @@ export declare type AssemblySymmetryQueryVariables = Exact<{
     entry_id: Scalars['String'];
 }>;
 export declare type AssemblySymmetryQuery = {
-    readonly assembly?: Maybe<{
-        readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<{
+    readonly assembly?: {
+        readonly rcsb_struct_symmetry?: ReadonlyArray<{
             readonly kind: string;
             readonly oligomeric_state: string;
-            readonly stoichiometry: ReadonlyArray<Maybe<string>>;
+            readonly stoichiometry: ReadonlyArray<string | null | undefined>;
             readonly symbol: string;
             readonly type: string;
-            readonly clusters: ReadonlyArray<Maybe<{
-                readonly avg_rmsd?: Maybe<number>;
-                readonly members: ReadonlyArray<Maybe<{
+            readonly clusters: ReadonlyArray<{
+                readonly avg_rmsd?: number | null | undefined;
+                readonly members: ReadonlyArray<{
                     readonly asym_id: string;
-                    readonly pdbx_struct_oper_list_ids?: Maybe<ReadonlyArray<Maybe<string>>>;
-                }>>;
-            }>>;
-            readonly rotation_axes?: Maybe<ReadonlyArray<Maybe<{
-                readonly order?: Maybe<number>;
-                readonly start: ReadonlyArray<Maybe<number>>;
-                readonly end: ReadonlyArray<Maybe<number>>;
-            }>>>;
-        }>>>;
-    }>;
+                    readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null | undefined> | null | undefined;
+                } | null | undefined>;
+            } | null | undefined>;
+            readonly rotation_axes?: ReadonlyArray<{
+                readonly order?: number | null | undefined;
+                readonly start: ReadonlyArray<number | null | undefined>;
+                readonly end: ReadonlyArray<number | null | undefined>;
+            } | null | undefined> | null | undefined;
+        } | null | undefined> | null | undefined;
+    } | null | undefined;
 };

package/lib/extensions/rcsb/validation-report/behavior.d.ts

@@ -12,7 +12,7 @@ export declare const RCSBValidationReport: import("../../../mol-state/transforme
 }>;
 export declare const ValidationReportGeometryQualityPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;
@@ -48,7 +48,7 @@ export declare const ValidationReportGeometryQualityPreset: StructureRepresentat
 }>;
 export declare const ValidationReportDensityFitPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;
@@ -76,7 +76,7 @@ export declare const ValidationReportDensityFitPreset: StructureRepresentationPr
 }>;
 export declare const ValidationReportRandomCoilIndexPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;

package/lib/extensions/rcsb/validation-report/representation.d.ts

@@ -32,7 +32,11 @@ export declare const IntraUnitClashParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type IntraUnitClashParams = typeof IntraUnitClashParams;
 export declare function IntraUnitClashVisual(materialId: number): UnitsVisual<IntraUnitClashParams>;
@@ -57,7 +61,11 @@ export declare const InterUnitClashParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type InterUnitClashParams = typeof InterUnitClashParams;
 export declare function InterUnitClashVisual(materialId: number): ComplexVisual<InterUnitClashParams>;
@@ -83,7 +91,11 @@ export declare const ClashesParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type ClashesParams = typeof ClashesParams;
 export declare function getClashesParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -108,7 +120,11 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type ClashesRepresentation = StructureRepresentation<ClashesParams>;
 export declare function ClashesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ClashesParams>): ClashesRepresentation;
@@ -134,5 +150,9 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 }, ValidationReport.Tag.Clashes>;

package/lib/mol-canvas3d/canvas3d.d.ts

@@ -98,13 +98,14 @@ export declare const Canvas3DParams: {
         selectStrength: number;
         markerPriority: number;
         xrayEdgeFalloff: number;
-        style: PD.NamedParams<PD.Normalize<{
-            lightIntensity: any;
-            ambientIntensity: any;
-            metalness: any;
-            roughness: any;
-            reflectivity: any;
-        }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "matte"> | PD.NamedParams<PD.Normalize<unknown>, "flat"> | PD.NamedParams<PD.Normalize<unknown>, "glossy"> | PD.NamedParams<PD.Normalize<unknown>, "metallic"> | PD.NamedParams<PD.Normalize<unknown>, "plastic">;
+        light: PD.Normalize<{
+            inclination: number;
+            azimuth: number;
+            color: import("../mol-util/color").Color;
+            intensity: number;
+        }>[];
+        ambientColor: import("../mol-util/color").Color;
+        ambientIntensity: number;
         clip: PD.Normalize<{
             variant: any;
             objects: any;
@@ -164,6 +165,7 @@ export declare const Canvas3DParams: {
             flatShaded: any;
             xrayShaded: any;
             quality: any;
+            material: any;
         }>, "on">;
     }>>;
 };
@@ -244,13 +246,14 @@ export declare const DefaultCanvas3DParams: PD.Values<{
         selectStrength: number;
         markerPriority: number;
         xrayEdgeFalloff: number;
-        style: PD.NamedParams<PD.Normalize<{
-            lightIntensity: any;
-            ambientIntensity: any;
-            metalness: any;
-            roughness: any;
-            reflectivity: any;
-        }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "matte"> | PD.NamedParams<PD.Normalize<unknown>, "flat"> | PD.NamedParams<PD.Normalize<unknown>, "glossy"> | PD.NamedParams<PD.Normalize<unknown>, "metallic"> | PD.NamedParams<PD.Normalize<unknown>, "plastic">;
+        light: PD.Normalize<{
+            inclination: number;
+            azimuth: number;
+            color: import("../mol-util/color").Color;
+            intensity: number;
+        }>[];
+        ambientColor: import("../mol-util/color").Color;
+        ambientIntensity: number;
         clip: PD.Normalize<{
             variant: any;
             objects: any;
@@ -310,6 +313,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             flatShaded: any;
             xrayShaded: any;
             quality: any;
+            material: any;
         }>, "on">;
     }>>;
 }>;

package/lib/mol-canvas3d/helper/camera-helper.d.ts

@@ -11,7 +11,7 @@ import { MarkerAction } from '../../mol-util/marker-action';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera, ICamera } from '../camera';
 export declare const CameraHelperParams: {
-    axes: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    axes: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         alpha: number;
         ignoreLight: boolean;
         colorX: import("../../mol-util/color").Color;
@@ -22,8 +22,12 @@ export declare const CameraHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
-    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+        material: PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>;
+    }>, "on">>;
 };
 export declare type CameraHelperParams = typeof CameraHelperParams;
 export declare type CameraHelperProps = PD.Values<CameraHelperParams>;

package/lib/mol-canvas3d/helper/handle-helper.d.ts

@@ -24,7 +24,11 @@ export declare const HandleHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+        material: PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>;
     }>, "on">>;
 };
 export declare type HandleHelperParams = typeof HandleHelperParams;