molstar 2.3.8 → 3.0.0-dev.0

package/lib/mol-io/reader/sdf/parser-v3-util.js

@@ -0,0 +1,84 @@
+import { Column } from '../../../mol-data/db';
+import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
+import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+export function isV3(versionLine) {
+    return versionLine.trim().endsWith('V3000');
+}
+export function handleCountsV3(tokenizer) {
+    var atomCount = TokenBuilder.create(tokenizer.data, 1);
+    var bondCount = TokenBuilder.create(tokenizer.data, 1);
+    Tokenizer.eatLine(tokenizer); // BEGIN CTAB
+    skipSingleValue(tokenizer); // M
+    skipSingleValue(tokenizer); // V30
+    skipSingleValue(tokenizer); // COUNTS
+    addSingleValue(tokenizer, atomCount);
+    addSingleValue(tokenizer, bondCount);
+    Tokenizer.eatLine(tokenizer);
+    return {
+        atomCount: TokenColumn(atomCount)(Column.Schema.int).value(0),
+        bondCount: TokenColumn(bondCount)(Column.Schema.int).value(0)
+    };
+}
+export function handleAtomsV3(tokenizer, atomCount) {
+    var x = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var y = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var z = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var type_symbol = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    for (var i = 0; i < atomCount; ++i) {
+        Tokenizer.markLine(tokenizer);
+        skipSingleValue(tokenizer); // M
+        skipSingleValue(tokenizer); // V30
+        skipSingleValue(tokenizer); // Index
+        var position = tokenizer.position;
+        addSingleValue(tokenizer, type_symbol);
+        addSingleValue(tokenizer, x);
+        addSingleValue(tokenizer, y);
+        addSingleValue(tokenizer, z);
+        tokenizer.position = position;
+    }
+    Tokenizer.eatLine(tokenizer); // Previous Line
+    Tokenizer.eatLine(tokenizer); // END ATOM
+    return {
+        count: atomCount,
+        x: TokenColumn(x)(Column.Schema.float),
+        y: TokenColumn(y)(Column.Schema.float),
+        z: TokenColumn(z)(Column.Schema.float),
+        type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+    };
+}
+export function handleBondsV3(tokenizer, bondCount) {
+    var atomIdxA = TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var atomIdxB = TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var order = TokenBuilder.create(tokenizer.data, bondCount * 2);
+    for (var i = 0; i < bondCount; ++i) {
+        Tokenizer.markLine(tokenizer);
+        skipSingleValue(tokenizer); // M
+        skipSingleValue(tokenizer); // V30
+        skipSingleValue(tokenizer); // Index
+        var position = tokenizer.position;
+        addSingleValue(tokenizer, order);
+        addSingleValue(tokenizer, atomIdxA);
+        addSingleValue(tokenizer, atomIdxB);
+        tokenizer.position = position;
+    }
+    Tokenizer.eatLine(tokenizer); // Previous Line
+    Tokenizer.eatLine(tokenizer); // END BOND
+    return {
+        count: bondCount,
+        atomIdxA: TokenColumn(atomIdxA)(Column.Schema.float),
+        atomIdxB: TokenColumn(atomIdxB)(Column.Schema.float),
+        order: TokenColumn(order)(Column.Schema.float),
+    };
+}
+function skipSingleValue(tokenizer) {
+    Tokenizer.skipWhitespace(tokenizer);
+    Tokenizer.eatValue(tokenizer);
+}
+function addSingleValue(tokenizer, tokens) {
+    var valueStart = tokenizer.position;
+    Tokenizer.skipWhitespace(tokenizer);
+    Tokenizer.eatValue(tokenizer);
+    Tokenizer.trim(tokenizer, valueStart, tokenizer.position);
+    TokenBuilder.addUnchecked(tokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+}
+//# sourceMappingURL=parser-v3-util.js.map

package/lib/mol-io/reader/sdf/parser-v3-util.js.map

@@ -0,0 +1 @@
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package/lib/mol-io/reader/sdf/parser.d.ts

@@ -8,7 +8,7 @@ import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
-/** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 */
+/** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 & 79 */
 export interface SdfFileCompound {
     readonly molFile: MolFile;
     readonly dataItems: {

package/lib/mol-io/reader/sdf/parser.js

@@ -11,6 +11,7 @@ import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+import { handleAtomsV3, handleBondsV3, handleCountsV3, isV3 } from './parser-v3-util';
 var delimiter = '$$$$';
 function handleDataItems(tokenizer) {
     var dataHeader = TokenBuilder.create(tokenizer.data, 32);
@@ -46,12 +47,19 @@ function handleDataItems(tokenizer) {
         data: TokenColumn(data)(Column.Schema.str)
     };
 }
+function handleCountsV2(countsAndVersion) {
+    return {
+        atomCount: +countsAndVersion.substr(0, 3),
+        bondCount: +countsAndVersion.substr(3, 3)
+    };
+}
 function handleMolFile(tokenizer) {
     var title = Tokenizer.readLine(tokenizer).trim();
     var program = Tokenizer.readLine(tokenizer).trim();
     var comment = Tokenizer.readLine(tokenizer).trim();
-    var counts = Tokenizer.readLine(tokenizer);
-    var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
+    var countsAndVersion = Tokenizer.readLine(tokenizer);
+    var molIsV3 = isV3(countsAndVersion);
+    var _a = molIsV3 ? handleCountsV3(tokenizer) : handleCountsV2(countsAndVersion), atomCount = _a.atomCount, bondCount = _a.bondCount;
     if (Number.isNaN(atomCount) || Number.isNaN(bondCount)) {
         // try to skip to next molecule
         while (tokenizer.position < tokenizer.length) {
@@ -61,8 +69,8 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
-    var atoms = handleAtoms(tokenizer, atomCount);
-    var bonds = handleBonds(tokenizer, bondCount);
+    var atoms = molIsV3 ? handleAtomsV3(tokenizer, atomCount) : handleAtoms(tokenizer, atomCount);
+    var bonds = molIsV3 ? handleBondsV3(tokenizer, bondCount) : handleBonds(tokenizer, bondCount);
     var dataItems = handleDataItems(tokenizer);
     return {
         molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },

package/lib/mol-io/reader/sdf/parser.js.map

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package/lib/mol-math/linear-algebra/3d/vec3.d.ts

@@ -138,6 +138,12 @@ declare namespace Vec3 {
      * Computes the dihedral angles of 4 points, reports in radians.
      */
     function dihedralAngle(a: Vec3, b: Vec3, c: Vec3, d: Vec3): number;
+    /**
+     * @param inclination in radians [0, PI]
+     * @param azimuth in radians [0, 2 * PI]
+     * @param radius [0, +Inf]
+     */
+    function directionFromSpherical(out: Vec3, inclination: number, azimuth: number, radius: number): Vec3;
     /**
      * Returns whether or not the vectors have exactly the same elements in the same position (when compared with ===)
      */

package/lib/mol-math/linear-algebra/3d/vec3.js

@@ -465,6 +465,15 @@ function Vec3() {
         return dot(tmp_dh_cb, tmp_dh_cross) > 0 ? _angle : -_angle;
     }
     Vec3.dihedralAngle = dihedralAngle;
+    /**
+     * @param inclination in radians [0, PI]
+     * @param azimuth in radians [0, 2 * PI]
+     * @param radius [0, +Inf]
+     */
+    function directionFromSpherical(out, inclination, azimuth, radius) {
+        return Vec3.set(out, radius * Math.cos(azimuth) * Math.sin(inclination), radius * Math.sin(azimuth) * Math.sin(inclination), radius * Math.cos(inclination));
+    }
+    Vec3.directionFromSpherical = directionFromSpherical;
     /**
      * Returns whether or not the vectors have exactly the same elements in the same position (when compared with ===)
      */

package/lib/mol-math/linear-algebra/3d/vec3.js.map

@@ -1 +1 @@
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package/lib/mol-model/loci.d.ts

@@ -54,56 +54,56 @@ declare namespace Loci {
     export function getPrincipalAxes(loci: Loci): PrincipalAxes | undefined;
     const Granularity: {
         element: (loci: Loci) => Loci;
-        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci;
+        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
-        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | Shape.Loci | ShapeGroup.Loci | {
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
+        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
         } | {
             kind: "empty-loci";
-        } | DataLoci<unknown, unknown>;
+        } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
     };
     export type Granularity = keyof typeof Granularity;
-    export const GranularityOptions: ["residue" | "entity" | "operator" | "model" | "element" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances", string][];
+    export const GranularityOptions: ["element" | "operator" | "residue" | "entity" | "model" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances", string][];
     /** Exclude `Instances` granularity kinds */
-    export function simpleGranularity(granularity: Granularity): "residue" | "entity" | "operator" | "model" | "element" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances";
+    export function simpleGranularity(granularity: Granularity): "element" | "operator" | "residue" | "entity" | "model" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances";
     export function applyGranularity(loci: Loci, granularity: Granularity): Loci;
     /**
      * Converts structure related loci to StructureElement.Loci and applies

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

@@ -38,7 +38,7 @@ export declare namespace Shape {
     function getTheme(shape: Shape): Theme;
     function groupIterator(shape: Shape): LocationIterator;
     function createTransform(transforms: Mat4[], transformData?: TransformData): TransformData;
-    function createRenderObject<G extends Geometry>(shape: Shape<G>, props: PD.Values<Geometry.Params<G>>): import("../../mol-gl/render-object").GraphicsRenderObject<"points" | "lines" | "text" | "spheres" | "mesh" | "cylinders" | "direct-volume" | "image" | "texture-mesh">;
+    function createRenderObject<G extends Geometry>(shape: Shape<G>, props: PD.Values<Geometry.Params<G>>): import("../../mol-gl/render-object").GraphicsRenderObject<"text" | "image" | "points" | "spheres" | "cylinders" | "lines" | "mesh" | "direct-volume" | "texture-mesh">;
     interface Loci {
         readonly kind: 'shape-loci';
         readonly shape: Shape;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 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>
@@ -41,7 +41,7 @@ declare const StructureProperties: {
         microheterogeneityCompIds: StructureElement.Property<string[]>;
         secondary_structure_type: StructureElement.Property<SecondaryStructureType>;
         secondary_structure_key: StructureElement.Property<number>;
-        chem_comp_type: StructureElement.Property<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
+        chem_comp_type: StructureElement.Property<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
     };
     chain: {
         key: StructureElement.Property<import("../model").ChainIndex>;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 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>
@@ -83,18 +83,18 @@ var residue = {
     hasMicroheterogeneity: p(hasMicroheterogeneity),
     microheterogeneityCompIds: p(microheterogeneityCompIds),
     secondary_structure_type: p(function (l) {
-        var _a, _b;
+        var _a;
         if (!Unit.isAtomic(l.unit))
             notAtomic();
         var secStruc = (_a = SecondaryStructureProvider.get(l.structure).value) === null || _a === void 0 ? void 0 : _a.get(l.unit.invariantId);
-        return (_b = secStruc === null || secStruc === void 0 ? void 0 : secStruc.type[l.unit.residueIndex[l.element]]) !== null && _b !== void 0 ? _b : 536870912 /* NA */;
+        return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* NA */;
     }),
     secondary_structure_key: p(function (l) {
-        var _a, _b;
+        var _a;
         if (!Unit.isAtomic(l.unit))
             notAtomic();
         var secStruc = (_a = SecondaryStructureProvider.get(l.structure).value) === null || _a === void 0 ? void 0 : _a.get(l.unit.invariantId);
-        return (_b = secStruc === null || secStruc === void 0 ? void 0 : secStruc.key[l.unit.residueIndex[l.element]]) !== null && _b !== void 0 ? _b : -1;
+        return secStruc ? secStruc.key[secStruc.getIndex(l.unit.residueIndex[l.element])] : -1;
     }),
     chem_comp_type: p(function (l) { return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l)).type; }),
 };

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

@@ -1 +1 @@
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package/lib/mol-model-formats/shape/ply.d.ts

@@ -22,16 +22,20 @@ export declare const PlyShapeParams: {
         green: string;
         blue: string;
     }>, "vertex">>;
-    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "none"> | PD.NamedParams<PD.Normalize<{
         group: string;
-    }>, "vertex"> | PD.NamedParams<PD.Normalize<unknown>, "none">>;
+    }>, "vertex">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     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.Converted<import("../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type PlyShapeParams = typeof PlyShapeParams;
 export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapeProvider<PlyFile, Mesh, {
@@ -46,14 +50,18 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
         green: string;
         blue: string;
     }>, "vertex">>;
-    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    grouping: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "none"> | PD.NamedParams<PD.Normalize<{
         group: string;
-    }>, "vertex"> | PD.NamedParams<PD.Normalize<unknown>, "none">>;
+    }>, "vertex">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     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.Converted<import("../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 }>>;