molstar 4.0.1 → 4.2.0

package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts

@@ -47,6 +47,7 @@ export declare const NucleotideBlockParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts

@@ -50,6 +50,7 @@ export declare const NucleotideRingParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts

@@ -39,6 +39,7 @@ export declare const OrientationEllipsoidMeshParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts

@@ -39,6 +39,7 @@ export declare const PolymerBackboneCylinderParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -79,6 +80,7 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts

@@ -47,6 +47,7 @@ export declare const PolymerBackboneSphereParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -95,6 +96,7 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts

@@ -41,6 +41,7 @@ export declare const PolymerDirectionParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts

@@ -45,6 +45,7 @@ export declare const PolymerGapParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts

@@ -65,6 +65,7 @@ export declare const PolymerTraceParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts

@@ -50,6 +50,7 @@ export declare const PolymerTubeParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/visual.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -19,6 +19,7 @@ import { Clipping } from '../mol-theme/clipping';
 import { Geometry } from '../mol-geo/geometry/geometry';
 import { Substance } from '../mol-theme/substance';
 import { LocationCallback } from './util';
+import { Emissive } from '../mol-theme/emissive';
 export interface VisualContext {
     readonly runtime: RuntimeContext;
     readonly webgl?: WebGLContext;
@@ -40,11 +41,13 @@ interface Visual<D, P extends PD.Params> {
     setTransform: (matrix?: Mat4, instanceMatrices?: Float32Array | null) => void;
     setOverpaint: (overpaint: Overpaint, webgl?: WebGLContext) => void;
     setTransparency: (transparency: Transparency, webgl?: WebGLContext) => void;
+    setEmissive: (emissive: Emissive, webgl?: WebGLContext) => void;
     setSubstance: (substance: Substance, webgl?: WebGLContext) => void;
     setClipping: (clipping: Clipping) => void;
     setThemeStrength: (strength: {
         overpaint: number;
         transparency: number;
+        emissive: number;
         substance: number;
     }) => void;
     destroy: () => void;
@@ -69,11 +72,13 @@ declare namespace Visual {
     };
     export function setOverpaint(renderObject: GraphicsRenderObject | undefined, overpaint: Overpaint, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext): void;
     export function setTransparency(renderObject: GraphicsRenderObject | undefined, transparency: Transparency, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext): void;
+    export function setEmissive(renderObject: GraphicsRenderObject | undefined, emissive: Emissive, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext): void;
     export function setSubstance(renderObject: GraphicsRenderObject | undefined, substance: Substance, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext): void;
     export function setClipping(renderObject: GraphicsRenderObject | undefined, clipping: Clipping, lociApply: LociApply, clear: boolean): void;
     export function setThemeStrength(renderObject: GraphicsRenderObject | undefined, strength: {
         overpaint: number;
         transparency: number;
+        emissive: number;
         substance: number;
     }): void;
     export function setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array | null): void;

package/lib/commonjs/mol-repr/visual.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -21,6 +21,7 @@ const base_1 = require("../mol-geo/geometry/base");
 const color_smoothing_1 = require("../mol-geo/geometry/mesh/color-smoothing");
 const color_smoothing_2 = require("../mol-geo/geometry/texture-mesh/color-smoothing");
 const substance_data_1 = require("../mol-geo/geometry/substance-data");
+const emissive_data_1 = require("../mol-geo/geometry/emissive-data");
 var Visual;
 (function (Visual) {
     function setVisibility(renderObject, visible) {
@@ -217,6 +218,58 @@ var Visual;
         }
     }
     Visual.setTransparency = setTransparency;
+    function setEmissive(renderObject, emissive, lociApply, clear, smoothing) {
+        if (!renderObject)
+            return;
+        const { tEmissive, dEmissiveType, emissiveAverage, dEmissive, uGroupCount, instanceCount, instanceGranularity: instanceGranularity } = renderObject.values;
+        const count = instanceGranularity.ref.value
+            ? instanceCount.ref.value
+            : uGroupCount.ref.value * instanceCount.ref.value;
+        // ensure texture has right size and type
+        const type = instanceGranularity.ref.value ? 'instance' : 'groupInstance';
+        (0, emissive_data_1.createEmissive)(emissive.layers.length ? count : 0, type, renderObject.values);
+        const { array } = tEmissive.ref.value;
+        // clear if requested
+        if (clear)
+            (0, emissive_data_1.clearEmissive)(array, 0, count);
+        for (let i = 0, il = emissive.layers.length; i < il; ++i) {
+            const { loci, value } = emissive.layers[i];
+            const apply = (interval) => {
+                const start = int_1.Interval.start(interval);
+                const end = int_1.Interval.end(interval);
+                return (0, emissive_data_1.applyEmissiveValue)(array, start, end, value);
+            };
+            lociApply(loci, apply, false);
+        }
+        mol_util_1.ValueCell.update(tEmissive, tEmissive.ref.value);
+        mol_util_1.ValueCell.updateIfChanged(emissiveAverage, (0, emissive_data_1.getEmissiveAverage)(array, count));
+        mol_util_1.ValueCell.updateIfChanged(dEmissiveType, type);
+        mol_util_1.ValueCell.updateIfChanged(dEmissive, emissive.layers.length > 0);
+        if (emissive.layers.length === 0)
+            return;
+        if (type === 'instance')
+            return;
+        if (smoothing && (0, base_1.hasColorSmoothingProp)(smoothing.props)) {
+            const { geometry, props, webgl } = smoothing;
+            if (geometry.kind === 'mesh') {
+                const { resolution, emissiveTexture } = geometry.meta;
+                const csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, true, resolution);
+                if (csp) {
+                    (0, color_smoothing_1.applyMeshEmissiveSmoothing)(renderObject.values, csp.resolution, csp.stride, webgl, emissiveTexture);
+                    geometry.meta.emissiveTexture = renderObject.values.tEmissiveGrid.ref.value;
+                }
+            }
+            else if (webgl && geometry.kind === 'texture-mesh') {
+                const { resolution, emissiveTexture } = geometry.meta;
+                const csp = (0, base_1.getColorSmoothingProps)(props.smoothColors, true, resolution);
+                if (csp) {
+                    (0, color_smoothing_2.applyTextureMeshEmissiveSmoothing)(renderObject.values, csp.resolution, csp.stride, webgl, emissiveTexture);
+                    geometry.meta.emissiveTexture = renderObject.values.tEmissiveGrid.ref.value;
+                }
+            }
+        }
+    }
+    Visual.setEmissive = setEmissive;
     function setSubstance(renderObject, substance, lociApply, clear, smoothing) {
         if (!renderObject)
             return;
@@ -303,6 +356,7 @@ var Visual;
         if (renderObject) {
             mol_util_1.ValueCell.updateIfChanged(renderObject.values.uOverpaintStrength, strength.overpaint);
             mol_util_1.ValueCell.updateIfChanged(renderObject.values.uTransparencyStrength, strength.transparency);
+            mol_util_1.ValueCell.updateIfChanged(renderObject.values.uEmissiveStrength, strength.emissive);
             mol_util_1.ValueCell.updateIfChanged(renderObject.values.uSubstanceStrength, strength.substance);
         }
     }

package/lib/commonjs/mol-repr/volume/direct-volume.d.ts

@@ -67,6 +67,7 @@ export declare const DirectVolumeParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -118,6 +119,7 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -171,6 +173,7 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/volume/isosurface.d.ts

@@ -112,6 +112,7 @@ export declare function IsosurfaceVisual(materialId: number, volume: Volume, key
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -190,6 +191,7 @@ export declare const IsosurfaceMeshParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -263,6 +265,7 @@ export declare const IsosurfaceWireframeParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -336,6 +339,7 @@ export declare const IsosurfaceParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -416,6 +420,7 @@ export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: V
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -497,6 +502,7 @@ export declare const IsosurfaceRepresentationProvider: VolumeRepresentationProvi
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/volume/registry.d.ts

@@ -76,6 +76,7 @@ export declare namespace VolumeRepresentationRegistry {
                     scale: any;
                 }>[];
             }>>;
+            emissive: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             lod: import("../../mol-util/param-definition").ParamDefinition.Vec3;
             cellSize: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -153,6 +154,7 @@ export declare namespace VolumeRepresentationRegistry {
                     scale: any;
                 }>[];
             }>>;
+            emissive: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             lod: import("../../mol-util/param-definition").ParamDefinition.Vec3;
             cellSize: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -203,6 +205,7 @@ export declare namespace VolumeRepresentationRegistry {
                     scale: any;
                 }>[];
             }>>;
+            emissive: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             lod: import("../../mol-util/param-definition").ParamDefinition.Vec3;
             cellSize: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -259,6 +262,7 @@ export declare namespace VolumeRepresentationRegistry {
                     scale: any;
                 }>[];
             }>>;
+            emissive: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             lod: import("../../mol-util/param-definition").ParamDefinition.Vec3;
             cellSize: import("../../mol-util/param-definition").ParamDefinition.Numeric;

package/lib/commonjs/mol-repr/volume/representation.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -57,6 +57,7 @@ export declare const VolumeParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/volume/representation.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -232,6 +232,9 @@ function VolumeVisual(builder, materialId) {
         setTransparency(transparency) {
             return visual_1.Visual.setTransparency(renderObject, transparency, lociApply, true);
         },
+        setEmissive(emissive) {
+            return visual_1.Visual.setEmissive(renderObject, emissive, lociApply, true);
+        },
         setSubstance(substance) {
             return visual_1.Visual.setSubstance(renderObject, substance, lociApply, true);
         },
@@ -341,6 +344,8 @@ function VolumeRepresentation(label, ctx, getParams, visualCtor, getLoci, getKey
             visual.setOverpaint(state.overpaint);
         if (state.transparency !== undefined && visual)
             visual.setTransparency(state.transparency);
+        if (state.emissive !== undefined && visual)
+            visual.setEmissive(state.emissive);
         if (state.substance !== undefined && visual)
             visual.setSubstance(state.substance);
         if (state.clipping !== undefined && visual)
@@ -351,7 +356,7 @@ function VolumeRepresentation(label, ctx, getParams, visualCtor, getLoci, getKey
             visual.setThemeStrength(state.themeStrength);
     }
     function setState(state) {
-        const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, transform, themeStrength, syncManually, markerActions } = state;
+        const { visible, alphaFactor, pickable, overpaint, transparency, emissive, substance, clipping, transform, themeStrength, syncManually, markerActions } = state;
         const newState = {};
         if (visible !== undefined)
             newState.visible = visible;
@@ -363,6 +368,8 @@ function VolumeRepresentation(label, ctx, getParams, visualCtor, getLoci, getKey
             newState.overpaint = overpaint;
         if (transparency !== undefined)
             newState.transparency = transparency;
+        if (emissive !== undefined)
+            newState.emissive = emissive;
         if (substance !== undefined)
             newState.substance = substance;
         if (clipping !== undefined)

package/lib/commonjs/mol-repr/volume/segment.d.ts

@@ -68,6 +68,7 @@ export declare function SegmentVisual(materialId: number, volume: Volume, key: n
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -125,6 +126,7 @@ export declare const SegmentMeshParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -184,6 +186,7 @@ export declare const SegmentParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -241,6 +244,7 @@ export declare function getSegmentParams(ctx: ThemeRegistryContext, volume: Volu
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -299,6 +303,7 @@ export declare const SegmentRepresentationProvider: VolumeRepresentationProvider
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-repr/volume/slice.d.ts

@@ -75,6 +75,7 @@ export declare const SliceParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -145,6 +146,7 @@ export declare function getSliceParams(ctx: ThemeRegistryContext, volume: Volume
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -216,6 +218,7 @@ export declare const SliceRepresentationProvider: VolumeRepresentationProvider<{
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/mol-script/language/symbol-table/core.d.ts

@@ -14,9 +14,9 @@ export declare namespace Types {
     const AnyValueVar: Type.Variable<any>;
     const ConstrainedVar: Type.Variable<any>;
     const Regex: Type.Value<RegExp>;
-    const Set: <T extends Type>(t?: T | undefined) => Type.Container<Set<T["@type"]>>;
-    const List: <T extends Type>(t?: T | undefined) => Type.Container<List<T["@type"]>>;
-    const Fn: <T extends Type>(t?: T | undefined, alias?: string) => Type.Container<(env: any) => T["@type"]>;
+    const Set: <T extends Type>(t?: T) => Type.Container<Set<T["@type"]>>;
+    const List: <T extends Type>(t?: T) => Type.Container<List<T["@type"]>>;
+    const Fn: <T extends Type>(t?: T, alias?: string) => Type.Container<(env: any) => T['@type']>;
     const Flags: <T extends Type>(t: T, alias?: string) => Type.Container<number>;
     const BitFlags: Type.Container<number>;
 }

package/lib/commonjs/mol-state/tree/immutable.d.ts

@@ -76,7 +76,7 @@ declare namespace StateTree {
     /**
      * Get all nodes in a subtree, leafs come first.
      */
-    export function subtreePostOrder(tree: StateTree, root: StateTransform): StateTransform<import("../transformer").StateTransformer<import("../object").StateObject<any, import("../object").StateObject.Type<any>>, import("../object").StateObject<any, import("../object").StateObject.Type<any>>, any>>[];
+    export function subtreePostOrder(tree: StateTree, root: StateTransform): StateTransform<import("..").StateTransformer<import("..").StateObject<any, import("..").StateObject.Type<any>>, import("..").StateObject<any, import("..").StateObject.Type<any>>, any>>[];
     export interface Serialized {
         /** Transforms serialized in pre-order */
         transforms: StateTransform.Serialized[];

package/lib/commonjs/mol-state/tree/transient.d.ts

@@ -22,7 +22,7 @@ declare class TransientTree implements StateTree {
     private changeNodes;
     private changeChildren;
     private changeDependencies;
-    get root(): StateTransform<import("../transformer").StateTransformer<import("../object").StateObject<any, import("../object").StateObject.Type<any>>, import("../object").StateObject<any, import("../object").StateObject.Type<any>>, any>>;
+    get root(): StateTransform<import("..").StateTransformer<import("..").StateObject<any, import("..").StateObject.Type<any>>, import("..").StateObject<any, import("..").StateObject.Type<any>>, any>>;
     asTransient(): TransientTree;
     private addChild;
     private removeChild;
@@ -34,7 +34,7 @@ declare class TransientTree implements StateTree {
     setParams(ref: StateTransform.Ref, params: any): boolean;
     /** Calls Transform.definition.params.areEqual if available, otherwise uses shallowEqual to check if the params changed */
     setTags(ref: StateTransform.Ref, tags: string | string[] | undefined): boolean;
-    assignState(ref: StateTransform.Ref, state?: Partial<StateTransform.State>): StateTransform<import("../transformer").StateTransformer<import("../object").StateObject<any, import("../object").StateObject.Type<any>>, import("../object").StateObject<any, import("../object").StateObject.Type<any>>, any>>;
+    assignState(ref: StateTransform.Ref, state?: Partial<StateTransform.State>): StateTransform<import("..").StateTransformer<import("..").StateObject<any, import("..").StateObject.Type<any>>, import("..").StateObject<any, import("..").StateObject.Type<any>>, any>>;
     remove(ref: StateTransform.Ref): StateTransform[];
     asImmutable(): StateTree;
     constructor(tree: StateTree);

package/lib/commonjs/mol-theme/color/external-volume.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Cai Huiyu <szmun.caihy@gmail.com>
  */
 import type { ColorTheme } from '../color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -27,6 +28,7 @@ export declare const ExternalVolumeColorThemeParams: {
         };
     }>, "relative-value">>;
     defaultColor: PD.Color;
+    normalOffset: PD.Numeric;
 };
 export type ExternalVolumeColorThemeParams = typeof ExternalVolumeColorThemeParams;
 export declare function ExternalVolumeColorTheme(ctx: ThemeDataContext, props: PD.Values<ExternalVolumeColorThemeParams>): ColorTheme<ExternalVolumeColorThemeParams>;

package/lib/commonjs/mol-theme/color/external-volume.js

@@ -1,8 +1,9 @@
 "use strict";
 /**
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Cai Huiyu <szmun.caihy@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ExternalVolumeColorThemeProvider = exports.ExternalVolumeColorTheme = exports.ExternalVolumeColorThemeParams = void 0;
@@ -13,7 +14,7 @@ const location_iterator_1 = require("../../mol-geo/util/location-iterator");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const interpolate_1 = require("../../mol-math/interpolate");
 const categories_1 = require("./categories");
-const Description = `Assigns a color based volume value at a given vertex.`;
+const Description = `Assigns a color based on volume value at a given vertex.`;
 exports.ExternalVolumeColorThemeParams = {
     volume: param_definition_1.ParamDefinition.ValueRef((ctx) => {
         const volumes = ctx.state.data.selectQ(q => q.root.subtree().filter(c => { var _a; return volume_1.Volume.is((_a = c.obj) === null || _a === void 0 ? void 0 : _a.data); }));
@@ -40,6 +41,7 @@ exports.ExternalVolumeColorThemeParams = {
         })
     }),
     defaultColor: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xcccccc)),
+    normalOffset: param_definition_1.ParamDefinition.Numeric(0., { min: 0, max: 20, step: 0.1 }, { description: 'Offset vertex position along its normal by given amount.' }),
 };
 function ExternalVolumeColorTheme(ctx, props) {
     let volume;
@@ -77,7 +79,11 @@ function ExternalVolumeColorTheme(ctx, props) {
             if (!(0, location_iterator_1.isPositionLocation)(location)) {
                 return props.defaultColor;
             }
+            // Offset the vertex position along its normal
             linear_algebra_1.Vec3.copy(gridCoords, location.position);
+            if (props.normalOffset > 0) {
+                linear_algebra_1.Vec3.scaleAndAdd(gridCoords, gridCoords, location.normal, props.normalOffset);
+            }
             linear_algebra_1.Vec3.transformMat4(gridCoords, gridCoords, cartnToGrid);
             const i = Math.floor(gridCoords[0]);
             const j = Math.floor(gridCoords[1]);

package/lib/commonjs/mol-theme/color.d.ts

@@ -1029,6 +1029,7 @@ declare namespace ColorTheme {
                 };
             }>, "relative-value">>;
             defaultColor: PD.Color;
+            normalOffset: PD.Numeric;
         }, "external-volume", ColorType>;
     };
     type _BuiltIn = typeof BuiltIn;

package/lib/commonjs/mol-theme/emissive.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Loci } from '../mol-model/loci';
+import { Structure, StructureElement } from '../mol-model/structure';
+import { Script } from '../mol-script/script';
+export { Emissive };
+type Emissive<T extends Loci = Loci> = {
+    readonly kind: T['kind'];
+    readonly layers: ReadonlyArray<Emissive.Layer<T>>;
+};
+declare function Emissive<T extends Loci>(kind: T['kind'], layers: ReadonlyArray<Emissive.Layer<T>>): Emissive;
+declare namespace Emissive {
+    type Layer<T extends Loci = Loci> = {
+        readonly loci: T;
+        readonly value: number;
+    };
+    const Empty: Emissive;
+    function areEqual(eA: Emissive, eB: Emissive): boolean;
+    function isEmpty(emissive: Emissive): boolean;
+    function remap(emissive: Emissive, structure: Structure): Emissive;
+    function merge(emissive: Emissive): Emissive;
+    function filter(emissive: Emissive, filter: Structure): Emissive;
+    type ScriptLayer = {
+        script: Script;
+        value: number;
+    };
+    function ofScript(scriptLayers: ScriptLayer[], structure: Structure): Emissive;
+    type BundleLayer = {
+        bundle: StructureElement.Bundle;
+        value: number;
+    };
+    function ofBundle(bundleLayers: BundleLayer[], structure: Structure): Emissive;
+    function toBundle(emissive: Emissive<StructureElement.Loci>): {
+        kind: string;
+        layers: BundleLayer[];
+    };
+}