molstar 2.3.9 → 3.0.0-dev.2

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

@@ -28,7 +28,11 @@ export declare const NucleotideRingParams: {
     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 NucleotideRingParams = typeof NucleotideRingParams;
 export declare function NucleotideRingVisual(materialId: number): UnitsVisual<NucleotideRingParams>;

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

@@ -20,7 +20,11 @@ export declare const OrientationEllipsoidMeshParams: {
     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 OrientationEllipsoidMeshParams = typeof OrientationEllipsoidMeshParams;
 export declare function OrientationEllipsoidMeshVisual(materialId: number): UnitsVisual<OrientationEllipsoidMeshParams>;

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

@@ -18,7 +18,11 @@ export declare const PolymerBackboneCylinderParams: {
     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;
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -34,7 +38,11 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
     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;
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

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

@@ -17,7 +17,11 @@ export declare const PolymerBackboneSphereParams: {
     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;
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -32,7 +36,11 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
     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;
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

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

@@ -22,7 +22,11 @@ export declare const PolymerDirectionParams: {
     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 PolymerDirectionParams = typeof PolymerDirectionParams;
 export declare function PolymerDirectionVisual(materialId: number): UnitsVisual<PolymerDirectionParams>;

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

@@ -25,7 +25,11 @@ export declare const PolymerGapParams: {
     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 PolymerGapParams = typeof PolymerGapParams;
 export declare function PolymerGapVisual(materialId: number): UnitsVisual<PolymerGapParams>;

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

@@ -43,7 +43,11 @@ export declare const PolymerTraceParams: {
     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 PolymerTraceParams = typeof PolymerTraceParams;
 export declare function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTraceParams>;

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

@@ -31,7 +31,11 @@ export declare const PolymerTubeParams: {
     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 PolymerTubeParams = typeof PolymerTubeParams;
 export declare function PolymerTubeVisual(materialId: number): UnitsVisual<PolymerTubeParams>;

package/lib/mol-repr/structure/visual/util/bond.d.ts

@@ -16,14 +16,14 @@ export declare const BondParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
 };
 export declare const DefaultBondProps: PD.Values<{
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
 }>;
 export declare type BondProps = typeof DefaultBondProps;
 export declare const BondCylinderParams: {
@@ -32,7 +32,7 @@ export declare const BondCylinderParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -51,7 +51,7 @@ export declare const DefaultBondCylinderProps: PD.Values<{
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -70,7 +70,7 @@ export declare const BondLineParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     aromaticDashCount: PD.Numeric;
@@ -81,7 +81,7 @@ export declare const DefaultBondLineProps: PD.Values<{
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     aromaticDashCount: PD.Numeric;

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

@@ -16,6 +16,8 @@ import { Overpaint } from '../mol-theme/overpaint';
 import { Interval } from '../mol-data/int';
 import { Transparency } from '../mol-theme/transparency';
 import { Clipping } from '../mol-theme/clipping';
+import { Geometry } from '../mol-geo/geometry/geometry';
+import { Substance } from '../mol-theme/substance';
 export interface VisualContext {
     readonly runtime: RuntimeContext;
     readonly webgl?: WebGLContext;
@@ -25,6 +27,7 @@ interface Visual<D, P extends PD.Params> {
     /** Number of addressable groups in all instances of the visual */
     readonly groupCount: number;
     readonly renderObject: GraphicsRenderObject | undefined;
+    readonly geometryVersion: number;
     createOrUpdate: (ctx: VisualContext, theme: Theme, props: PD.Values<P>, data?: D) => Promise<void> | void;
     getLoci: (pickingId: PickingId) => Loci;
     mark: (loci: Loci, action: MarkerAction) => boolean;
@@ -33,26 +36,34 @@ interface Visual<D, P extends PD.Params> {
     setPickable: (pickable: boolean) => void;
     setColorOnly: (colorOnly: boolean) => void;
     setTransform: (matrix?: Mat4, instanceMatrices?: Float32Array | null) => void;
-    setOverpaint: (overpaint: Overpaint) => void;
-    setTransparency: (transparency: Transparency) => void;
+    setOverpaint: (overpaint: Overpaint, webgl?: WebGLContext) => void;
+    setTransparency: (transparency: Transparency, webgl?: WebGLContext) => void;
+    setSubstance: (substance: Substance, webgl?: WebGLContext) => void;
     setClipping: (clipping: Clipping) => void;
     destroy: () => void;
     mustRecreate?: (data: D, props: PD.Values<P>, webgl?: WebGLContext) => boolean;
 }
 declare namespace Visual {
-    type LociApply = (loci: Loci, apply: (interval: Interval) => boolean, isMarking: boolean) => boolean;
-    function setVisibility(renderObject: GraphicsRenderObject | undefined, visible: boolean): void;
-    function setAlphaFactor(renderObject: GraphicsRenderObject | undefined, alphaFactor: number): void;
-    function setPickable(renderObject: GraphicsRenderObject | undefined, pickable: boolean): void;
-    function setColorOnly(renderObject: GraphicsRenderObject | undefined, colorOnly: boolean): void;
-    type PreviousMark = {
+    export type LociApply = (loci: Loci, apply: (interval: Interval) => boolean, isMarking: boolean) => boolean;
+    export function setVisibility(renderObject: GraphicsRenderObject | undefined, visible: boolean): void;
+    export function setAlphaFactor(renderObject: GraphicsRenderObject | undefined, alphaFactor: number): void;
+    export function setPickable(renderObject: GraphicsRenderObject | undefined, pickable: boolean): void;
+    export function setColorOnly(renderObject: GraphicsRenderObject | undefined, colorOnly: boolean): void;
+    export type PreviousMark = {
         loci: Loci;
         action: MarkerAction;
         status: MarkerInfo['status'];
     };
-    function mark(renderObject: GraphicsRenderObject | undefined, loci: Loci, action: MarkerAction, lociApply: LociApply, previous?: PreviousMark): boolean;
-    function setOverpaint(renderObject: GraphicsRenderObject | undefined, overpaint: Overpaint, lociApply: LociApply, clear: boolean): void;
-    function setTransparency(renderObject: GraphicsRenderObject | undefined, transparency: Transparency, lociApply: LociApply, clear: boolean): void;
-    function setClipping(renderObject: GraphicsRenderObject | undefined, clipping: Clipping, lociApply: LociApply, clear: boolean): void;
-    function setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array | null): void;
+    export function mark(renderObject: GraphicsRenderObject | undefined, loci: Loci, action: MarkerAction, lociApply: LociApply, previous?: PreviousMark): boolean;
+    type SmoothingContext = {
+        geometry: Geometry;
+        props: PD.Values<any>;
+        webgl?: WebGLContext;
+    };
+    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 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 setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array | null): void;
+    export {};
 }

package/lib/mol-repr/visual.js

@@ -14,6 +14,10 @@ import { Interval } from '../mol-data/int';
 import { createTransparency, clearTransparency, applyTransparencyValue, getTransparencyAverage } from '../mol-geo/geometry/transparency-data';
 import { createClipping, applyClippingGroups, clearClipping } from '../mol-geo/geometry/clipping-data';
 import { getMarkersAverage } from '../mol-geo/geometry/marker-data';
+import { getColorSmoothingProps, hasColorSmoothingProp } from '../mol-geo/geometry/base';
+import { applyMeshOverpaintSmoothing, applyMeshSubstanceSmoothing, applyMeshTransparencySmoothing } from '../mol-geo/geometry/mesh/color-smoothing';
+import { applyTextureMeshOverpaintSmoothing, applyTextureMeshSubstanceSmoothing, applyTextureMeshTransparencySmoothing } from '../mol-geo/geometry/texture-mesh/color-smoothing';
+import { applySubstanceMaterial, clearSubstance, createSubstance } from '../mol-geo/geometry/substance-data';
 export { Visual };
 var Visual;
 (function (Visual) {
@@ -104,10 +108,10 @@ var Visual;
         return changed;
     }
     Visual.mark = mark;
-    function setOverpaint(renderObject, overpaint, lociApply, clear) {
+    function setOverpaint(renderObject, overpaint, lociApply, clear, smoothing) {
         if (!renderObject)
             return;
-        var _a = renderObject.values, tOverpaint = _a.tOverpaint, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tOverpaint = _a.tOverpaint, dOverpaintType = _a.dOverpaintType, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
         // ensure texture has right size
         createOverpaint(overpaint.layers.length ? count : 0, renderObject.values);
@@ -116,7 +120,7 @@ var Visual;
         if (clear)
             clearOverpaint(array, 0, count);
         var _loop_1 = function (i, il) {
-            var _b = overpaint.layers[i], loci = _b.loci, color = _b.color, clear_1 = _b.clear;
+            var _d = overpaint.layers[i], loci = _d.loci, color = _d.color, clear_1 = _d.clear;
             var apply = function (interval) {
                 var start = Interval.start(interval);
                 var end = Interval.end(interval);
@@ -130,12 +134,34 @@ var Visual;
             _loop_1(i, il);
         }
         ValueCell.update(tOverpaint, tOverpaint.ref.value);
+        ValueCell.updateIfChanged(dOverpaintType, 'groupInstance');
+        if (overpaint.layers.length === 0)
+            return;
+        if (smoothing && hasColorSmoothingProp(smoothing.props)) {
+            var geometry = smoothing.geometry, props = smoothing.props, webgl = smoothing.webgl;
+            if (geometry.kind === 'mesh') {
+                var _b = geometry.meta, resolution = _b.resolution, overpaintTexture = _b.overpaintTexture;
+                var csp = getColorSmoothingProps(props.smoothColors, true, resolution);
+                if (csp) {
+                    applyMeshOverpaintSmoothing(renderObject.values, csp.resolution, csp.stride, webgl, overpaintTexture);
+                    geometry.meta.overpaintTexture = renderObject.values.tOverpaintGrid.ref.value;
+                }
+            }
+            else if (webgl && geometry.kind === 'texture-mesh') {
+                var _c = geometry.meta, resolution = _c.resolution, overpaintTexture = _c.overpaintTexture;
+                var csp = getColorSmoothingProps(props.smoothColors, true, resolution);
+                if (csp) {
+                    applyTextureMeshOverpaintSmoothing(renderObject.values, csp.resolution, csp.stride, webgl, overpaintTexture);
+                    geometry.meta.overpaintTexture = renderObject.values.tOverpaintGrid.ref.value;
+                }
+            }
+        }
     }
     Visual.setOverpaint = setOverpaint;
-    function setTransparency(renderObject, transparency, lociApply, clear) {
+    function setTransparency(renderObject, transparency, lociApply, clear, smoothing) {
         if (!renderObject)
             return;
-        var _a = renderObject.values, tTransparency = _a.tTransparency, transparencyAverage = _a.transparencyAverage, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tTransparency = _a.tTransparency, dTransparencyType = _a.dTransparencyType, transparencyAverage = _a.transparencyAverage, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
         // ensure texture has right size and variant
         createTransparency(transparency.layers.length ? count : 0, renderObject.values);
@@ -144,7 +170,7 @@ var Visual;
         if (clear)
             clearTransparency(array, 0, count);
         var _loop_2 = function (i, il) {
-            var _b = transparency.layers[i], loci = _b.loci, value = _b.value;
+            var _d = transparency.layers[i], loci = _d.loci, value = _d.value;
             var apply = function (interval) {
                 var start = Interval.start(interval);
                 var end = Interval.end(interval);
@@ -157,8 +183,80 @@ var Visual;
         }
         ValueCell.update(tTransparency, tTransparency.ref.value);
         ValueCell.updateIfChanged(transparencyAverage, getTransparencyAverage(array, count));
+        ValueCell.updateIfChanged(dTransparencyType, 'groupInstance');
+        if (transparency.layers.length === 0)
+            return;
+        if (smoothing && hasColorSmoothingProp(smoothing.props)) {
+            var geometry = smoothing.geometry, props = smoothing.props, webgl = smoothing.webgl;
+            if (geometry.kind === 'mesh') {
+                var _b = geometry.meta, resolution = _b.resolution, transparencyTexture = _b.transparencyTexture;
+                var csp = getColorSmoothingProps(props.smoothColors, true, resolution);
+                if (csp) {
+                    applyMeshTransparencySmoothing(renderObject.values, csp.resolution, csp.stride, webgl, transparencyTexture);
+                    geometry.meta.transparencyTexture = renderObject.values.tTransparencyGrid.ref.value;
+                }
+            }
+            else if (webgl && geometry.kind === 'texture-mesh') {
+                var _c = geometry.meta, resolution = _c.resolution, transparencyTexture = _c.transparencyTexture;
+                var csp = getColorSmoothingProps(props.smoothColors, true, resolution);
+                if (csp) {
+                    applyTextureMeshTransparencySmoothing(renderObject.values, csp.resolution, csp.stride, webgl, transparencyTexture);
+                    geometry.meta.transparencyTexture = renderObject.values.tTransparencyGrid.ref.value;
+                }
+            }
+        }
     }
     Visual.setTransparency = setTransparency;
+    function setSubstance(renderObject, substance, lociApply, clear, smoothing) {
+        if (!renderObject)
+            return;
+        var _a = renderObject.values, tSubstance = _a.tSubstance, dSubstanceType = _a.dSubstanceType, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var count = uGroupCount.ref.value * instanceCount.ref.value;
+        // ensure texture has right size
+        createSubstance(substance.layers.length ? count : 0, renderObject.values);
+        var array = tSubstance.ref.value.array;
+        // clear all if requested
+        if (clear)
+            clearSubstance(array, 0, count);
+        var _loop_3 = function (i, il) {
+            var _d = substance.layers[i], loci = _d.loci, material = _d.material, clear_2 = _d.clear;
+            var apply = function (interval) {
+                var start = Interval.start(interval);
+                var end = Interval.end(interval);
+                return clear_2
+                    ? clearSubstance(array, start, end)
+                    : applySubstanceMaterial(array, start, end, material);
+            };
+            lociApply(loci, apply, false);
+        };
+        for (var i = 0, il = substance.layers.length; i < il; ++i) {
+            _loop_3(i, il);
+        }
+        ValueCell.update(tSubstance, tSubstance.ref.value);
+        ValueCell.updateIfChanged(dSubstanceType, 'groupInstance');
+        if (substance.layers.length === 0)
+            return;
+        if (smoothing && hasColorSmoothingProp(smoothing.props)) {
+            var geometry = smoothing.geometry, props = smoothing.props, webgl = smoothing.webgl;
+            if (geometry.kind === 'mesh') {
+                var _b = geometry.meta, resolution = _b.resolution, substanceTexture = _b.substanceTexture;
+                var csp = getColorSmoothingProps(props.smoothColors, true, resolution);
+                if (csp) {
+                    applyMeshSubstanceSmoothing(renderObject.values, csp.resolution, csp.stride, webgl, substanceTexture);
+                    geometry.meta.substanceTexture = renderObject.values.tSubstanceGrid.ref.value;
+                }
+            }
+            else if (webgl && geometry.kind === 'texture-mesh') {
+                var _c = geometry.meta, resolution = _c.resolution, substanceTexture = _c.substanceTexture;
+                var csp = getColorSmoothingProps(props.smoothColors, true, resolution);
+                if (csp) {
+                    applyTextureMeshSubstanceSmoothing(renderObject.values, csp.resolution, csp.stride, webgl, substanceTexture);
+                    geometry.meta.substanceTexture = renderObject.values.tSubstanceGrid.ref.value;
+                }
+            }
+        }
+    }
+    Visual.setSubstance = setSubstance;
     function setClipping(renderObject, clipping, lociApply, clear) {
         if (!renderObject)
             return;
@@ -170,7 +268,7 @@ var Visual;
         // clear if requested
         if (clear)
             clearClipping(array, 0, count);
-        var _loop_3 = function (i, il) {
+        var _loop_4 = function (i, il) {
             var _b = clipping.layers[i], loci = _b.loci, groups = _b.groups;
             var apply = function (interval) {
                 var start = Interval.start(interval);
@@ -180,7 +278,7 @@ var Visual;
             lociApply(loci, apply, false);
         };
         for (var i = 0, il = clipping.layers.length; i < il; ++i) {
-            _loop_3(i, il);
+            _loop_4(i, il);
         }
         ValueCell.update(tClipping, tClipping.ref.value);
     }

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

@@ -26,10 +26,10 @@ export declare const DirectVolumeParams: {
     quality: {
         isEssential: boolean;
         type: "select";
-        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
         cycle?: boolean | undefined;
         isOptional?: boolean | undefined;
-        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../mol-util/legend").Legend | undefined;
@@ -70,16 +70,20 @@ export declare const DirectVolumeParams: {
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type DirectVolumeParams = typeof DirectVolumeParams;
 export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume: Volume): {
     quality: {
         isEssential: boolean;
         type: "select";
-        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
         cycle?: boolean | undefined;
         isOptional?: boolean | undefined;
-        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../mol-util/legend").Legend | undefined;
@@ -120,6 +124,10 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type DirectVolumeProps = PD.Values<DirectVolumeParams>;
 export declare function DirectVolumeVisual(materialId: number): VolumeVisual<DirectVolumeParams>;
@@ -128,10 +136,10 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
     quality: {
         isEssential: boolean;
         type: "select";
-        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
         cycle?: boolean | undefined;
         isOptional?: boolean | undefined;
-        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../mol-util/legend").Legend | undefined;
@@ -172,4 +180,8 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 }, "direct-volume">;