molstar 3.0.0-dev.4 → 3.0.0-dev.8

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

@@ -60,6 +60,16 @@ export declare const UnitsMeshParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsMeshParams = typeof UnitsMeshParams;
 export interface UnitsMeshVisualBuilder<P extends UnitsMeshParams> extends UnitsVisualBuilder<P, Mesh> {
@@ -81,6 +91,16 @@ export declare const UnitsSpheresParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsSpheresParams = typeof UnitsSpheresParams;
 export interface UnitsSpheresVisualBuilder<P extends UnitsSpheresParams> extends UnitsVisualBuilder<P, Spheres> {
@@ -103,6 +123,16 @@ export declare const UnitsCylindersParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsCylindersParams = typeof UnitsCylindersParams;
 export interface UnitsCylindersVisualBuilder<P extends UnitsCylindersParams> extends UnitsVisualBuilder<P, Cylinders> {
@@ -121,6 +151,16 @@ export declare const UnitsPointsParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsPointsParams = typeof UnitsPointsParams;
 export interface UnitsPointVisualBuilder<P extends UnitsPointsParams> extends UnitsVisualBuilder<P, Points> {
@@ -138,6 +178,16 @@ export declare const UnitsLinesParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsLinesParams = typeof UnitsLinesParams;
 export interface UnitsLinesVisualBuilder<P extends UnitsLinesParams> extends UnitsVisualBuilder<P, Lines> {
@@ -172,6 +222,16 @@ export declare const UnitsTextParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsTextParams = typeof UnitsTextParams;
 export interface UnitsTextVisualBuilder<P extends UnitsTextParams> extends UnitsVisualBuilder<P, Text> {
@@ -180,27 +240,9 @@ export declare function UnitsTextVisual<P extends UnitsTextParams>(builder: Unit
 export declare const UnitsDirectVolumeParams: {
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
@@ -210,6 +252,16 @@ export declare const UnitsDirectVolumeParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsDirectVolumeParams = typeof UnitsDirectVolumeParams;
 export interface UnitsDirectVolumeVisualBuilder<P extends UnitsDirectVolumeParams> extends UnitsVisualBuilder<P, DirectVolume> {
@@ -232,6 +284,16 @@ export declare const UnitsTextureMeshParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsTextureMeshParams = typeof UnitsTextureMeshParams;
 export interface UnitsTextureMeshVisualBuilder<P extends UnitsTextureMeshParams> extends UnitsVisualBuilder<P, TextureMesh> {

package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts

@@ -42,6 +42,16 @@ export declare const InterUnitBondCylinderParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -81,6 +91,16 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts

@@ -26,6 +26,16 @@ export declare const InterUnitBondLineParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InterUnitBondLineParams = typeof InterUnitBondLineParams;
 export declare function InterUnitBondLineVisual(materialId: number): ComplexVisual<InterUnitBondLineParams>;

package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts

@@ -43,6 +43,16 @@ export declare const IntraUnitBondCylinderParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -82,6 +92,16 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js

@@ -71,13 +71,13 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
                 _a = [bI, aI], aI = _a[0], bI = _a[1];
             if (offset[aI + 1] - offset[aI] === 1)
                 _b = [bI, aI], aI = _b[0], bI = _b[1];
-            var aR = elementRingIndices.get(aI);
+            var aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
             var maxSize = 0;
             for (var i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
                 var _bI = b[i];
                 if (_bI !== bI && _bI !== aI) {
                     if (aR) {
-                        var _bR = elementRingIndices.get(_bI);
+                        var _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
                         if (!_bR)
                             continue;
                         var size = arrayIntersectionSize(aR, _bR);

package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts

@@ -26,6 +26,16 @@ export declare const IntraUnitBondLineParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type IntraUnitBondLineParams = typeof IntraUnitBondLineParams;
 export declare function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUnitBondLineParams>;

package/lib/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -50,13 +50,13 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
                 _a = [bI, aI], aI = _a[0], bI = _a[1];
             if (offset[aI + 1] - offset[aI] === 1)
                 _b = [bI, aI], aI = _b[0], bI = _b[1];
-            var aR = elementRingIndices.get(aI);
+            var aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
             var maxSize = 0;
             for (var i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
                 var _bI = b[i];
                 if (_bI !== bI && _bI !== aI) {
                     if (aR) {
-                        var _bR = elementRingIndices.get(_bI);
+                        var _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
                         if (!_bR)
                             continue;
                         var size = arrayIntersectionSize(aR, _bR);

package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts

@@ -34,6 +34,16 @@ export declare const CarbohydrateLinkParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CarbohydrateLinkParams = typeof CarbohydrateLinkParams;
 export declare function CarbohydrateLinkVisual(materialId: number): ComplexVisual<CarbohydrateLinkParams>;

package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts

@@ -24,6 +24,16 @@ export declare const CarbohydrateSymbolParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CarbohydrateSymbolParams = typeof CarbohydrateSymbolParams;
 export declare function CarbohydrateSymbolVisual(materialId: number): ComplexVisual<CarbohydrateSymbolParams>;

package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts

@@ -34,6 +34,16 @@ export declare const CarbohydrateTerminalLinkParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CarbohydrateTerminalLinkParams = typeof CarbohydrateTerminalLinkParams;
 export declare function CarbohydrateTerminalLinkVisual(materialId: number): ComplexVisual<CarbohydrateTerminalLinkParams>;

package/lib/mol-repr/structure/visual/element-cross.d.ts

@@ -25,6 +25,16 @@ export declare const ElementCrossParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type ElementCrossParams = typeof ElementCrossParams;
 export declare function createElementCross(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementCrossParams>, lines: Lines): Lines;

package/lib/mol-repr/structure/visual/element-point.d.ts

@@ -24,6 +24,16 @@ export declare const ElementPointParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type ElementPointParams = typeof ElementPointParams;
 export declare function createElementPoint(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementPointParams>, points: Points): Points;

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

@@ -28,6 +28,16 @@ export declare const ElementSphereParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -52,6 +62,16 @@ export declare function ElementSphereVisual(materialId: number, structure: Struc
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

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

@@ -29,6 +29,16 @@ export declare const EllipsoidMeshParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type EllipsoidMeshParams = typeof EllipsoidMeshParams;
 export declare function EllipsoidMeshVisual(materialId: number): UnitsVisual<EllipsoidMeshParams>;

package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts

@@ -14,27 +14,9 @@ export declare const GaussianDensityVolumeParams: {
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
@@ -44,6 +26,16 @@ export declare const GaussianDensityVolumeParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams;
 export declare function GaussianDensityVolumeVisual(materialId: number): ComplexVisual<GaussianDensityVolumeParams>;
@@ -55,27 +47,9 @@ export declare const UnitsGaussianDensityVolumeParams: {
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
@@ -85,6 +59,16 @@ export declare const UnitsGaussianDensityVolumeParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsGaussianDensityVolumeParams = typeof UnitsGaussianDensityVolumeParams;
 export declare function UnitsGaussianDensityVolumeVisual(materialId: number): UnitsVisual<UnitsGaussianDensityVolumeParams>;

package/lib/mol-repr/structure/visual/gaussian-density-volume.js

@@ -15,7 +15,7 @@ import { UnitsDirectVolumeParams, UnitsDirectVolumeVisual } from '../units-visua
 import { getStructureExtraRadius, getUnitExtraRadius } from './util/common';
 function createGaussianDensityVolume(ctx, structure, theme, props, directVolume) {
     return __awaiter(this, void 0, void 0, function () {
-        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, vol, sphere;
+        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -24,14 +24,15 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
                         throw new Error('GaussianDensityVolume requires `webgl` and `blendMinMax` extension');
                     }
                     oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined;
-                    return [4 /*yield*/, computeStructureGaussianDensityTexture(structure, props, webgl, oldTexture).runInContext(runtime)];
+                    return [4 /*yield*/, computeStructureGaussianDensityTexture(structure, theme.size, props, webgl, oldTexture).runInContext(runtime)];
                 case 1:
                     densityTextureData = _a.sent();
                     transform = densityTextureData.transform, texture = densityTextureData.texture, bbox = densityTextureData.bbox, gridDim = densityTextureData.gridDim;
                     stats = { min: 0, max: 1, mean: 0.04, sigma: 0.01 };
                     unitToCartn = Mat4.mul(Mat4(), transform, Mat4.fromScaling(Mat4(), gridDim));
                     cellDim = Mat4.getScaling(Vec3(), transform);
-                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, directVolume);
+                    axisOrder = Vec3.create(0, 1, 2);
+                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
                     sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
@@ -69,7 +70,7 @@ export function GaussianDensityVolumeVisual(materialId) {
 //
 function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, directVolume) {
     return __awaiter(this, void 0, void 0, function () {
-        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, vol, sphere;
+        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -81,14 +82,15 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
                         throw new Error('GaussianDensityVolume requires `webgl`');
                     }
                     oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined;
-                    return [4 /*yield*/, computeUnitGaussianDensityTexture(structure, unit, props, webgl, oldTexture).runInContext(runtime)];
+                    return [4 /*yield*/, computeUnitGaussianDensityTexture(structure, unit, theme.size, props, webgl, oldTexture).runInContext(runtime)];
                 case 1:
                     densityTextureData = _a.sent();
                     transform = densityTextureData.transform, texture = densityTextureData.texture, bbox = densityTextureData.bbox, gridDim = densityTextureData.gridDim;
                     stats = { min: 0, max: 1, mean: 0.04, sigma: 0.01 };
                     unitToCartn = Mat4.mul(Mat4(), transform, Mat4.fromScaling(Mat4(), gridDim));
                     cellDim = Mat4.getScaling(Vec3(), transform);
-                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, directVolume);
+                    axisOrder = Vec3.create(0, 1, 2);
+                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
                     sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts

@@ -35,6 +35,16 @@ export declare const GaussianSurfaceMeshParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type GaussianSurfaceMeshParams = typeof GaussianSurfaceMeshParams;
 export declare const StructureGaussianSurfaceMeshParams: {
@@ -64,6 +74,16 @@ export declare const StructureGaussianSurfaceMeshParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type StructureGaussianSurfaceMeshParams = typeof StructureGaussianSurfaceMeshParams;
 export declare function GaussianSurfaceVisual(materialId: number, structure: Structure, props: PD.Values<GaussianSurfaceMeshParams>, webgl?: WebGLContext): UnitsVisual<{
@@ -93,6 +113,16 @@ export declare function GaussianSurfaceVisual(materialId: number, structure: Str
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }>;
 export declare function StructureGaussianSurfaceVisual(materialId: number, structure: Structure, props: PD.Values<StructureGaussianSurfaceMeshParams>, webgl?: WebGLContext): ComplexVisual<{
     ignoreHydrogens: PD.BooleanParam;
@@ -121,6 +151,16 @@ export declare function StructureGaussianSurfaceVisual(materialId: number, struc
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }>;
 export declare function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<GaussianSurfaceMeshParams>;
 export declare function StructureGaussianSurfaceMeshVisual(materialId: number): ComplexVisual<StructureGaussianSurfaceMeshParams>;