molstar 3.4.0 → 3.6.1

package/lib/mol-repr/structure/representation/cartoon.d.ts

@@ -19,6 +19,7 @@ export declare const CartoonParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -57,6 +58,7 @@ export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: S
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -96,6 +98,7 @@ export declare const CartoonRepresentationProvider: StructureRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

package/lib/mol-repr/structure/representation/ellipsoid.d.ts

@@ -36,6 +36,7 @@ export declare const EllipsoidParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -87,6 +88,7 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -139,6 +141,7 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

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

@@ -47,6 +47,7 @@ export declare const GaussianSurfaceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 };
 export declare type GaussianSurfaceParams = typeof GaussianSurfaceParams;
@@ -89,6 +90,7 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 };
 export declare type GaussianSurfaceRepresentation = StructureRepresentation<GaussianSurfaceParams>;
@@ -132,5 +134,6 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 }, "gaussian-surface">;

package/lib/mol-repr/structure/representation/molecular-surface.d.ts

@@ -46,6 +46,7 @@ export declare const MolecularSurfaceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 };
 export declare type MolecularSurfaceParams = typeof MolecularSurfaceParams;
@@ -87,6 +88,7 @@ export declare function getMolecularSurfaceParams(ctx: ThemeRegistryContext, str
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 };
 export declare type MolecularSurfaceRepresentation = StructureRepresentation<MolecularSurfaceParams>;
@@ -129,5 +131,6 @@ export declare const MolecularSurfaceRepresentationProvider: StructureRepresenta
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 }, "molecular-surface">;

package/lib/mol-repr/structure/representation/orientation.d.ts

@@ -20,6 +20,7 @@ export declare const OrientationParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -52,6 +53,7 @@ export declare function getOrientationParams(ctx: ThemeRegistryContext, structur
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -85,6 +87,7 @@ export declare const OrientationRepresentationProvider: StructureRepresentationP
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

package/lib/mol-repr/structure/representation/putty.d.ts

@@ -20,6 +20,7 @@ export declare const PuttyParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -54,6 +55,7 @@ export declare function getPuttyParams(ctx: ThemeRegistryContext, structure: Str
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -89,6 +91,7 @@ export declare const PuttyRepresentationProvider: StructureRepresentationProvide
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

package/lib/mol-repr/structure/representation/spacefill.d.ts

@@ -20,6 +20,7 @@ export declare const SpacefillParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -54,6 +55,7 @@ export declare function getSpacefillParams(ctx: ThemeRegistryContext, structure:
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -89,6 +91,7 @@ export declare const SpacefillRepresentationProvider: StructureRepresentationPro
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

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

@@ -51,6 +51,7 @@ export declare const UnitsMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -82,6 +83,7 @@ export declare const UnitsSpheresParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -114,6 +116,7 @@ export declare const UnitsCylindersParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -275,6 +278,7 @@ export declare const UnitsTextureMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -33,6 +33,7 @@ export declare const InterUnitBondCylinderParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -82,6 +83,7 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -34,6 +34,7 @@ export declare const IntraUnitBondCylinderParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -83,6 +84,7 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -25,6 +25,7 @@ export declare const CarbohydrateLinkParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -15,6 +15,7 @@ export declare const CarbohydrateSymbolParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -25,6 +25,7 @@ export declare const CarbohydrateTerminalLinkParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -19,6 +19,7 @@ export declare const ElementSphereParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -53,6 +54,7 @@ export declare function ElementSphereVisual(materialId: number, structure: Struc
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -20,6 +20,7 @@ export declare const EllipsoidMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -12,7 +12,6 @@ import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 import { eachElement, eachSerialElement, ElementIterator, getElementLoci, getSerialElementLoci } from './util/element';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { UnitsDirectVolumeParams, UnitsDirectVolumeVisual } from '../units-visual';
-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, axisOrder, vol, sphere;
@@ -33,7 +32,7 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
                     cellDim = Mat4.getScaling(Vec3(), transform);
                     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));
+                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
             }
@@ -91,7 +90,7 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
                     cellDim = Mat4.getScaling(Vec3(), transform);
                     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));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
             }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -26,6 +26,7 @@ export declare const GaussianSurfaceMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -65,6 +66,7 @@ export declare const StructureGaussianSurfaceMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -104,6 +106,7 @@ export declare function GaussianSurfaceVisual(materialId: number, structure: Str
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -142,6 +145,7 @@ export declare function StructureGaussianSurfaceVisual(materialId: number, struc
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,7 +14,7 @@ import { TextureMesh } from '../../../mol-geo/geometry/texture-mesh/texture-mesh
 import { extractIsosurface } from '../../../mol-gl/compute/marching-cubes/isosurface';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { ComplexMeshParams, ComplexMeshVisual, ComplexTextureMeshVisual, ComplexTextureMeshParams } from '../complex-visual';
-import { getUnitExtraRadius, getStructureExtraRadius, getVolumeSliceInfo } from './util/common';
+import { getVolumeSliceInfo } from './util/common';
 import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
 import { applyTextureMeshColorSmoothing } from '../../../mol-geo/geometry/texture-mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
@@ -51,14 +51,14 @@ export function StructureGaussianSurfaceVisual(materialId, structure, props, web
 //
 function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var smoothness, _a, transform, field, idField, radiusFactor, resolution, params, surface, sphere;
+        var smoothness, _a, transform, field, idField, radiusFactor, resolution, maxRadius, params, surface, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: Math.exp(-smoothness) / radiusFactor,
                         scalarField: field,
@@ -71,7 +71,7 @@ function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         Mesh.uniformTriangleGroup(surface);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     return [2 /*return*/, surface];
             }
@@ -128,14 +128,14 @@ export function GaussianSurfaceMeshVisual(materialId) {
 //
 function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var smoothness, _a, transform, field, idField, radiusFactor, resolution, params, surface, sphere;
+        var smoothness, _a, transform, field, idField, radiusFactor, resolution, maxRadius, params, surface, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, computeStructureGaussianDensity(structure, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: Math.exp(-smoothness) / radiusFactor,
                         scalarField: field,
@@ -148,7 +148,7 @@ function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh)
                     Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         Mesh.uniformTriangleGroup(surface);
-                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     return [2 /*return*/, surface];
             }
@@ -225,7 +225,7 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                     axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
-                    boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
                     return [2 /*return*/, surface];
@@ -308,7 +308,7 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                     axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
-                    boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+                    boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
                     return [2 /*return*/, surface];

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,17 +11,16 @@ import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/
 import { UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { Sphere3D } from '../../../mol-math/geometry';
-import { getUnitExtraRadius } from './util/common';
 function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
     return __awaiter(this, void 0, void 0, function () {
-        var smoothness, _a, transform, field, idField, params, wireframe, sphere;
+        var smoothness, _a, transform, field, idField, maxRadius, params, wireframe, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: Math.exp(-smoothness),
                         scalarField: field,
@@ -31,7 +30,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
                 case 2:
                     wireframe = _b.sent();
                     Lines.transform(wireframe, transform);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     wireframe.setBoundingSphere(sphere);
                     return [2 /*return*/, wireframe];
             }

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

@@ -22,6 +22,7 @@ export declare const MolecularSurfaceMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-repr/structure/visual/molecular-surface-mesh.js

@@ -11,7 +11,7 @@ import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { computeUnitMolecularSurface } from './util/molecular-surface';
 import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
-import { CommonSurfaceParams, getUnitExtraRadius } from './util/common';
+import { CommonSurfaceParams } from './util/common';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
@@ -19,12 +19,12 @@ export var MolecularSurfaceMeshParams = __assign(__assign(__assign(__assign({},
 //
 function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var _a, transform, field, idField, resolution, params, surface, iterations, sphere;
+        var _a, transform, field, idField, resolution, maxRadius, params, surface, iterations, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, resolution = _a.resolution;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, resolution = _a.resolution, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: props.probeRadius,
                         scalarField: field,
@@ -40,7 +40,7 @@ function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         Mesh.uniformTriangleGroup(surface);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     surface.meta.resolution = resolution;
                     return [2 /*return*/, surface];

package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,18 +11,18 @@ import { Lines } from '../../../mol-geo/geometry/lines/lines';
 import { computeUnitMolecularSurface } from './util/molecular-surface';
 import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/algorithm';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
-import { CommonSurfaceParams, getUnitExtraRadius } from './util/common';
+import { CommonSurfaceParams } from './util/common';
 import { Sphere3D } from '../../../mol-math/geometry';
 export var MolecularSurfaceWireframeParams = __assign(__assign(__assign(__assign({}, UnitsLinesParams), MolecularSurfaceCalculationParams), CommonSurfaceParams), { sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }) });
 //
 function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lines) {
     return __awaiter(this, void 0, void 0, function () {
-        var _a, transform, field, idField, params, wireframe, sphere;
+        var _a, transform, field, idField, maxRadius, params, wireframe, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
-                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
+                    _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, maxRadius = _a.maxRadius;
                     params = {
                         isoLevel: props.probeRadius,
                         scalarField: field,
@@ -32,7 +32,7 @@ function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lin
                 case 2:
                     wireframe = _b.sent();
                     Lines.transform(wireframe, transform);
-                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius + getUnitExtraRadius(unit));
+                    sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
                     wireframe.setBoundingSphere(sphere);
                     return [2 /*return*/, wireframe];
             }

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

@@ -24,6 +24,7 @@ export declare const NucleotideBlockParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -27,6 +27,7 @@ export declare const NucleotideRingParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -19,6 +19,7 @@ export declare const OrientationEllipsoidMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -17,6 +17,7 @@ export declare const PolymerBackboneCylinderParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -50,6 +51,7 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -16,6 +16,7 @@ export declare const PolymerBackboneSphereParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -48,6 +49,7 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;