molstar 3.4.0 → 3.6.1

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

@@ -15,7 +15,6 @@ var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var element_1 = require("./util/element");
 var geometry_1 = require("../../../mol-math/geometry");
 var units_visual_1 = require("../units-visual");
-var common_1 = require("./util/common");
 function createGaussianDensityVolume(ctx, structure, theme, props, directVolume) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
         var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
@@ -36,7 +35,7 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
                     cellDim = linear_algebra_1.Mat4.getScaling((0, linear_algebra_1.Vec3)(), transform);
                     axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
                     vol = direct_volume_1.DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, props.radiusOffset + (0, common_1.getStructureExtraRadius)(structure));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, densityTextureData.maxRadius);
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
             }
@@ -95,7 +94,7 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
                     cellDim = linear_algebra_1.Mat4.getScaling((0, linear_algebra_1.Vec3)(), transform);
                     axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
                     vol = direct_volume_1.DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.radiusOffset + (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, densityTextureData.maxRadius);
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
             }

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -56,14 +56,14 @@ exports.StructureGaussianSurfaceVisual = StructureGaussianSurfaceVisual;
 //
 function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
     return tslib_1.__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 tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, (0, gaussian_1.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,
@@ -76,7 +76,7 @@ function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     mesh_1.Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         mesh_1.Mesh.uniformTriangleGroup(surface);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.radiusOffset + (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     return [2 /*return*/, surface];
             }
@@ -134,14 +134,14 @@ exports.GaussianSurfaceMeshVisual = GaussianSurfaceMeshVisual;
 //
 function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh) {
     return tslib_1.__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 tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, (0, gaussian_1.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,
@@ -154,7 +154,7 @@ function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh)
                     mesh_1.Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         mesh_1.Mesh.uniformTriangleGroup(surface);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, props.radiusOffset + (0, common_1.getStructureExtraRadius)(structure));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     return [2 /*return*/, surface];
             }
@@ -232,7 +232,7 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                     axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = (0, isosurface_1.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 = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.radiusOffset + (0, common_1.getStructureExtraRadius)(structure));
+                    boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, densityTextureData.maxRadius);
                     surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
                     return [2 /*return*/, surface];
@@ -316,7 +316,7 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                     axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = (0, isosurface_1.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 = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, props.radiusOffset + (0, common_1.getStructureExtraRadius)(structure));
+                    boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, densityTextureData.maxRadius);
                     surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
                     return [2 /*return*/, surface];

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -14,17 +14,16 @@ var algorithm_1 = require("../../../mol-geo/util/marching-cubes/algorithm");
 var units_visual_1 = require("../units-visual");
 var element_1 = require("./util/element");
 var geometry_1 = require("../../../mol-math/geometry");
-var common_1 = require("./util/common");
 function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
     return tslib_1.__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 tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
                     return [4 /*yield*/, (0, gaussian_1.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,
@@ -34,7 +33,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
                 case 2:
                     wireframe = _b.sent();
                     lines_1.Lines.transform(wireframe, transform);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.radiusOffset + (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, maxRadius);
                     wireframe.setBoundingSphere(sphere);
                     return [2 /*return*/, wireframe];
             }

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

@@ -22,12 +22,12 @@ exports.MolecularSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1._
 //
 function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
     return tslib_1.__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 tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, (0, molecular_surface_2.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,
@@ -43,7 +43,7 @@ function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     mesh_1.Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         mesh_1.Mesh.uniformTriangleGroup(surface);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, maxRadius);
                     surface.setBoundingSphere(sphere);
                     surface.meta.resolution = resolution;
                     return [2 /*return*/, surface];

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -20,12 +20,12 @@ exports.MolecularSurfaceWireframeParams = tslib_1.__assign(tslib_1.__assign(tsli
 //
 function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lines) {
     return tslib_1.__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 tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, (0, molecular_surface_2.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,
@@ -35,7 +35,7 @@ function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lin
                 case 2:
                     wireframe = _b.sent();
                     lines_1.Lines.transform(wireframe, transform);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.probeRadius + (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, maxRadius);
                     wireframe.setBoundingSphere(sphere);
                     return [2 /*return*/, wireframe];
             }

package/lib/commonjs/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/commonjs/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/commonjs/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/commonjs/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/commonjs/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;

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

@@ -21,6 +21,7 @@ export declare const PolymerDirectionParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

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

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

@@ -42,6 +42,7 @@ export declare const PolymerTraceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -30,6 +30,7 @@ export declare const PolymerTubeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-repr/structure/visual/util/common.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>
  */
@@ -85,5 +85,3 @@ export declare function getStructureConformationAndRadius(structure: Structure,
 export declare function isHydrogen(unit: Unit, element: ElementIndex): boolean;
 export declare function isH(atomicNumber: ArrayLike<number>, element: ElementIndex): boolean;
 export declare function isTrace(unit: Unit, element: ElementIndex): boolean;
-export declare function getUnitExtraRadius(unit: Unit): number;
-export declare function getStructureExtraRadius(structure: Structure): number;

package/lib/commonjs/mol-repr/structure/visual/util/common.js

@@ -1,11 +1,11 @@
 "use strict";
 /**
- * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getStructureExtraRadius = exports.getUnitExtraRadius = exports.isTrace = exports.isH = exports.isHydrogen = exports.getStructureConformationAndRadius = exports.getUnitConformationAndRadius = exports.DefaultCommonSurfaceProps = exports.CommonSurfaceParams = exports.getConformation = exports.ensureReasonableResolution = exports.getVolumeSliceInfo = exports.includesUnitKind = exports.UnitKindOptions = exports.UnitKindInfo = exports.createUnitsTransform = exports.getAltResidueLociFromId = exports.getAltResidueLoci = exports.getResidueLoci = void 0;
+exports.isTrace = exports.isH = exports.isHydrogen = exports.getStructureConformationAndRadius = exports.getUnitConformationAndRadius = exports.DefaultCommonSurfaceProps = exports.CommonSurfaceParams = exports.getConformation = exports.ensureReasonableResolution = exports.getVolumeSliceInfo = exports.includesUnitKind = exports.UnitKindOptions = exports.UnitKindInfo = exports.createUnitsTransform = exports.getAltResidueLociFromId = exports.getAltResidueLoci = exports.getResidueLoci = void 0;
 var tslib_1 = require("tslib");
 var structure_1 = require("../../../../mol-model/structure");
 var linear_algebra_1 = require("../../../../mol-math/linear-algebra");
@@ -289,28 +289,3 @@ function isTrace(unit, element) {
     return false;
 }
 exports.isTrace = isTrace;
-function getUnitExtraRadius(unit) {
-    if (structure_1.Unit.isAtomic(unit))
-        return 4;
-    var max = 0;
-    var elements = unit.elements;
-    var r = unit.conformation.r;
-    for (var i = 0, _i = elements.length; i < _i; i++) {
-        var _r = r(elements[i]);
-        if (_r > max)
-            max = _r;
-    }
-    return max + 1;
-}
-exports.getUnitExtraRadius = getUnitExtraRadius;
-function getStructureExtraRadius(structure) {
-    var max = 0;
-    for (var _a = 0, _b = structure.unitSymmetryGroups; _a < _b.length; _a++) {
-        var ug = _b[_a];
-        var r = getUnitExtraRadius(ug.units[0]);
-        if (r > max)
-            max = r;
-    }
-    return max;
-}
-exports.getStructureExtraRadius = getStructureExtraRadius;

package/lib/commonjs/mol-repr/util.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>
  */
@@ -31,6 +31,7 @@ export interface QualityProps {
     doubleSided: boolean;
     xrayShaded: boolean;
     alpha: number;
+    allowTransparentBackfaces: boolean;
 }
 export declare const DefaultQualityThresholds: {
     lowestElementCount: number;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -169,7 +169,7 @@ function getQualityProps(props, data) {
     // max resolution based on volume (for 'auto' quality)
     resolution = Math.max(resolution, volume / 500000000);
     resolution = Math.min(resolution, 20);
-    if ((props.alpha !== undefined && props.alpha < 1) || !!props.xrayShaded) {
+    if (!props.allowTransparentBackfaces && ((props.alpha !== undefined && props.alpha < 1) || !!props.xrayShaded)) {
         doubleSided = false;
     }
     return {

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

@@ -93,6 +93,7 @@ export declare function IsosurfaceVisual(materialId: number, volume: Volume, pro
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -166,6 +167,7 @@ export declare const IsosurfaceMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -328,6 +330,7 @@ export declare const IsosurfaceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 };
 export declare type IsosurfaceParams = typeof IsosurfaceParams;
@@ -403,6 +406,7 @@ export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: V
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 };
 export declare type IsosurfaceRepresentation = VolumeRepresentation<IsosurfaceParams>;
@@ -479,5 +483,6 @@ export declare const IsosurfaceRepresentationProvider: VolumeRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
 }, "isosurface">;

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

@@ -82,6 +82,7 @@ export declare namespace VolumeRepresentationRegistry {
             flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            allowTransparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
         }, "isosurface">;
         slice: import("./representation").VolumeRepresentationProvider<{

package/lib/commonjs/mol-script/language/builder.d.ts

@@ -10,6 +10,7 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
+            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;