molstar 3.3.1 → 3.6.0

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;

package/lib/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/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/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/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/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/mol-repr/structure/visual/util/common.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>
  */
@@ -273,26 +273,3 @@ export function isTrace(unit, element) {
         return true;
     return false;
 }
-export function getUnitExtraRadius(unit) {
-    if (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;
-}
-export 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;
-}

package/lib/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/mol-repr/util.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>
  */
@@ -165,7 +165,7 @@ export 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/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/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/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>>;

package/lib/mol-script/language/parser.js

@@ -6,6 +6,7 @@
 import { MonadicParser as P } from '../../mol-util/monadic-parser';
 import { Expression } from './expression';
 import { MolScriptBuilder as B } from './builder';
+import { assertUnreachable } from '../../mol-util/type-helpers';
 export function parseMolScript(input) {
     return Language.parse(input);
 }
@@ -59,15 +60,15 @@ var Language;
                     case '[': return B.core.type.list(withoutComments(expr.nodes).map(visitExpr));
                     case '{': return B.core.type.set(withoutComments(expr.nodes).map(visitExpr));
                     case '(': {
+                        if (expr.nodes[0].kind === 'comment')
+                            throw new Error('Invalid expression');
                         var head = visitExpr(expr.nodes[0]);
                         return Expression.Apply(head, getArgs(expr.nodes));
                     }
+                    default: assertUnreachable(expr.bracket);
                 }
-                return 0;
-            }
-            default: {
-                throw new Error('should not happen');
             }
+            default: assertUnreachable(expr);
         }
     }
     function getArgs(nodes) {
@@ -98,6 +99,8 @@ var Language;
                 }
                 if (i >= _i)
                     throw new Error("There must be a value foolowed a named arg ':".concat(name_1, "'."));
+                if (nodes[i].kind === 'comment')
+                    throw new Error('Invalid expression');
                 args[name_1] = visitExpr(nodes[i]);
                 if (isNaN(+name_1))
                     allNumeric = false;

package/lib/mol-task/util/scheduler.d.ts

@@ -5,8 +5,8 @@
  */
 /// <reference types="node" />
 declare const Scheduler: {
-    setImmediate: ((callback: (...args: any[]) => void, ...args: any[]) => number) | typeof setImmediate;
-    clearImmediate: ((handle: number) => void) | typeof clearImmediate;
+    setImmediate: typeof setImmediate | ((callback: (...args: any[]) => void, ...args: any[]) => number);
+    clearImmediate: typeof clearImmediate | ((handle: number) => void);
     immediatePromise(): Promise<void>;
     delay<T>(timeout: number, value?: T | undefined): Promise<T>;
 };

package/lib/mol-task/util/scheduler.js

@@ -5,7 +5,7 @@
  */
 import { __spreadArray } from "tslib";
 function createImmediateActions() {
-    var global = (function () {
+    var thisGlobal = (function () {
         var _window = typeof window !== 'undefined' && window;
         var _self = typeof self !== 'undefined' && typeof WorkerGlobalScope !== 'undefined' && self instanceof WorkerGlobalScope && self;
         var _global = typeof global !== 'undefined' && global;
@@ -65,14 +65,14 @@ function createImmediateActions() {
         };
     }
     function canUsePostMessage() {
-        if (global && global.postMessage && !global.importScripts) {
+        if (thisGlobal && thisGlobal.postMessage && !thisGlobal.importScripts) {
             var postMessageIsAsynchronous_1 = true;
-            var oldOnMessage = global.onmessage;
-            global.onmessage = function () {
+            var oldOnMessage = thisGlobal.onmessage;
+            thisGlobal.onmessage = function () {
                 postMessageIsAsynchronous_1 = false;
             };
-            global.postMessage('', '*');
-            global.onmessage = oldOnMessage;
+            thisGlobal.postMessage('', '*');
+            thisGlobal.onmessage = oldOnMessage;
             return postMessageIsAsynchronous_1;
         }
     }
@@ -82,7 +82,7 @@ function createImmediateActions() {
         // * http://www.whatwg.org/specs/web-apps/current-work/multipage/comms.html#crossDocumentMessages
         var messagePrefix = 'setImmediate$' + Math.random() + '$';
         var onGlobalMessage = function (event) {
-            if (event.source === global &&
+            if (event.source === thisGlobal &&
                 typeof event.data === 'string' &&
                 event.data.indexOf(messagePrefix) === 0) {
                 runIfPresent(+event.data.slice(messagePrefix.length));

package/lib/mol-theme/color/hydrophobicity.js

@@ -45,8 +45,8 @@ export function HydrophobicityColorTheme(ctx, props) {
     var scale = ColorScale.create({
         listOrName: props.list.colors,
         domain: [max, min],
-        minLabel: 'Hydrophobic',
-        maxLabel: 'Hydrophilic'
+        minLabel: 'Hydrophilic',
+        maxLabel: 'Hydrophobic'
     });
     function color(location) {
         var compId;

package/lib/mol-util/data-source.js

@@ -93,6 +93,7 @@ function getCompression(name) {
         /\.zip$/i.test(name) ? DataCompressionMethod.Zip :
             DataCompressionMethod.None;
 }
+var reFilterPath = /^(__MACOSX|.DS_Store)/;
 function decompress(ctx, data, compression) {
     return __awaiter(this, void 0, void 0, function () {
         var _a, parsed, names;
@@ -111,7 +112,7 @@ function decompress(ctx, data, compression) {
                 case 3: return [4 /*yield*/, unzip(ctx, data.buffer)];
                 case 4:
                     parsed = _b.sent();
-                    names = Object.keys(parsed);
+                    names = Object.keys(parsed).filter(function (n) { return !reFilterPath.test(n); });
                     if (names.length !== 1)
                         throw new Error('can only decompress zip files with a single entry');
                     return [2 /*return*/, parsed[names[0]]];

package/lib/mol-util/file-info.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 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>
  */
@@ -11,8 +11,6 @@ export interface FileInfo {
     ext: string;
     base: string;
     dir: string;
-    compressed: string | boolean;
-    binary: boolean;
     protocol: string;
     query: string;
     src: FileInput;

package/lib/mol-util/file-info.js

@@ -1,16 +1,13 @@
 /**
- * Copyright (c) 2018 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>
  */
 // TODO only support compressed files for which uncompression support is available???
 // TODO store globally with decompression plugins?
 var compressedExtList = ['gz', 'zip'];
-// TODO store globally with parser plugins?
-var binaryExtList = ['bcif', 'ccp4', 'dcd'];
 export function getFileInfo(file) {
     var path;
-    var compressed;
     var protocol = '';
     if (file instanceof File) {
         path = file.name;
@@ -35,15 +32,10 @@ export function getFileInfo(file) {
     }
     var dir = path.substring(0, path.lastIndexOf('/') + 1);
     if (compressedExtList.includes(ext)) {
-        compressed = ext;
         var n = path.length - ext.length - 1;
         ext = (path.substr(0, n).split('.').pop() || '').toLowerCase();
         var m = base.length - ext.length - 1;
         base = base.substr(0, m);
     }
-    else {
-        compressed = false;
-    }
-    var binary = binaryExtList.includes(ext);
-    return { path: path, name: name, ext: ext, base: base, dir: dir, compressed: compressed, binary: binary, protocol: protocol, query: query, src: file };
+    return { path: path, name: name, ext: ext, base: base, dir: dir, protocol: protocol, query: query, src: file };
 }

package/lib/mol-util/index.d.ts

@@ -27,3 +27,4 @@ export declare const assign: (<T>(o: T, ...from: any[]) => T);
 export declare const merge: (<T>(source: T, ...rest: Partial<T>[]) => T);
 export declare function formatTime(d: Date): string;
 export declare function formatProgress(p: Progress): string;
+export declare function formatBytes(count: number): string;