molstar 3.5.0 → 3.7.0

package/lib/commonjs/cli/cifschema/util/schema.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/examples/alpha-orbitals/index.js

@@ -11,7 +11,7 @@ var rxjs_1 = require("rxjs");
 var operators_1 = require("rxjs/operators");
 var transforms_1 = require("../../extensions/alpha-orbitals/transforms");
 var grid3d_1 = require("../../mol-gl/compute/grid3d");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var config_1 = require("../../mol-plugin/config");
@@ -30,15 +30,15 @@ var AlphaOrbitalsExample = /** @class */ (function () {
         this.currentParams = tslib_1.__assign({}, this.state.value);
     }
     AlphaOrbitalsExample.prototype.init = function (target) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var defaultSpec, _b;
-            return tslib_1.__generator(this, function (_c) {
-                switch (_c.label) {
+            var defaultSpec, _a;
+            var _this = this;
+            return tslib_1.__generator(this, function (_b) {
+                switch (_b.label) {
                     case 0:
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
-                        _b = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, defaultSpec), { layout: {
+                        _a = this;
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, defaultSpec), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false
@@ -56,17 +56,22 @@ var AlphaOrbitalsExample = /** @class */ (function () {
                                     [config_1.PluginConfig.Viewport.ShowAnimation, false],
                                 ] }))];
                     case 1:
-                        _b.plugin = _c.sent();
+                        _a.plugin = _b.sent();
                         this.plugin.managers.interactivity.setProps({ granularity: 'element' });
-                        if (!(0, grid3d_1.canComputeGrid3dOnGPU)((_a = this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl)) {
-                            commands_1.PluginCommands.Toast.Show(this.plugin, {
-                                title: 'Error',
-                                message: "Browser/device does not support required WebGL extension (OES_texture_float)."
-                            });
-                            return [2 /*return*/];
-                        }
-                        this.load(tslib_1.__assign({ moleculeSdf: example_data_1.DemoMoleculeSDF }, example_data_1.DemoOrbitals));
-                        (0, controls_1.mountControls)(this, document.getElementById('controls'));
+                        this.plugin.behaviors.canvas3d.initialized.subscribe(function (init) {
+                            var _a;
+                            if (!init)
+                                return;
+                            if (!(0, grid3d_1.canComputeGrid3dOnGPU)((_a = _this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl)) {
+                                commands_1.PluginCommands.Toast.Show(_this.plugin, {
+                                    title: 'Error',
+                                    message: "Browser/device does not support required WebGL extension (OES_texture_float)."
+                                });
+                                return;
+                            }
+                            _this.load(tslib_1.__assign({ moleculeSdf: example_data_1.DemoMoleculeSDF }, example_data_1.DemoOrbitals));
+                            (0, controls_1.mountControls)(_this, document.getElementById('controls'));
+                        });
                         return [2 /*return*/];
                 }
             });

package/lib/commonjs/examples/basic-wrapper/index.js

@@ -10,7 +10,7 @@ var pdbe_1 = require("../../extensions/pdbe");
 var loci_1 = require("../../mol-model/loci");
 var structure_1 = require("../../mol-model/structure");
 var model_index_1 = require("../../mol-plugin-state/animation/built-in/model-index");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var script_1 = require("../../mol-script/script");
@@ -186,7 +186,7 @@ var BasicWrapper = /** @class */ (function () {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false

package/lib/commonjs/examples/lighting/index.js

@@ -6,7 +6,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var assets_1 = require("../../mol-util/assets");
@@ -66,7 +66,7 @@ var LightingDemo = /** @class */ (function () {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false

package/lib/commonjs/examples/proteopedia-wrapper/index.js

@@ -11,7 +11,7 @@ var canvas3d_1 = require("../../mol-canvas3d/canvas3d");
 var model_index_1 = require("../../mol-plugin-state/animation/built-in/model-index");
 var structure_representation_params_1 = require("../../mol-plugin-state/helpers/structure-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var transformers_1 = require("../../mol-plugin/behavior/dynamic/volume-streaming/transformers");
 var commands_1 = require("../../mol-plugin/commands");
@@ -241,7 +241,7 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
                                     model_index_1.AnimateModelIndex
                                 ], layout: {
                                     initial: {

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -42,6 +42,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    transparentBackfaces: string;
     bumpFrequency: number;
     bumpAmplitude: number;
 }>>;

package/lib/commonjs/extensions/anvil/representation.d.ts

@@ -18,6 +18,7 @@ declare const BilayerPlanesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -98,6 +99,7 @@ export declare const MembraneOrientationParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 };
@@ -134,6 +136,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 };
@@ -170,6 +173,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 }, "membrane-orientation">;

package/lib/commonjs/extensions/cellpack/representation.d.ts

@@ -44,6 +44,7 @@ export declare const MBParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -17,6 +17,7 @@ export declare const ConfalPyramidsParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -46,6 +47,7 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -76,6 +78,7 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts

@@ -24,6 +24,7 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    transparentBackfaces: string;
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts

@@ -16,6 +16,7 @@ export declare const AssemblySymmetryParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts

@@ -31,6 +31,7 @@ export declare const IntraUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -73,6 +74,7 @@ export declare const InterUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -116,6 +118,7 @@ export declare const ClashesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -158,6 +161,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -201,6 +205,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-canvas3d/canvas3d.d.ts

@@ -166,6 +166,7 @@ export declare const Canvas3DParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            transparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;
@@ -319,6 +320,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            transparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;

package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts

@@ -22,6 +22,7 @@ export declare const CameraHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
+        transparentBackfaces: string;
         bumpFrequency: number;
         bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts

@@ -24,6 +24,7 @@ export declare const HandleHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
+        transparentBackfaces: string;
         bumpFrequency: number;
         bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/commonjs/mol-canvas3d/helper/helper.d.ts

@@ -33,6 +33,7 @@ export declare const HelperParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            transparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;
@@ -65,6 +66,7 @@ export declare const DefaultHelperProps: PD.Values<{
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            transparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;

package/lib/commonjs/mol-canvas3d/passes/image.d.ts

@@ -60,6 +60,7 @@ export declare const ImageParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            transparentBackfaces: any;
             bumpFrequency: any;
             bumpAmplitude: any;
             quality: any;

package/lib/commonjs/mol-data/db/column.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -28,6 +28,7 @@ declare namespace Column {
         export type Str = {
             '@type': 'str';
             T: string;
+            transform?: 'uppercase' | 'lowercase';
         } & Base<'str'>;
         export type Int = {
             '@type': 'int';
@@ -50,6 +51,7 @@ declare namespace Column {
         export type Aliased<T> = {
             '@type': 'aliased';
             T: T;
+            transform?: T extends string ? 'uppercase' | 'lowercase' : never;
         } & Base<T extends string ? 'str' : 'int'>;
         export type List<T extends number | string> = {
             '@type': 'list';
@@ -58,16 +60,21 @@ declare namespace Column {
             itemParse: (x: string) => T;
         } & Base<'list'>;
         export const str: Str;
+        export const ustr: Str;
+        export const lstr: Str;
         export const int: Int;
         export const coord: Coordinate;
         export const float: Float;
-        export function Str(defaultValue?: string): Str;
+        export function Str(options?: {
+            defaultValue?: string;
+            transform?: 'uppercase' | 'lowercase';
+        }): Str;
         export function Int(defaultValue?: number): Int;
         export function Float(defaultValue?: number): Float;
         export function Tensor(space: Tensors.Space, baseType?: Int | Float): Tensor;
         export function Vector(dim: number, baseType?: Int | Float): Tensor;
         export function Matrix(rows: number, cols: number, baseType?: Int | Float): Tensor;
-        export function Aliased<T>(t: Str | Int, defaultValue?: T): Aliased<T>;
+        export function Aliased<T>(t: Str | Int): Aliased<T>;
         export function List<T extends number | string>(separator: string, itemParse: (x: string) => T, defaultValue?: T[]): List<T>;
         export {};
     }

package/lib/commonjs/mol-data/db/column.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -17,13 +17,12 @@ var Column;
     (function (Schema) {
         // T also serves as a default value for undefined columns
         Schema.str = { '@type': 'str', T: '', valueType: 'str' };
+        Schema.ustr = { '@type': 'str', T: '', valueType: 'str', transform: 'uppercase' };
+        Schema.lstr = { '@type': 'str', T: '', valueType: 'str', transform: 'lowercase' };
         Schema.int = { '@type': 'int', T: 0, valueType: 'int' };
         Schema.coord = { '@type': 'coord', T: 0, valueType: 'float' };
         Schema.float = { '@type': 'float', T: 0, valueType: 'float' };
-        function Str(defaultValue) {
-            if (defaultValue === void 0) { defaultValue = ''; }
-            return { '@type': 'str', T: defaultValue, valueType: 'str' };
-        }
+        function Str(options) { var _a; return { '@type': 'str', T: (_a = options === null || options === void 0 ? void 0 : options.defaultValue) !== null && _a !== void 0 ? _a : '', transform: options === null || options === void 0 ? void 0 : options.transform, valueType: 'str' }; }
         Schema.Str = Str;
         ;
         function Int(defaultValue) {
@@ -53,9 +52,7 @@ var Column;
             return Tensor(linear_algebra_1.Tensor.ColumnMajorMatrix(rows, cols, baseType['@type'] === 'int' ? Int32Array : Float64Array), baseType);
         }
         Schema.Matrix = Matrix;
-        function Aliased(t, defaultValue) {
-            if (typeof defaultValue !== 'undefined')
-                return tslib_1.__assign(tslib_1.__assign({}, t), { T: defaultValue });
+        function Aliased(t) {
             return t;
         }
         Schema.Aliased = Aliased;
@@ -268,8 +265,13 @@ function lambdaColumn(_a) {
 function arrayColumn(_a) {
     var array = _a.array, schema = _a.schema, valueKind = _a.valueKind;
     var rowCount = array.length;
+    var defaultValue = schema.T;
     var value = schema.valueType === 'str'
-        ? function (row) { var v = array[row]; return typeof v === 'string' ? v : '' + v; }
+        ? schema.transform === 'lowercase'
+            ? function (row) { var v = array[row]; return typeof v === 'string' ? v.toLowerCase() : "".concat(v !== null && v !== void 0 ? v : defaultValue).toLowerCase(); }
+            : schema.transform === 'uppercase'
+                ? function (row) { var v = array[row]; return typeof v === 'string' ? v.toUpperCase() : "".concat(v !== null && v !== void 0 ? v : defaultValue).toUpperCase(); }
+                : function (row) { var v = array[row]; return typeof v === 'string' ? v : "".concat(v !== null && v !== void 0 ? v : defaultValue); }
         : function (row) { return array[row]; };
     var isTyped = ColumnHelpers.isTypedArray(array);
     return {
@@ -280,15 +282,35 @@ function arrayColumn(_a) {
         value: value,
         valueKind: valueKind ? valueKind : function (row) { return 0 /* Present */; },
         toArray: schema.valueType === 'str'
-            ? function (params) {
-                var _a = ColumnHelpers.getArrayBounds(rowCount, params), start = _a.start, end = _a.end;
-                var ret = new (params && typeof params.array !== 'undefined' ? params.array : array.constructor)(end - start);
-                for (var i = 0, _i = end - start; i < _i; i++) {
-                    var v = array[start + i];
-                    ret[i] = typeof v === 'string' ? v : '' + v;
+            ? schema.transform === 'lowercase'
+                ? function (params) {
+                    var _a = ColumnHelpers.getArrayBounds(rowCount, params), start = _a.start, end = _a.end;
+                    var ret = new (params && typeof params.array !== 'undefined' ? params.array : array.constructor)(end - start);
+                    for (var i = 0, _i = end - start; i < _i; i++) {
+                        var v = array[start + i];
+                        ret[i] = typeof v === 'string' ? v.toLowerCase() : "".concat(v !== null && v !== void 0 ? v : defaultValue).toLowerCase();
+                    }
+                    return ret;
                 }
-                return ret;
-            }
+                : schema.transform === 'uppercase'
+                    ? function (params) {
+                        var _a = ColumnHelpers.getArrayBounds(rowCount, params), start = _a.start, end = _a.end;
+                        var ret = new (params && typeof params.array !== 'undefined' ? params.array : array.constructor)(end - start);
+                        for (var i = 0, _i = end - start; i < _i; i++) {
+                            var v = array[start + i];
+                            ret[i] = typeof v === 'string' ? v.toUpperCase() : "".concat(v !== null && v !== void 0 ? v : defaultValue).toUpperCase();
+                        }
+                        return ret;
+                    }
+                    : function (params) {
+                        var _a = ColumnHelpers.getArrayBounds(rowCount, params), start = _a.start, end = _a.end;
+                        var ret = new (params && typeof params.array !== 'undefined' ? params.array : array.constructor)(end - start);
+                        for (var i = 0, _i = end - start; i < _i; i++) {
+                            var v = array[start + i];
+                            ret[i] = typeof v === 'string' ? v : "".concat(v !== null && v !== void 0 ? v : defaultValue);
+                        }
+                        return ret;
+                    }
             : isTyped
                 ? function (params) { return ColumnHelpers.typedArrayWindow(array, params); }
                 : function (params) {

package/lib/commonjs/mol-geo/geometry/color-data.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>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -9,7 +9,7 @@ import { TextureImage } from '../../mol-gl/renderable/util';
 import { Color } from '../../mol-util/color';
 import { Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
 import { LocationIterator } from '../util/location-iterator';
-import { ColorTheme } from '../../mol-theme/color';
+import { ColorTheme, ColorVolume } from '../../mol-theme/color';
 import { Texture } from '../../mol-gl/webgl/texture';
 export declare type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance' | 'volume' | 'volumeInstance' | 'direct';
 export declare type ColorData = {
@@ -26,10 +26,4 @@ export declare type ColorData = {
 export declare function createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any>, colorData?: ColorData): ColorData;
 export declare function createValueColor(value: Color, colorData?: ColorData): ColorData;
 export declare function createTextureColor(colors: TextureImage<Uint8Array>, type: ColorType, colorData?: ColorData): ColorData;
-interface ColorVolume {
-    colors: Texture;
-    dimension: Vec3;
-    transform: Vec4;
-}
 export declare function createGridColor(grid: ColorVolume, type: ColorType, colorData?: ColorData): ColorData;
-export {};

package/lib/commonjs/mol-geo/geometry/color-data.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>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -34,8 +34,20 @@ function _createColors(locationIt, positionIt, colorTheme, colorData) {
         case 'groupInstance': return createGroupInstanceColor(locationIt, colorTheme.color, colorData);
         case 'vertex': return createVertexColor(positionIt, colorTheme.color, colorData);
         case 'vertexInstance': return createVertexInstanceColor(positionIt, colorTheme.color, colorData);
-        case 'volume': return createGridColor(colorTheme.grid, 'volume', colorData);
-        case 'volumeInstance': return createGridColor(colorTheme.grid, 'volumeInstance', colorData);
+        case 'volume':
+            if (colorTheme.grid) {
+                return createGridColor(colorTheme.grid, 'volume', colorData);
+            }
+            else {
+                throw new Error('Grid missing for "volume" color theme');
+            }
+        case 'volumeInstance':
+            if (colorTheme.grid) {
+                return createGridColor(colorTheme.grid, 'volumeInstance', colorData);
+            }
+            else {
+                throw new Error('Grid missing for "volume" color theme');
+            }
         case 'direct': return createDirectColor(colorData);
     }
 }
@@ -184,6 +196,7 @@ function createVertexInstanceColor(locationIt, color, colorData) {
     }
     return createTextureColor(colors, 'vertexInstance', colorData);
 }
+//
 function createGridColor(grid, type, colorData) {
     var colors = grid.colors, dimension = grid.dimension, transform = grid.transform;
     var width = colors.getWidth();

package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -43,13 +43,15 @@ export declare namespace Cylinders {
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
+        transparentBackfaces: PD.Select<string>;
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
-            roughness: number; /** Number of cylinders */
+            roughness: number;
+            /** Number of cylinders */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -110,7 +110,7 @@ var Cylinders;
     }
     Cylinders.transform = transform;
     //
-    Cylinders.Params = tslib_1.__assign(tslib_1.__assign({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
+    Cylinders.Params = tslib_1.__assign(tslib_1.__assign({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), transparentBackfaces: param_definition_1.ParamDefinition.Select('off', param_definition_1.ParamDefinition.arrayToOptions(['off', 'on', 'opaque']), base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
     Cylinders.Utils = {
         Params: Cylinders.Params,
         createEmpty: createEmpty,
@@ -156,7 +156,7 @@ var Cylinders;
         var padding = (0, size_data_1.getMaxSize)(size) * props.sizeFactor;
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ dGeometryType: mol_util_1.ValueCell.create('cylinders'), aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
+        return tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ dGeometryType: mol_util_1.ValueCell.create('cylinders'), aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), dOpaqueBackfaces: mol_util_1.ValueCell.create(props.transparentBackfaces === 'opaque'), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
     }
     function createValuesSimple(cylinders, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -169,6 +169,7 @@ var Cylinders;
         mol_util_1.ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        mol_util_1.ValueCell.updateIfChanged(values.dOpaqueBackfaces, props.transparentBackfaces === 'opaque');
         mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }

package/lib/commonjs/mol-geo/geometry/mesh/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>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -62,6 +62,7 @@ export declare namespace Mesh {
         flatShaded: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
+        transparentBackfaces: PD.Select<string>;
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;