molstar 2.3.9 → 2.4.0

package/lib/commonjs/mol-util/color/lists.d.ts

@@ -68,7 +68,7 @@ export declare const ColorLists: {
 };
 export declare type ColorListName = keyof typeof ColorLists;
 export declare const ColorListNames: string[];
-export declare const ColorListOptions: ["orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "red-yellow-blue" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue", string, string][];
-export declare const ColorListOptionsScale: ["orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "red-yellow-blue" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue", string, string][];
-export declare const ColorListOptionsSet: ["orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "red-yellow-blue" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue", string, string][];
+export declare const ColorListOptions: ["red-yellow-blue" | "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue", string, string][];
+export declare const ColorListOptionsScale: ["red-yellow-blue" | "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue", string, string][];
+export declare const ColorListOptionsSet: ["red-yellow-blue" | "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue", string, string][];
 export declare function getColorListFromName(name: ColorListName): ColorList;

package/lib/commonjs/mol-util/color/palette.d.ts

@@ -10,38 +10,38 @@ import { ParamDefinition as PD } from '../param-definition';
 declare type PaletteType = 'generate' | 'colors';
 declare const DefaultGetPaletteProps: {
     type: PaletteType;
-    colorList: "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "red-yellow-blue" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue";
+    colorList: "red-yellow-blue" | "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue";
 };
 declare type GetPaletteProps = typeof DefaultGetPaletteProps;
 export declare function getPaletteParams(props?: Partial<GetPaletteProps>): {
     palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        list: {
-            kind: "interpolate" | "set";
-            colors: import("./color").ColorListEntry[];
-        };
-    }>, "colors"> | PD.NamedParams<PD.Normalize<{
         maxCount: number;
         hue: [number, number];
         chroma: [number, number];
         luminance: [number, number];
         clusteringStepCount: number;
         minSampleCount: number;
-    }>, "generate">>;
-};
-declare const DefaultPaletteProps: PD.Values<{
-    palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    }>, "generate"> | PD.NamedParams<PD.Normalize<{
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("./color").ColorListEntry[];
         };
-    }>, "colors"> | PD.NamedParams<PD.Normalize<{
+    }>, "colors">>;
+};
+declare const DefaultPaletteProps: PD.Values<{
+    palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
         maxCount: number;
         hue: [number, number];
         chroma: [number, number];
         luminance: [number, number];
         clusteringStepCount: number;
         minSampleCount: number;
-    }>, "generate">>;
+    }>, "generate"> | PD.NamedParams<PD.Normalize<{
+        list: {
+            kind: "set" | "interpolate";
+            colors: import("./color").ColorListEntry[];
+        };
+    }>, "colors">>;
 }>;
 declare type PaletteProps = typeof DefaultPaletteProps;
 declare const DefaultLabelOptions: {

package/lib/commonjs/mol-util/color/scale.d.ts

@@ -21,7 +21,7 @@ export interface ColorScale {
 export declare const DefaultColorScaleProps: {
     domain: [number, number];
     reverse: boolean;
-    listOrName: "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "red-yellow-blue" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue" | ColorListEntry[];
+    listOrName: "red-yellow-blue" | "orange-red" | "purple-blue" | "blue-purple" | "oranges" | "blue-green" | "yellow-orange-brown" | "yellow-green" | "reds" | "red-purple" | "greens" | "yellow-green-blue" | "purples" | "green-blue" | "greys" | "yellow-orange-red" | "purple-red" | "blues" | "purple-blue-green" | "spectral" | "red-yellow-green" | "red-blue" | "pink-yellow-green" | "purple-green" | "brown-white-green" | "red-grey" | "orange-purple" | "set-2" | "accent" | "set-1" | "set-3" | "dark-2" | "paired" | "pastel-2" | "pastel-1" | "many-distinct" | "magma" | "inferno" | "plasma" | "viridis" | "cividis" | "twilight" | "turbo" | "rainbow" | "red-white-blue" | ColorListEntry[];
     minLabel: string | undefined;
     maxLabel: string | undefined;
 };

package/lib/commonjs/servers/model/config.d.ts

@@ -53,7 +53,7 @@ declare const DefaultModelServerConfig: {
      *
      * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
      */
-    sourceMap: ([string, string] | [string, string, "bcif" | "cif" | "cif.gz" | "bcif.gz"])[];
+    sourceMap: ([string, string] | [string, string, "cif" | "bcif" | "cif.gz" | "bcif.gz"])[];
 };
 export declare const ModelServerFetchFormats: readonly ["cif", "bcif", "cif.gz", "bcif.gz"];
 export declare type ModelServerFetchFormats = (typeof ModelServerFetchFormats)[number];
@@ -108,7 +108,7 @@ export declare const ModelServerConfig: {
      *
      * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
      */
-    sourceMap: ([string, string] | [string, string, "bcif" | "cif" | "cif.gz" | "bcif.gz"])[];
+    sourceMap: ([string, string] | [string, string, "cif" | "bcif" | "cif.gz" | "bcif.gz"])[];
 };
 export declare const ModelServerConfigTemplate: ModelServerConfig;
 export declare function configureServer(): void;

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

@@ -10,7 +10,7 @@ import { StructureRepresentation, StructureRepresentationProvider } from '../../
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { ThemeRegistryContext } from '../../../mol-theme/theme';
 export declare const ConfalPyramidsParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -22,7 +22,7 @@ export declare const ConfalPyramidsParams: {
 };
 export declare type ConfalPyramidsParams = typeof ConfalPyramidsParams;
 export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, structure: Structure): {
-    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -35,7 +35,7 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
 export declare type ConfalPyramidsRepresentation = StructureRepresentation<ConfalPyramidsParams>;
 export declare function ConfalPyramidsRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ConfalPyramidsParams>): ConfalPyramidsRepresentation;
 export declare const ConfalPyramidsRepresentationProvider: StructureRepresentationProvider<{
-    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/extensions/geo-export/controls.js

@@ -94,7 +94,7 @@ var GeometryControls = /** @class */ (function (_super) {
                             }];
                     case 7:
                         e_1 = _e.sent();
-                        this.plugin.log.error('' + e_1);
+                        this.plugin.log.error('Error during geometry export');
                         throw e_1;
                     case 8: return [2 /*return*/];
                 }

package/lib/extensions/geo-export/controls.js.map

@@ -1 +1 @@
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+{"version":3,"file":"controls.js","sourceRoot":"","sources":["../../../src/extensions/geo-export/controls.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AACjD,OAAO,EAAE,KAAK,EAAE,MAAM,yBAAyB,CAAC;AAChD,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AAEnE,OAAO,EAAE,IAAI,EAAE,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,iBAAiB,EAAE,MAAM,gCAAgC,CAAC;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,iCAAiC,CAAC;AACxE,OAAO,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAC;AAE/C,MAAM,CAAC,IAAM,cAAc,GAAG;IAC1B,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,KAAK,EAAE;QACrB,CAAC,KAAK,EAAE,wBAAwB,CAAC;QACjC,CAAC,KAAK,EAAE,YAAY,CAAC;QACrB,CAAC,KAAK,EAAE,kBAAkB,CAAC;QAC3B,CAAC,MAAM,EAAE,qCAAqC,CAAC;KAClD,CAAC;CACL,CAAC;AAEF;IAAsC,oCAAe;IA0DjD,0BAAoB,MAAqB;QAAzC,YACI,iBAAO,SACV;QAFmB,YAAM,GAAN,MAAM,CAAe;QAzDhC,eAAS,GAAG;YACjB,MAAM,EAAE,KAAI,CAAC,EAAE,CAAC,QAAQ,CAAmC,EAAE,CAAC,gBAAgB,CAAC,cAAc,CAAC,CAAC;SAClG,CAAA;;IAyDD,CAAC;IAvDO,sCAAW,GAAnB;QACI,IAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,cAAc,CAAC,UAAU,CAAC,WAAW,CAAC,iBAAiB,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,GAAI,CAAC,IAAI,EAAX,CAAW,CAAC,CAAC;QAC5I,IAAM,SAAS,GAAG,IAAI,GAAG,EAAU,CAAC;QACpC,MAAM,CAAC,OAAO,CAAC,UAAA,CAAC,IAAI,OAAA,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,EAAtC,CAAsC,CAAC,CAAC;QAC5D,IAAM,QAAQ,GAAG,QAAQ,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACvD,OAAO,UAAG,QAAQ,IAAI,eAAe,CAAE,CAAC;IAC5C,CAAC;IAED,yCAAc,GAAd;QAAA,iBA2CC;QA1CG,IAAM,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,iBAAiB,EAAE,UAAM,GAAG;;;;;;;wBAEvC,aAAa,GAAG,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,gBAAgB,EAAG,CAAC;wBAC1D,QAAQ,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;wBAE9B,KAAK,GAAG,QAAQ,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,KAAK,CAAC,QAAQ,CAAC,KAAM,CAAC,CAAC;wBAC9D,cAAc,GAAG,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,qBAAsB,CAAC;wBAC9D,WAAW,GAAG,KAAK,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,cAAc,CAAC,CAAC;wBAC5D,oBAAoB,SAAwD,CAAC;wBACjF,QAAQ,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE;4BACxC,KAAK,KAAK;gCACN,oBAAoB,GAAG,IAAI,WAAW,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;gCAC3D,MAAM;4BACV,KAAK,KAAK;gCACN,oBAAoB,GAAG,IAAI,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAC;gCAC9D,MAAM;4BACV,KAAK,KAAK;gCACN,oBAAoB,GAAG,IAAI,WAAW,CAAC,WAAW,CAAC,CAAC;gCACpD,MAAM;4BACV,KAAK,MAAM;gCACP,oBAAoB,GAAG,IAAI,YAAY,CAAC,KAAK,EAAE,WAAW,EAAE,cAAc,CAAC,MAAM,CAAC,CAAC;gCACnF,MAAM;4BACV,OAAO,CAAC,CAAC,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;yBACnD;wBAEQ,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM;;;6BAAE,CAAA,CAAC,GAAG,EAAE,CAAA;wBAC7C,qBAAM,GAAG,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,2BAAoB,CAAC,cAAI,EAAE,CAAE,EAAE,CAAC,EAAA;;wBAA5D,SAA4D,CAAC;wBAC7D,qBAAM,oBAAoB,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,KAAM,EAAE,GAAG,CAAC,EAAA;;wBAAnF,SAAmF,CAAC;;;wBAFrC,EAAE,CAAC,CAAA;;4BAKzC,qBAAM,oBAAoB,CAAC,OAAO,CAAC,GAAG,CAAC,EAAA;;wBAA9C,IAAI,GAAG,SAAuC;wBACpD,sBAAO;gCACH,IAAI,MAAA;gCACJ,QAAQ,EAAE,QAAQ,GAAG,GAAG,GAAG,oBAAoB,CAAC,aAAa;6BAChE,EAAC;;;wBAEF,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,8BAA8B,CAAC,CAAC;wBACtD,MAAM,GAAC,CAAC;;;;aAEf,CAAC,CAAC;QAEH,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3D,CAAC;IAKL,uBAAC;AAAD,CAAC,AA7DD,CAAsC,eAAe,GA6DpD"}

package/lib/extensions/geo-export/glb-exporter.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Style } from '../../mol-gl/renderer';
 import { Box3D } from '../../mol-math/geometry';

package/lib/extensions/geo-export/glb-exporter.js

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { __awaiter, __extends, __generator, __spreadArray } from "tslib";
 import { asciiWrite } from '../../mol-io/common/ascii';
@@ -21,6 +22,11 @@ var UNSIGNED_INT = 5125;
 var FLOAT = 5126;
 var ARRAY_BUFFER = 34962;
 var ELEMENT_ARRAY_BUFFER = 34963;
+var GLTF_MAGIC_BYTE = 0x46546C67;
+var JSON_CHUNK_TYPE = 0x4E4F534A;
+var BIN_CHUNK_TYPE = 0x004E4942;
+var JSON_PAD_CHAR = 0x20;
+var BIN_PAD_CHAR = 0x00;
 var GlbExporter = /** @class */ (function (_super) {
     __extends(GlbExporter, _super);
     function GlbExporter(style, boundingBox) {
@@ -110,20 +116,14 @@ var GlbExporter = /** @class */ (function (_super) {
             indexAccessorIndex: isGeoTexture ? undefined : this.addBuffer(indexBuffer, UNSIGNED_INT, 'SCALAR', drawCount, ELEMENT_ARRAY_BUFFER)
         };
     };
-    GlbExporter.prototype.addColorBuffer = function (values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors) {
-        var groupCount = values.uGroupCount.ref.value;
+    GlbExporter.prototype.addColorBuffer = function (geoData, interpolatedColors, interpolatedOverpaint, interpolatedTransparency) {
+        var values = geoData.values, vertexCount = geoData.vertexCount;
         var uAlpha = values.uAlpha.ref.value;
-        var dTransparency = values.dTransparency.ref.value;
-        var tTransparency = values.tTransparency.ref.value;
         var colorArray = new Uint8Array(vertexCount * 4);
         for (var i = 0; i < vertexCount; ++i) {
-            var color = GlbExporter.getColor(values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors, i);
-            var alpha = uAlpha;
-            if (dTransparency) {
-                var group = isGeoTexture ? GlbExporter.getGroup(groups, i) : groups[i];
-                var transparency = tTransparency.array[instanceIndex * groupCount + group] / 255;
-                alpha *= 1 - transparency;
-            }
+            var color = GlbExporter.getColor(i, geoData, interpolatedColors, interpolatedOverpaint);
+            var transparency = GlbExporter.getTransparency(i, geoData, interpolatedTransparency);
+            var alpha = uAlpha * (1 - transparency);
             color = Color.sRGBToLinear(color);
             Color.toArray(color, colorArray, i * 4);
             colorArray[i * 4 + 3] = Math.round(alpha * 255);
@@ -136,19 +136,29 @@ var GlbExporter = /** @class */ (function (_super) {
     };
     GlbExporter.prototype.addMeshWithColors = function (input) {
         return __awaiter(this, void 0, void 0, function () {
-            var mesh, values, isGeoTexture, webgl, ctx, t, colorType, dTransparency, aTransform, instanceCount, interpolatedColors, stride, sameGeometryBuffers, sameColorBuffer, vertexAccessorIndex, normalAccessorIndex, indexAccessorIndex, colorAccessorIndex, meshIndex, instanceIndex, _a, vertices, normals, indices, groups, vertexCount, drawCount, accessorIndices, node;
+            var mesh, values, isGeoTexture, webgl, ctx, t, colorType, overpaintType, transparencyType, dTransparency, aTransform, instanceCount, interpolatedColors, stride, interpolatedOverpaint, stride, interpolatedTransparency, stride, sameGeometryBuffers, sameColorBuffer, vertexAccessorIndex, normalAccessorIndex, indexAccessorIndex, colorAccessorIndex, meshIndex, instanceIndex, _a, vertices, normals, indices, groups, vertexCount, drawCount, accessorIndices, node;
             return __generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         mesh = input.mesh, values = input.values, isGeoTexture = input.isGeoTexture, webgl = input.webgl, ctx = input.ctx;
                         t = Mat4();
                         colorType = values.dColorType.ref.value;
+                        overpaintType = values.dOverpaintType.ref.value;
+                        transparencyType = values.dTransparencyType.ref.value;
                         dTransparency = values.dTransparency.ref.value;
                         aTransform = values.aTransform.ref.value;
                         instanceCount = values.uInstanceCount.ref.value;
                         if (colorType === 'volume' || colorType === 'volumeInstance') {
                             stride = isGeoTexture ? 4 : 3;
-                            interpolatedColors = GlbExporter.getInterpolatedColors(mesh.vertices, mesh.vertexCount, values, stride, colorType, webgl);
+                            interpolatedColors = GlbExporter.getInterpolatedColors(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: colorType });
+                        }
+                        if (overpaintType === 'volumeInstance') {
+                            stride = isGeoTexture ? 4 : 3;
+                            interpolatedOverpaint = GlbExporter.getInterpolatedOverpaint(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: overpaintType });
+                        }
+                        if (transparencyType === 'volumeInstance') {
+                            stride = isGeoTexture ? 4 : 3;
+                            interpolatedTransparency = GlbExporter.getInterpolatedTransparency(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: transparencyType });
                         }
                         sameGeometryBuffers = mesh !== undefined;
                         sameColorBuffer = sameGeometryBuffers && colorType !== 'instance' && !colorType.endsWith('Instance') && !dTransparency;
@@ -177,7 +187,7 @@ var GlbExporter = /** @class */ (function (_super) {
                             }
                             // create a color buffer if needed
                             if (instanceIndex === 0 || !sameColorBuffer) {
-                                colorAccessorIndex = this.addColorBuffer(values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors);
+                                colorAccessorIndex = this.addColorBuffer({ values: values, groups: groups, vertexCount: vertexCount, instanceIndex: instanceIndex, isGeoTexture: isGeoTexture }, interpolatedColors, interpolatedOverpaint, interpolatedTransparency);
                             }
                             // glTF mesh
                             meshIndex = this.meshes.length;
@@ -259,12 +269,12 @@ var GlbExporter = /** @class */ (function (_super) {
                 jsonString = JSON.stringify(gltf);
                 jsonBuffer = new Uint8Array(jsonString.length);
                 asciiWrite(jsonBuffer, jsonString);
-                _a = createChunk(0x4E4F534A, [jsonBuffer.buffer], jsonBuffer.length, 0x20), jsonChunk = _a[0], jsonChunkLength = _a[1];
-                _b = createChunk(0x004E4942, this.binaryBuffer, binaryBufferLength, 0x00), binaryChunk = _b[0], binaryChunkLength = _b[1];
+                _a = createChunk(JSON_CHUNK_TYPE, [jsonBuffer.buffer], jsonBuffer.length, JSON_PAD_CHAR), jsonChunk = _a[0], jsonChunkLength = _a[1];
+                _b = createChunk(BIN_CHUNK_TYPE, this.binaryBuffer, binaryBufferLength, BIN_PAD_CHAR), binaryChunk = _b[0], binaryChunkLength = _b[1];
                 glbBufferLength = 12 + jsonChunkLength + binaryChunkLength;
                 header = new ArrayBuffer(12);
                 headerDataView = new DataView(header);
-                headerDataView.setUint32(0, 0x46546C67, true); // magic number "glTF"
+                headerDataView.setUint32(0, GLTF_MAGIC_BYTE, true); // magic number "glTF"
                 headerDataView.setUint32(4, 2, true); // version
                 headerDataView.setUint32(8, glbBufferLength, true); // length
                 glbBuffer = __spreadArray(__spreadArray([header], jsonChunk, true), binaryChunk, true);

package/lib/extensions/geo-export/glb-exporter.js.map

@@ -1 +1 @@
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package/lib/extensions/geo-export/mesh-exporter.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { GraphicsRenderObject } from '../../mol-gl/render-object';
 import { BaseValues } from '../../mol-gl/renderable/schema';
@@ -25,12 +26,39 @@ export interface AddMeshInput {
     webgl: WebGLContext | undefined;
     ctx: RuntimeContext;
 }
+export declare type MeshGeoData = {
+    values: BaseValues;
+    groups: Float32Array | Uint8Array;
+    vertexCount: number;
+    instanceIndex: number;
+    isGeoTexture: boolean;
+};
 export declare abstract class MeshExporter<D extends RenderObjectExportData> implements RenderObjectExporter<D> {
     abstract readonly fileExtension: string;
     private static getSizeFromTexture;
     private static getSize;
     protected static getGroup(groups: Float32Array | Uint8Array, i: number): number;
-    protected static getInterpolatedColors(vertices: Float32Array, vertexCount: number, values: BaseValues, stride: number, colorType: 'volume' | 'volumeInstance', webgl: WebGLContext): Uint8Array;
+    protected static getInterpolatedColors(webgl: WebGLContext, input: {
+        vertices: Float32Array;
+        vertexCount: number;
+        values: BaseValues;
+        stride: 3 | 4;
+        colorType: 'volume' | 'volumeInstance';
+    }): Uint8Array;
+    protected static getInterpolatedOverpaint(webgl: WebGLContext, input: {
+        vertices: Float32Array;
+        vertexCount: number;
+        values: BaseValues;
+        stride: 3 | 4;
+        colorType: 'volumeInstance';
+    }): Uint8Array;
+    protected static getInterpolatedTransparency(webgl: WebGLContext, input: {
+        vertices: Float32Array;
+        vertexCount: number;
+        values: BaseValues;
+        stride: 3 | 4;
+        colorType: 'volumeInstance';
+    }): Uint8Array;
     protected static quantizeColors(colorArray: Uint8Array, vertexCount: number): void;
     protected static getInstance(input: AddMeshInput, instanceIndex: number): {
         vertices: Float32Array;
@@ -40,7 +68,8 @@ export declare abstract class MeshExporter<D extends RenderObjectExportData> imp
         vertexCount: number;
         drawCount: number;
     };
-    protected static getColor(values: BaseValues, groups: Float32Array | Uint8Array, vertexCount: number, instanceIndex: number, isGeoTexture: boolean, interpolatedColors: Uint8Array | undefined, vertexIndex: number): Color;
+    protected static getColor(vertexIndex: number, geoData: MeshGeoData, interpolatedColors?: Uint8Array, interpolatedOverpaint?: Uint8Array): Color;
+    protected static getTransparency(vertexIndex: number, geoData: MeshGeoData, interpolatedTransparency?: Uint8Array): number;
     protected abstract addMeshWithColors(input: AddMeshInput): void;
     private addMesh;
     private addLines;

package/lib/extensions/geo-export/mesh-exporter.js

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { __awaiter, __generator } from "tslib";
 import { sort, arraySwap } from '../../mol-data/util';
@@ -14,6 +15,7 @@ import { sizeDataFactor } from '../../mol-geo/geometry/size-data';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { Color } from '../../mol-util/color/color';
 import { decodeFloatRGB } from '../../mol-util/float-packing';
+import { readAlphaTexture, readTexture } from '../../mol-gl/compute/util';
 var GeoExportName = 'geo-export';
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3fromArray = Vec3.fromArray;
@@ -56,22 +58,37 @@ var MeshExporter = /** @class */ (function () {
         }
         return decodeFloatRGB(r, g, b);
     };
-    MeshExporter.getInterpolatedColors = function (vertices, vertexCount, values, stride, colorType, webgl) {
+    MeshExporter.getInterpolatedColors = function (webgl, input) {
+        var values = input.values, vertexCount = input.vertexCount, vertices = input.vertices, colorType = input.colorType, stride = input.stride;
         var colorGridTransform = values.uColorGridTransform.ref.value;
         var colorGridDim = values.uColorGridDim.ref.value;
         var colorTexDim = values.uColorTexDim.ref.value;
         var aTransform = values.aTransform.ref.value;
         var instanceCount = values.uInstanceCount.ref.value;
-        if (!webgl.namedFramebuffers[GeoExportName]) {
-            webgl.namedFramebuffers[GeoExportName] = webgl.resources.framebuffer();
-        }
-        var framebuffer = webgl.namedFramebuffers[GeoExportName];
-        var width = colorTexDim[0], height = colorTexDim[1];
-        var colorGrid = new Uint8Array(width * height * 4);
-        framebuffer.bind();
-        values.tColorGrid.ref.value.attachFramebuffer(framebuffer, 0);
-        webgl.readPixels(0, 0, width, height, colorGrid);
-        var interpolated = getTrilinearlyInterpolated({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: colorGrid, gridDim: colorGridDim, gridTexDim: colorTexDim, gridTransform: colorGridTransform, vertexStride: stride, colorStride: 4 });
+        var colorGrid = readTexture(webgl, values.tColorGrid.ref.value).array;
+        var interpolated = getTrilinearlyInterpolated({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: colorGrid, gridDim: colorGridDim, gridTexDim: colorTexDim, gridTransform: colorGridTransform, vertexStride: stride, colorStride: 4, outputStride: 3 });
+        return interpolated.array;
+    };
+    MeshExporter.getInterpolatedOverpaint = function (webgl, input) {
+        var values = input.values, vertexCount = input.vertexCount, vertices = input.vertices, colorType = input.colorType, stride = input.stride;
+        var overpaintGridTransform = values.uOverpaintGridTransform.ref.value;
+        var overpaintGridDim = values.uOverpaintGridDim.ref.value;
+        var overpaintTexDim = values.uOverpaintTexDim.ref.value;
+        var aTransform = values.aTransform.ref.value;
+        var instanceCount = values.uInstanceCount.ref.value;
+        var overpaintGrid = readTexture(webgl, values.tOverpaintGrid.ref.value).array;
+        var interpolated = getTrilinearlyInterpolated({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: overpaintGrid, gridDim: overpaintGridDim, gridTexDim: overpaintTexDim, gridTransform: overpaintGridTransform, vertexStride: stride, colorStride: 4, outputStride: 4 });
+        return interpolated.array;
+    };
+    MeshExporter.getInterpolatedTransparency = function (webgl, input) {
+        var values = input.values, vertexCount = input.vertexCount, vertices = input.vertices, colorType = input.colorType, stride = input.stride;
+        var transparencyGridTransform = values.uTransparencyGridTransform.ref.value;
+        var transparencyGridDim = values.uTransparencyGridDim.ref.value;
+        var transparencyTexDim = values.uTransparencyTexDim.ref.value;
+        var aTransform = values.aTransform.ref.value;
+        var instanceCount = values.uInstanceCount.ref.value;
+        var transparencyGrid = readAlphaTexture(webgl, values.tTransparencyGrid.ref.value).array;
+        var interpolated = getTrilinearlyInterpolated({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: transparencyGrid, gridDim: transparencyGridDim, gridTexDim: transparencyTexDim, gridTransform: transparencyGridTransform, vertexStride: stride, colorStride: 4, outputStride: 1, itemOffset: 3 });
         return interpolated.array;
     };
     MeshExporter.quantizeColors = function (colorArray, vertexCount) {
@@ -153,11 +170,13 @@ var MeshExporter = /** @class */ (function () {
             };
         }
     };
-    MeshExporter.getColor = function (values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors, vertexIndex) {
+    MeshExporter.getColor = function (vertexIndex, geoData, interpolatedColors, interpolatedOverpaint) {
+        var values = geoData.values, instanceIndex = geoData.instanceIndex, isGeoTexture = geoData.isGeoTexture, groups = geoData.groups, vertexCount = geoData.vertexCount;
         var groupCount = values.uGroupCount.ref.value;
         var colorType = values.dColorType.ref.value;
         var uColor = values.uColor.ref.value;
         var tColor = values.tColor.ref.value.array;
+        var overpaintType = values.dOverpaintType.ref.value;
         var dOverpaint = values.dOverpaint.ref.value;
         var tOverpaint = values.tOverpaint.ref.value.array;
         var color;
@@ -193,13 +212,66 @@ var MeshExporter = /** @class */ (function () {
             default: throw new Error('Unsupported color type.');
         }
         if (dOverpaint) {
-            var group = isGeoTexture ? MeshExporter.getGroup(groups, vertexIndex) : groups[vertexIndex];
-            var overpaintColor = Color.fromArray(tOverpaint, (instanceIndex * groupCount + group) * 4);
-            var overpaintAlpha = tOverpaint[(instanceIndex * groupCount + group) * 4 + 3] / 255;
+            var overpaintColor = void 0;
+            var overpaintAlpha = void 0;
+            switch (overpaintType) {
+                case 'groupInstance': {
+                    var group = isGeoTexture ? MeshExporter.getGroup(groups, vertexIndex) : groups[vertexIndex];
+                    var idx = (instanceIndex * groupCount + group) * 4;
+                    overpaintColor = Color.fromArray(tOverpaint, idx);
+                    overpaintAlpha = tOverpaint[idx + 3] / 255;
+                    break;
+                }
+                case 'vertexInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex) * 4;
+                    overpaintColor = Color.fromArray(tOverpaint, idx);
+                    overpaintAlpha = tOverpaint[idx + 3] / 255;
+                    break;
+                }
+                case 'volumeInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex) * 4;
+                    overpaintColor = Color.fromArray(interpolatedOverpaint, idx);
+                    overpaintAlpha = interpolatedOverpaint[idx + 3] / 255;
+                    break;
+                }
+                default: throw new Error('Unsupported overpaint type.');
+            }
+            // interpolate twice to avoid darkening due to empty overpaint
+            overpaintColor = Color.interpolate(color, overpaintColor, overpaintAlpha);
             color = Color.interpolate(color, overpaintColor, overpaintAlpha);
         }
         return color;
     };
+    MeshExporter.getTransparency = function (vertexIndex, geoData, interpolatedTransparency) {
+        var values = geoData.values, instanceIndex = geoData.instanceIndex, isGeoTexture = geoData.isGeoTexture, groups = geoData.groups, vertexCount = geoData.vertexCount;
+        var groupCount = values.uGroupCount.ref.value;
+        var dTransparency = values.dTransparency.ref.value;
+        var tTransparency = values.tTransparency.ref.value.array;
+        var transparencyType = values.dTransparencyType.ref.value;
+        var transparency = 0;
+        if (dTransparency) {
+            switch (transparencyType) {
+                case 'groupInstance': {
+                    var group = isGeoTexture ? MeshExporter.getGroup(groups, vertexIndex) : groups[vertexIndex];
+                    var idx = (instanceIndex * groupCount + group);
+                    transparency = tTransparency[idx] / 255;
+                    break;
+                }
+                case 'vertexInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex);
+                    transparency = tTransparency[idx] / 255;
+                    break;
+                }
+                case 'volumeInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex);
+                    transparency = interpolatedTransparency[idx] / 255;
+                    break;
+                }
+                default: throw new Error('Unsupported transparency type.');
+            }
+        }
+        return transparency;
+    };
     MeshExporter.prototype.addMesh = function (values, webgl, ctx) {
         return __awaiter(this, void 0, void 0, function () {
             var aPosition, aNormal, aGroup, originalData, indices, vertexCount, drawCount;