molstar 2.3.9 → 2.4.0

package/lib/commonjs/mol-geo/geometry/base.js.map

@@ -1 +1 @@
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+{"version":3,"file":"base.js","sourceRoot":"","sources":["../../../../src/mol-geo/geometry/base.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAGH,2CAA2C;AAE3C,+DAA6D;AAC7D,oEAAwE;AACxE,mDAA0E;AAE1E,oDAAwD;AACxD,qDAAwD;AACxD,yDAAkE;AAClE,wDAAgE;AAChE,0DAAwD;AAE3C,QAAA,iBAAiB,GAAG;IAC7B,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,SAAS,EAAE,EAAE;IACb,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,EAAE;IACZ,KAAK,EAAE,EAAE;IACT,OAAO,EAAE,EAAE;IACX,QAAQ,EAAE,EAAE;CACf,CAAC;AAEW,QAAA,kBAAkB,GAAG,MAAM,CAAC,IAAI,CAAC,yBAAiB,CAAoB,CAAC;AACvE,QAAA,oBAAoB,GAAG,kCAAE,CAAC,cAAc,CAAC,0BAAkB,CAAC,CAAC;AAE1E,EAAE;AAEW,QAAA,oBAAoB,GAAG;IAChC,YAAY,EAAE,kCAAE,CAAC,YAAY,CAAC,MAAM,EAAE;QAClC,IAAI,EAAE,kCAAE,CAAC,KAAK,CAAC,EAAE,CAAC;QAClB,EAAE,EAAE,kCAAE,CAAC,KAAK,CAAC;YACT,gBAAgB,EAAE,kCAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;YAChE,YAAY,EAAE,kCAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC;SAC5D,CAAC;QACF,GAAG,EAAE,kCAAE,CAAC,KAAK,CAAC,EAAE,CAAC;KACpB,CAAC;CACL,CAAC;AAGF,SAAgB,qBAAqB,CAAC,KAAqB;IACvD,OAAO,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;AAChC,CAAC;AAFD,sDAEC;AAED,SAAgB,sBAAsB,CAAC,YAA6D,EAAE,eAAyB,EAAE,UAAmB;IAChJ,IAAI,CAAC,YAAY,CAAC,IAAI,KAAK,IAAI,IAAI,CAAC,YAAY,CAAC,IAAI,KAAK,MAAM,IAAI,eAAe,CAAC,CAAC,IAAI,UAAU,IAAI,UAAU,GAAG,CAAC,EAAE;QACnH,IAAI,MAAM,GAAG,CAAC,CAAC;QACf,IAAI,YAAY,CAAC,IAAI,KAAK,IAAI,EAAE;YAC5B,UAAU,IAAI,YAAY,CAAC,MAAM,CAAC,gBAAgB,CAAC;YACnD,MAAM,GAAG,YAAY,CAAC,MAAM,CAAC,YAAY,CAAC;SAC7C;aAAM;YACH,6EAA6E;YAC7E,UAAU,IAAI,CAAC,GAAG,IAAA,wBAAU,EAAC,CAAC,EAAE,GAAG,EAAE,UAAU,CAAC,CAAC;YACjD,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,UAAU,CAAC,CAAC;YACvC,IAAI,UAAU,GAAG,GAAG;gBAAE,MAAM,GAAG,CAAC,CAAC;SACpC;QACD,OAAO,EAAE,UAAU,YAAA,EAAE,MAAM,QAAA,EAAE,CAAC;KACjC;IAAA,CAAC;AACN,CAAC;AAdD,wDAcC;AAED,EAAE;AAEF,IAAiB,YAAY,CAyD5B;AAzDD,WAAiB,YAAY;IACZ,mBAAM,GAAG;QAClB,KAAK,EAAE,kCAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,WAAW,EAAE,IAAI,EAAE,WAAW,EAAE,wDAAwD,EAAE,CAAC;QACpK,OAAO,EAAE,kCAAE,CAAC,MAAM,CAAgB,MAAM,EAAE,4BAAoB,EAAE,EAAE,WAAW,EAAE,IAAI,EAAE,WAAW,EAAE,iDAAiD,EAAE,CAAC;KACzJ,CAAC;IAGW,4BAAe,GAAY,EAAE,QAAQ,EAAE,SAAS,EAAE,CAAC;IACnD,mCAAsB,GAAY;QAC3C,QAAQ,EAAE,gBAAgB;QAC1B,MAAM,EAAE,UAAC,MAAyB,IAAK,OAAA,OAAO,MAAM,CAAC,OAAO,KAAK,WAAW,IAAI,MAAM,CAAC,OAAO,KAAK,QAAQ,EAApE,CAAoE;KAC9G,CAAC;IAIF,SAAgB,YAAY,CAAC,UAA4B,EAAE,SAAa,EAAE,SAAyB;QAAtE,2BAAA,EAAA,aAAa,kBAAU,CAAC,IAAI;QAAE,0BAAA,EAAA,aAAa;QACpE,IAAI,CAAC,SAAS;YAAE,SAAS,GAAG,IAAA,wCAAuB,GAAE,CAAC;QACtD,IAAM,gBAAgB,GAAG,IAAA,oCAAgB,EAAC,CAAC,EAAE,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,EAAE,cAAM,OAAA,uBAAY,EAAZ,CAAY,EAAE,KAAK,EAAE,cAAM,OAAA,KAAK,EAAL,CAAK,CAAC,CAAC;QAC3H,IAAM,KAAK,GAAU;YACjB,KAAK,EAAE,IAAA,2BAAiB,EAAC,EAAE,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,CAAC;YACnD,IAAI,EAAE,IAAA,0BAAgB,EAAC,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC;SACnD,CAAC;QACF,OAAO,EAAE,SAAS,WAAA,EAAE,gBAAgB,kBAAA,EAAE,KAAK,OAAA,EAAE,CAAC;IAClD,CAAC;IARe,yBAAY,eAQ3B,CAAA;IAED,SAAgB,YAAY,CAAC,KAAwB,EAAE,MAAc;QACjE,OAAO;YACH,KAAK,EAAE,oBAAS,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC;YACpC,MAAM,EAAE,oBAAS,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC;YACrC,YAAY,EAAE,oBAAS,CAAC,MAAM,CAAC,MAAM,CAAC,WAAW,CAAC;YAClD,WAAW,EAAE,oBAAS,CAAC,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC;YAChD,SAAS,EAAE,oBAAS,CAAC,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC;SAChD,CAAC;IACN,CAAC;IARe,yBAAY,eAQ3B,CAAA;IAED,SAAgB,YAAY,CAAC,MAAkB,EAAE,KAAwB;QACrE,oBAAS,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,uCAAuC;IACjG,CAAC;IAFe,yBAAY,eAE3B,CAAA;IAED,SAAgB,qBAAqB,CAAC,KAAsC;QAAtC,sBAAA,EAAA,UAAsC;QACxE,IAAM,MAAM,GAAG,KAAK,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,KAAK,CAAC,CAAC;QACpE,OAAO;YACH,QAAQ,EAAE,KAAK;YACf,OAAO,EAAE,IAAI;YACb,WAAW,EAAE,CAAC;YACd,QAAQ,EAAE,IAAI;YACd,SAAS,EAAE,KAAK;YAChB,MAAM,QAAA;YACN,UAAU,EAAE,MAAM;YAClB,MAAM,EAAE,KAAK;SAChB,CAAC;IACN,CAAC;IAZe,kCAAqB,wBAYpC,CAAA;IAED,SAAgB,qBAAqB,CAAC,KAAsB,EAAE,KAAwB;QAClF,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,IAAI,CAAC,CAAC;QACpD,KAAK,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC;IACpC,CAAC;IAHe,kCAAqB,wBAGpC,CAAA;AACL,CAAC,EAzDgB,YAAY,GAAZ,oBAAY,KAAZ,oBAAY,QAyD5B"}

package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts

@@ -34,7 +34,7 @@ export declare namespace DirectVolume {
     function createRenderModeParam(stats?: Grid['stats']): PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -56,7 +56,7 @@ export declare namespace DirectVolume {
         renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
             controlPoints: Vec2[];
             list: {
-                kind: "interpolate" | "set";
+                kind: "set" | "interpolate";
                 colors: import("../../../mol-util/color/color").ColorListEntry[];
             };
         }>, "volume"> | PD.NamedParams<PD.Normalize<{

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

@@ -16,7 +16,7 @@ export declare const InterpolationTypes: {
     bspline: string;
 };
 export declare type InterpolationTypes = keyof typeof InterpolationTypes;
-export declare const InterpolationTypeNames: ("nearest" | "bspline" | "catmulrom" | "mitchell")[];
+export declare const InterpolationTypeNames: ("bspline" | "nearest" | "catmulrom" | "mitchell")[];
 export { Image };
 interface Image {
     readonly kind: 'image';
@@ -31,7 +31,7 @@ declare namespace Image {
     function create(imageTexture: TextureImage<Uint8Array>, corners: Float32Array, groupTexture: TextureImage<Uint8Array>, image?: Image): Image;
     function createEmpty(image?: Image): Image;
     const Params: {
-        interpolation: PD.Select<"nearest" | "bspline" | "catmulrom" | "mitchell">;
+        interpolation: PD.Select<"bspline" | "nearest" | "catmulrom" | "mitchell">;
         alpha: PD.Numeric;
         quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     };

package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
+import { MeshValues } from '../../../mol-gl/renderable/mesh';
 import { TextureImage } from '../../../mol-gl/renderable/util';
 import { WebGLContext } from '../../../mol-gl/webgl/context';
 import { Texture } from '../../../mol-gl/webgl/texture';
@@ -20,6 +21,7 @@ interface ColorSmoothingInput {
     colorType: 'group' | 'groupInstance';
     boundingSphere: Sphere3D;
     invariantBoundingSphere: Sphere3D;
+    itemSize: 4 | 3 | 1;
 }
 export declare function calcMeshColorSmoothing(input: ColorSmoothingInput, resolution: number, stride: number, webgl?: WebGLContext, texture?: Texture): {
     kind: "volume";
@@ -48,8 +50,13 @@ interface ColorInterpolationInput {
     gridTexDim: Vec2;
     gridDim: Vec3;
     gridTransform: Vec4;
-    vertexStride: number;
-    colorStride: number;
+    vertexStride: 3 | 4;
+    colorStride: 1 | 3 | 4;
+    outputStride: 1 | 3 | 4;
+    itemOffset?: 0 | 1 | 2 | 3;
 }
 export declare function getTrilinearlyInterpolated(input: ColorInterpolationInput): TextureImage<Uint8Array>;
+export declare function applyMeshColorSmoothing(values: MeshValues, resolution: number, stride: number, webgl?: WebGLContext, colorTexture?: Texture): void;
+export declare function applyMeshOverpaintSmoothing(values: MeshValues, resolution: number, stride: number, webgl?: WebGLContext, colorTexture?: Texture): void;
+export declare function applyMeshTransparencySmoothing(values: MeshValues, resolution: number, stride: number, webgl?: WebGLContext, colorTexture?: Texture): void;
 export {};

package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js

@@ -5,14 +5,15 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTrilinearlyInterpolated = exports.calcMeshColorSmoothing = void 0;
+exports.applyMeshTransparencySmoothing = exports.applyMeshOverpaintSmoothing = exports.applyMeshColorSmoothing = exports.getTrilinearlyInterpolated = exports.calcMeshColorSmoothing = void 0;
 var util_1 = require("../../../mol-gl/renderable/util");
 var geometry_1 = require("../../../mol-math/geometry");
+var interpolate_1 = require("../../../mol-math/interpolate");
 var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var util_2 = require("../../../mol-repr/volume/util");
-var color_1 = require("../../../mol-util/color");
+var mol_util_1 = require("../../../mol-util");
 function calcMeshColorSmoothing(input, resolution, stride, webgl, texture) {
-    var colorType = input.colorType, vertexCount = input.vertexCount, groupCount = input.groupCount, positionBuffer = input.positionBuffer, transformBuffer = input.transformBuffer, groupBuffer = input.groupBuffer;
+    var colorType = input.colorType, vertexCount = input.vertexCount, groupCount = input.groupCount, positionBuffer = input.positionBuffer, transformBuffer = input.transformBuffer, groupBuffer = input.groupBuffer, itemSize = input.itemSize;
     var isInstanceType = colorType.endsWith('Instance');
     var box = geometry_1.Box3D.fromSphere3D((0, geometry_1.Box3D)(), isInstanceType ? input.boundingSphere : input.invariantBoundingSphere);
     var scaleFactor = 1 / resolution;
@@ -24,7 +25,6 @@ function calcMeshColorSmoothing(input, resolution, stride, webgl, texture) {
     var xn = gridDim[0], yn = gridDim[1];
     var _a = (0, util_2.getVolumeTexture2dLayout)(gridDim), width = _a.width, height = _a.height;
     // console.log({ width, height, dim });
-    var itemSize = 3;
     var data = new Float32Array(width * height * itemSize);
     var count = new Float32Array(width * height);
     var grid = new Uint8Array(width * height * itemSize);
@@ -53,10 +53,7 @@ function calcMeshColorSmoothing(input, resolution, stride, webgl, texture) {
             var y = Math.floor(vy);
             var z = Math.floor(vz);
             // group colors
-            var ci = i * groupCount + groupBuffer[j];
-            var r = colors[ci * 3];
-            var g = colors[ci * 3 + 1];
-            var b = colors[ci * 3 + 2];
+            var ci = (i * groupCount + groupBuffer[j]) * itemSize;
             // Extents of grid to consider for this atom
             var begX = Math.max(0, x - p);
             var begY = Math.max(0, y - p);
@@ -78,33 +75,36 @@ function calcMeshColorSmoothing(input, resolution, stride, webgl, texture) {
                             continue;
                         var s = p - d;
                         var index = getIndex(xi, yi, zi);
-                        data[index] += r * s;
-                        data[index + 1] += g * s;
-                        data[index + 2] += b * s;
-                        count[index / 3] += s;
+                        for (var k = 0; k < itemSize; ++k) {
+                            data[index + k] += colors[ci + k] * s;
+                        }
+                        count[index / itemSize] += s;
                     }
                 }
             }
         }
     }
     for (var i = 0, il = count.length; i < il; ++i) {
-        var i3 = i * 3;
+        var is = i * itemSize;
         var c = count[i];
-        grid[i3] = Math.round(data[i3] / c);
-        grid[i3 + 1] = Math.round(data[i3 + 1] / c);
-        grid[i3 + 2] = Math.round(data[i3 + 2] / c);
+        for (var k = 0; k < itemSize; ++k) {
+            grid[is + k] = Math.round(data[is + k] / c);
+        }
     }
     var gridTexDim = linear_algebra_1.Vec2.create(width, height);
     var gridTransform = linear_algebra_1.Vec4.create(min[0], min[1], min[2], scaleFactor);
     var type = isInstanceType ? 'volumeInstance' : 'volume';
     if (webgl) {
-        if (!texture)
-            texture = webgl.resources.texture('image-uint8', 'rgb', 'ubyte', 'linear');
+        if (!texture) {
+            var format = itemSize === 4 ? 'rgba' :
+                itemSize === 3 ? 'rgb' : 'alpha';
+            texture = webgl.resources.texture('image-uint8', format, 'ubyte', 'linear');
+        }
         texture.load(textureImage);
         return { kind: 'volume', texture: texture, gridTexDim: gridTexDim, gridDim: gridDim, gridTransform: gridTransform, type: type };
     }
     else {
-        var interpolated = getTrilinearlyInterpolated({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: transformBuffer, positionBuffer: positionBuffer, colorType: type, grid: grid, gridDim: gridDim, gridTexDim: gridTexDim, gridTransform: gridTransform, vertexStride: 3, colorStride: 3 });
+        var interpolated = getTrilinearlyInterpolated({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: transformBuffer, positionBuffer: positionBuffer, colorType: type, grid: grid, gridDim: gridDim, gridTexDim: gridTexDim, gridTransform: gridTransform, vertexStride: 3, colorStride: itemSize, outputStride: itemSize });
         return {
             kind: 'vertex',
             texture: interpolated,
@@ -116,9 +116,14 @@ function calcMeshColorSmoothing(input, resolution, stride, webgl, texture) {
 exports.calcMeshColorSmoothing = calcMeshColorSmoothing;
 function getTrilinearlyInterpolated(input) {
     var vertexCount = input.vertexCount, positionBuffer = input.positionBuffer, transformBuffer = input.transformBuffer, grid = input.grid, gridDim = input.gridDim, gridTexDim = input.gridTexDim, gridTransform = input.gridTransform, vertexStride = input.vertexStride, colorStride = input.colorStride;
+    var itemOffset = input.itemOffset || 0;
+    var outputStride = input.outputStride;
+    if (outputStride + itemOffset > colorStride) {
+        throw new Error('outputStride + itemOffset must NOT be larger than colorStride');
+    }
     var isInstanceType = input.colorType.endsWith('Instance');
     var instanceCount = isInstanceType ? input.instanceCount : 1;
-    var image = (0, util_1.createTextureImage)(Math.max(1, instanceCount * vertexCount), 3, Uint8Array);
+    var image = (0, util_1.createTextureImage)(Math.max(1, instanceCount * vertexCount), outputStride, Uint8Array);
     var array = image.array;
     var xn = gridDim[0], yn = gridDim[1];
     var width = gridTexDim[0];
@@ -149,24 +154,138 @@ function getTrilinearlyInterpolated(input) {
             var x0 = v0[0], y0 = v0[1], z0 = v0[2];
             var x1 = v1[0], y1 = v1[1], z1 = v1[2];
             var xd = vd[0], yd = vd[1], zd = vd[2];
-            var s000 = color_1.Color.fromArray(grid, getIndex(x0, y0, z0));
-            var s100 = color_1.Color.fromArray(grid, getIndex(x1, y0, z0));
-            var s001 = color_1.Color.fromArray(grid, getIndex(x0, y0, z1));
-            var s101 = color_1.Color.fromArray(grid, getIndex(x1, y0, z1));
-            var s010 = color_1.Color.fromArray(grid, getIndex(x0, y1, z0));
-            var s110 = color_1.Color.fromArray(grid, getIndex(x1, y1, z0));
-            var s011 = color_1.Color.fromArray(grid, getIndex(x0, y1, z1));
-            var s111 = color_1.Color.fromArray(grid, getIndex(x1, y1, z1));
-            var s00 = color_1.Color.interpolate(s000, s100, xd);
-            var s01 = color_1.Color.interpolate(s001, s101, xd);
-            var s10 = color_1.Color.interpolate(s010, s110, xd);
-            var s11 = color_1.Color.interpolate(s011, s111, xd);
-            var s0 = color_1.Color.interpolate(s00, s10, yd);
-            var s1 = color_1.Color.interpolate(s01, s11, yd);
-            color_1.Color.toArray(color_1.Color.interpolate(s0, s1, zd), array, (i * vertexCount + j) * 3);
+            var i000 = getIndex(x0, y0, z0) + itemOffset;
+            var i100 = getIndex(x1, y0, z0) + itemOffset;
+            var i001 = getIndex(x0, y0, z1) + itemOffset;
+            var i101 = getIndex(x1, y0, z1) + itemOffset;
+            var i010 = getIndex(x0, y1, z0) + itemOffset;
+            var i110 = getIndex(x1, y1, z0) + itemOffset;
+            var i011 = getIndex(x0, y1, z1) + itemOffset;
+            var i111 = getIndex(x1, y1, z1) + itemOffset;
+            var o = (i * vertexCount + j) * outputStride;
+            for (var k = 0; k < outputStride; ++k) {
+                var s000 = grid[i000 + k];
+                var s100 = grid[i100 + k];
+                var s001 = grid[i001 + k];
+                var s101 = grid[i101 + k];
+                var s010 = grid[i010 + k];
+                var s110 = grid[i110 + k];
+                var s011 = grid[i011 + k];
+                var s111 = grid[i111 + k];
+                var s00 = (0, interpolate_1.lerp)(s000, s100, xd);
+                var s01 = (0, interpolate_1.lerp)(s001, s101, xd);
+                var s10 = (0, interpolate_1.lerp)(s010, s110, xd);
+                var s11 = (0, interpolate_1.lerp)(s011, s111, xd);
+                var s0 = (0, interpolate_1.lerp)(s00, s10, yd);
+                var s1 = (0, interpolate_1.lerp)(s01, s11, yd);
+                array[o + k] = (0, interpolate_1.lerp)(s0, s1, zd);
+            }
         }
     }
     return image;
 }
 exports.getTrilinearlyInterpolated = getTrilinearlyInterpolated;
+//
+function isSupportedColorType(x) {
+    return x === 'group' || x === 'groupInstance';
+}
+function applyMeshColorSmoothing(values, resolution, stride, webgl, colorTexture) {
+    if (!isSupportedColorType(values.dColorType.ref.value))
+        return;
+    var smoothingData = calcMeshColorSmoothing({
+        vertexCount: values.uVertexCount.ref.value,
+        instanceCount: values.uInstanceCount.ref.value,
+        groupCount: values.uGroupCount.ref.value,
+        transformBuffer: values.aTransform.ref.value,
+        instanceBuffer: values.aInstance.ref.value,
+        positionBuffer: values.aPosition.ref.value,
+        groupBuffer: values.aGroup.ref.value,
+        colorData: values.tColor.ref.value,
+        colorType: values.dColorType.ref.value,
+        boundingSphere: values.boundingSphere.ref.value,
+        invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
+        itemSize: 3
+    }, resolution, stride, webgl, colorTexture);
+    if (smoothingData.kind === 'volume') {
+        mol_util_1.ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
+        mol_util_1.ValueCell.update(values.tColorGrid, smoothingData.texture);
+        mol_util_1.ValueCell.update(values.uColorTexDim, smoothingData.gridTexDim);
+        mol_util_1.ValueCell.update(values.uColorGridDim, smoothingData.gridDim);
+        mol_util_1.ValueCell.update(values.uColorGridTransform, smoothingData.gridTransform);
+    }
+    else if (smoothingData.kind === 'vertex') {
+        mol_util_1.ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
+        mol_util_1.ValueCell.update(values.tColor, smoothingData.texture);
+        mol_util_1.ValueCell.update(values.uColorTexDim, smoothingData.texDim);
+    }
+}
+exports.applyMeshColorSmoothing = applyMeshColorSmoothing;
+function isSupportedOverpaintType(x) {
+    return x === 'groupInstance';
+}
+function applyMeshOverpaintSmoothing(values, resolution, stride, webgl, colorTexture) {
+    if (!isSupportedOverpaintType(values.dOverpaintType.ref.value))
+        return;
+    var smoothingData = calcMeshColorSmoothing({
+        vertexCount: values.uVertexCount.ref.value,
+        instanceCount: values.uInstanceCount.ref.value,
+        groupCount: values.uGroupCount.ref.value,
+        transformBuffer: values.aTransform.ref.value,
+        instanceBuffer: values.aInstance.ref.value,
+        positionBuffer: values.aPosition.ref.value,
+        groupBuffer: values.aGroup.ref.value,
+        colorData: values.tOverpaint.ref.value,
+        colorType: values.dOverpaintType.ref.value,
+        boundingSphere: values.boundingSphere.ref.value,
+        invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
+        itemSize: 4
+    }, resolution, stride, webgl, colorTexture);
+    if (smoothingData.kind === 'volume') {
+        mol_util_1.ValueCell.updateIfChanged(values.dOverpaintType, smoothingData.type);
+        mol_util_1.ValueCell.update(values.tOverpaintGrid, smoothingData.texture);
+        mol_util_1.ValueCell.update(values.uOverpaintTexDim, smoothingData.gridTexDim);
+        mol_util_1.ValueCell.update(values.uOverpaintGridDim, smoothingData.gridDim);
+        mol_util_1.ValueCell.update(values.uOverpaintGridTransform, smoothingData.gridTransform);
+    }
+    else if (smoothingData.kind === 'vertex') {
+        mol_util_1.ValueCell.updateIfChanged(values.dOverpaintType, smoothingData.type);
+        mol_util_1.ValueCell.update(values.tOverpaint, smoothingData.texture);
+        mol_util_1.ValueCell.update(values.uOverpaintTexDim, smoothingData.texDim);
+    }
+}
+exports.applyMeshOverpaintSmoothing = applyMeshOverpaintSmoothing;
+function isSupportedTransparencyType(x) {
+    return x === 'groupInstance';
+}
+function applyMeshTransparencySmoothing(values, resolution, stride, webgl, colorTexture) {
+    if (!isSupportedTransparencyType(values.dTransparencyType.ref.value))
+        return;
+    var smoothingData = calcMeshColorSmoothing({
+        vertexCount: values.uVertexCount.ref.value,
+        instanceCount: values.uInstanceCount.ref.value,
+        groupCount: values.uGroupCount.ref.value,
+        transformBuffer: values.aTransform.ref.value,
+        instanceBuffer: values.aInstance.ref.value,
+        positionBuffer: values.aPosition.ref.value,
+        groupBuffer: values.aGroup.ref.value,
+        colorData: values.tTransparency.ref.value,
+        colorType: values.dTransparencyType.ref.value,
+        boundingSphere: values.boundingSphere.ref.value,
+        invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
+        itemSize: 1
+    }, resolution, stride, webgl, colorTexture);
+    if (smoothingData.kind === 'volume') {
+        mol_util_1.ValueCell.updateIfChanged(values.dTransparencyType, smoothingData.type);
+        mol_util_1.ValueCell.update(values.tTransparencyGrid, smoothingData.texture);
+        mol_util_1.ValueCell.update(values.uTransparencyTexDim, smoothingData.gridTexDim);
+        mol_util_1.ValueCell.update(values.uTransparencyGridDim, smoothingData.gridDim);
+        mol_util_1.ValueCell.update(values.uTransparencyGridTransform, smoothingData.gridTransform);
+    }
+    else if (smoothingData.kind === 'vertex') {
+        mol_util_1.ValueCell.updateIfChanged(values.dTransparencyType, smoothingData.type);
+        mol_util_1.ValueCell.update(values.tTransparency, smoothingData.texture);
+        mol_util_1.ValueCell.update(values.uTransparencyTexDim, smoothingData.texDim);
+    }
+}
+exports.applyMeshTransparencySmoothing = applyMeshTransparencySmoothing;
 //# sourceMappingURL=color-smoothing.js.map

package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js.map

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package/lib/commonjs/mol-geo/geometry/overpaint-data.d.ts

@@ -1,16 +1,21 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { ValueCell } from '../../mol-util/value-cell';
-import { Vec2 } from '../../mol-math/linear-algebra';
+import { Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
 import { TextureImage } from '../../mol-gl/renderable/util';
 import { Color } from '../../mol-util/color';
+import { Texture } from '../../mol-gl/webgl/texture';
 export declare type OverpaintData = {
     tOverpaint: ValueCell<TextureImage<Uint8Array>>;
     uOverpaintTexDim: ValueCell<Vec2>;
     dOverpaint: ValueCell<boolean>;
+    tOverpaintGrid: ValueCell<Texture>;
+    uOverpaintGridDim: ValueCell<Vec3>;
+    uOverpaintGridTransform: ValueCell<Vec4>;
+    dOverpaintType: ValueCell<string>;
 };
 export declare function applyOverpaintColor(array: Uint8Array, start: number, end: number, color: Color): boolean;
 export declare function clearOverpaint(array: Uint8Array, start: number, end: number): boolean;

package/lib/commonjs/mol-geo/geometry/overpaint-data.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,6 +10,7 @@ var value_cell_1 = require("../../mol-util/value-cell");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var util_1 = require("../../mol-gl/renderable/util");
 var color_1 = require("../../mol-util/color");
+var texture_1 = require("../../mol-gl/webgl/texture");
 function applyOverpaintColor(array, start, end, color) {
     for (var i = start; i < end; ++i) {
         color_1.Color.toArray(color, array, i * 4);
@@ -36,6 +37,10 @@ function createOverpaint(count, overpaintData) {
             tOverpaint: value_cell_1.ValueCell.create(overpaint),
             uOverpaintTexDim: value_cell_1.ValueCell.create(linear_algebra_1.Vec2.create(overpaint.width, overpaint.height)),
             dOverpaint: value_cell_1.ValueCell.create(count > 0),
+            tOverpaintGrid: value_cell_1.ValueCell.create((0, texture_1.createNullTexture)()),
+            uOverpaintGridDim: value_cell_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)),
+            uOverpaintGridTransform: value_cell_1.ValueCell.create(linear_algebra_1.Vec4.create(0, 0, 0, 1)),
+            dOverpaintType: value_cell_1.ValueCell.create('groupInstance'),
         };
     }
 }
@@ -52,6 +57,10 @@ function createEmptyOverpaint(overpaintData) {
             tOverpaint: value_cell_1.ValueCell.create(emptyOverpaintTexture),
             uOverpaintTexDim: value_cell_1.ValueCell.create(linear_algebra_1.Vec2.create(1, 1)),
             dOverpaint: value_cell_1.ValueCell.create(false),
+            tOverpaintGrid: value_cell_1.ValueCell.create((0, texture_1.createNullTexture)()),
+            uOverpaintGridDim: value_cell_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)),
+            uOverpaintGridTransform: value_cell_1.ValueCell.create(linear_algebra_1.Vec4.create(0, 0, 0, 1)),
+            dOverpaintType: value_cell_1.ValueCell.create('groupInstance'),
         };
     }
 }

package/lib/commonjs/mol-geo/geometry/overpaint-data.js.map

@@ -1 +1 @@
-{"version":3,"file":"overpaint-data.js","sourceRoot":"","sources":["../../../../src/mol-geo/geometry/overpaint-data.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAEH,wDAAsD;AACtD,gEAAqD;AACrD,qDAAgF;AAChF,8CAA6C;AAQ7C,SAAgB,mBAAmB,CAAC,KAAiB,EAAE,KAAa,EAAE,GAAW,EAAE,KAAY;IAC3F,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,GAAG,EAAE,EAAE,CAAC,EAAE;QAC9B,aAAK,CAAC,OAAO,CAAC,KAAK,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;QACnC,KAAK,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC;KAC1B;IACD,OAAO,IAAI,CAAC;AAChB,CAAC;AAND,kDAMC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,KAAa,EAAE,GAAW;IACxE,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,CAAC,CAAC;IAClC,OAAO,IAAI,CAAC;AAChB,CAAC;AAHD,wCAGC;AAED,SAAgB,eAAe,CAAC,KAAa,EAAE,aAA6B;IACxE,IAAM,SAAS,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC,EAAE,UAAU,EAAE,aAAa,IAAI,aAAa,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;IACnI,IAAI,aAAa,EAAE;QACf,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACtD,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,gBAAgB,EAAE,qBAAI,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;QACjG,sBAAS,CAAC,eAAe,CAAC,aAAa,CAAC,UAAU,EAAE,KAAK,GAAG,CAAC,CAAC,CAAC;QAC/D,OAAO,aAAa,CAAC;KACxB;SAAM;QACH,OAAO;YACH,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,SAAS,CAAC;YACvC,gBAAgB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;YAClF,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,CAAC;SAC1C,CAAC;KACL;AACL,CAAC;AAdD,0CAcC;AAED,IAAM,qBAAqB,GAAG,EAAE,KAAK,EAAE,IAAI,UAAU,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC;AAChF,SAAgB,oBAAoB,CAAC,aAA6B;IAC9D,IAAI,aAAa,EAAE;QACf,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,UAAU,EAAE,qBAAqB,CAAC,CAAC;QAClE,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,gBAAgB,EAAE,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QACpE,OAAO,aAAa,CAAC;KACxB;SAAM;QACH,OAAO;YACH,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAqB,CAAC;YACnD,gBAAgB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YACrD,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,KAAK,CAAC;SACtC,CAAC;KACL;AACL,CAAC;AAZD,oDAYC"}
+{"version":3,"file":"overpaint-data.js","sourceRoot":"","sources":["../../../../src/mol-geo/geometry/overpaint-data.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAEH,wDAAsD;AACtD,gEAAiE;AACjE,qDAAgF;AAChF,8CAA6C;AAC7C,sDAAwE;AAaxE,SAAgB,mBAAmB,CAAC,KAAiB,EAAE,KAAa,EAAE,GAAW,EAAE,KAAY;IAC3F,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,GAAG,EAAE,EAAE,CAAC,EAAE;QAC9B,aAAK,CAAC,OAAO,CAAC,KAAK,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;QACnC,KAAK,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC;KAC1B;IACD,OAAO,IAAI,CAAC;AAChB,CAAC;AAND,kDAMC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,KAAa,EAAE,GAAW;IACxE,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,CAAC,CAAC;IAClC,OAAO,IAAI,CAAC;AAChB,CAAC;AAHD,wCAGC;AAED,SAAgB,eAAe,CAAC,KAAa,EAAE,aAA6B;IACxE,IAAM,SAAS,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,CAAC,EAAE,UAAU,EAAE,aAAa,IAAI,aAAa,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;IACnI,IAAI,aAAa,EAAE;QACf,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACtD,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,gBAAgB,EAAE,qBAAI,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;QACjG,sBAAS,CAAC,eAAe,CAAC,aAAa,CAAC,UAAU,EAAE,KAAK,GAAG,CAAC,CAAC,CAAC;QAC/D,OAAO,aAAa,CAAC;KACxB;SAAM;QACH,OAAO;YACH,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,SAAS,CAAC;YACvC,gBAAgB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;YAClF,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,CAAC;YAEvC,cAAc,EAAE,sBAAS,CAAC,MAAM,CAAC,IAAA,2BAAiB,GAAE,CAAC;YACrD,iBAAiB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YACzD,uBAAuB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YAClE,cAAc,EAAE,sBAAS,CAAC,MAAM,CAAC,eAAe,CAAC;SACpD,CAAC;KACL;AACL,CAAC;AAnBD,0CAmBC;AAED,IAAM,qBAAqB,GAAG,EAAE,KAAK,EAAE,IAAI,UAAU,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC;AAChF,SAAgB,oBAAoB,CAAC,aAA6B;IAC9D,IAAI,aAAa,EAAE;QACf,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,UAAU,EAAE,qBAAqB,CAAC,CAAC;QAClE,sBAAS,CAAC,MAAM,CAAC,aAAa,CAAC,gBAAgB,EAAE,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QACpE,OAAO,aAAa,CAAC;KACxB;SAAM;QACH,OAAO;YACH,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAqB,CAAC;YACnD,gBAAgB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YACrD,UAAU,EAAE,sBAAS,CAAC,MAAM,CAAC,KAAK,CAAC;YAEnC,cAAc,EAAE,sBAAS,CAAC,MAAM,CAAC,IAAA,2BAAiB,GAAE,CAAC;YACrD,iBAAiB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YACzD,uBAAuB,EAAE,sBAAS,CAAC,MAAM,CAAC,qBAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YAClE,cAAc,EAAE,sBAAS,CAAC,MAAM,CAAC,eAAe,CAAC;SACpD,CAAC;KACL;AACL,CAAC;AAjBD,oDAiBC"}

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

@@ -35,7 +35,6 @@ export declare namespace Spheres {
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
         alpha: PD.Numeric;
-        /** Number of spheres */
         quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts

@@ -8,7 +8,7 @@ import { Texture } from '../../../mol-gl/webgl/texture';
 import { ValueSpec, AttributeSpec, UniformSpec, TextureSpec, DefineSpec } from '../../../mol-gl/renderable/schema';
 import { Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
 import { Sphere3D } from '../../../mol-math/geometry';
-import { TextureImage } from '../../../mol-gl/renderable/util';
+import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
 export declare const ColorAccumulateSchema: {
     drawCount: ValueSpec<"number">;
     instanceCount: ValueSpec<"number">;
@@ -23,7 +23,7 @@ export declare const ColorAccumulateSchema: {
     tPosition: TextureSpec<"texture">;
     tGroup: TextureSpec<"texture">;
     uColorTexDim: UniformSpec<"v2">;
-    tColor: TextureSpec<"image-uint8">;
+    tColor: TextureSpec<"texture">;
     dColorType: DefineSpec<"string">;
     uCurrentSlice: UniformSpec<"f">;
     uCurrentX: UniformSpec<"f">;
@@ -40,11 +40,12 @@ interface AccumulateInput {
     instanceBuffer: Float32Array;
     positionTexture: Texture;
     groupTexture: Texture;
-    colorData: TextureImage<Uint8Array>;
+    colorData: Texture;
     colorType: 'group' | 'groupInstance';
 }
 export declare const ColorNormalizeSchema: {
     tColor: TextureSpec<"texture">;
+    tCount: TextureSpec<"texture">;
     uTexSize: UniformSpec<"v2">;
     drawCount: ValueSpec<"number">;
     instanceCount: ValueSpec<"number">;
@@ -62,4 +63,7 @@ export declare function calcTextureMeshColorSmoothing(input: ColorSmoothingInput
     gridTransform: Vec4;
     type: string;
 };
+export declare function applyTextureMeshColorSmoothing(values: TextureMeshValues, resolution: number, stride: number, webgl: WebGLContext, colorTexture?: Texture): void;
+export declare function applyTextureMeshOverpaintSmoothing(values: TextureMeshValues, resolution: number, stride: number, webgl: WebGLContext, colorTexture?: Texture): void;
+export declare function applyTextureMeshTransparencySmoothing(values: TextureMeshValues, resolution: number, stride: number, webgl: WebGLContext, colorTexture?: Texture): void;
 export {};