npm - molstar - Versions diffs - 2.3.7 → 2.4.1 - Mend

molstar 2.3.7 → 2.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1699) hide show

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

@@ -72,7 +72,7 @@ export declare namespace DirectVolume {
         stepsPerCell: PD.Numeric;
         jumpLength: PD.Numeric;
         alpha: PD.Numeric;
-        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<DirectVolume, Params>;

package/lib/mol-geo/geometry/image/image.d.ts CHANGED Viewed

@@ -16,7 +16,7 @@ export declare const InterpolationTypes: {
     bspline: string;
 };
 export declare type InterpolationTypes = keyof typeof InterpolationTypes;
-export declare const InterpolationTypeNames: ("bspline" | "nearest" | "catmulrom" | "mitchell")[];
+export declare const InterpolationTypeNames: ("nearest" | "bspline" | "catmulrom" | "mitchell")[];
 export { Image };
 interface Image {
     readonly kind: 'image';
@@ -31,9 +31,9 @@ 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<"bspline" | "nearest" | "catmulrom" | "mitchell">;
+        interpolation: PD.Select<"nearest" | "bspline" | "catmulrom" | "mitchell">;
         alpha: PD.Numeric;
-        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Image, Params>;

package/lib/mol-geo/geometry/lines/lines.d.ts CHANGED Viewed

@@ -40,7 +40,7 @@ export declare namespace Lines {
         sizeFactor: PD.Numeric;
         lineSizeAttenuation: PD.BooleanParam;
         alpha: PD.Numeric;
-        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Lines, Params>;

package/lib/mol-geo/geometry/mesh/builder/tube.js CHANGED Viewed

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Vec3 } from '../../../../mol-math/linear-algebra';
-import { ChunkedArray } from '../../../../mol-data/util';
+import { cantorPairing, ChunkedArray } from '../../../../mol-data/util';
 var normalVector = Vec3();
 var surfacePoint = Vec3();
 var controlPoint = Vec3();
@@ -30,24 +30,26 @@ var v3dot = Vec3.dot;
 var v3unitX = Vec3.unitX;
 var caAdd3 = ChunkedArray.add3;
 var CosSinCache = new Map();
-function getCosSin(radialSegments) {
-    if (!CosSinCache.has(radialSegments)) {
+function getCosSin(radialSegments, shift) {
+    var offset = shift ? 1 : 0;
+    var hash = cantorPairing(radialSegments, offset);
+    if (!CosSinCache.has(hash)) {
         var cos = [];
         var sin = [];
         for (var j = 0; j < radialSegments; ++j) {
-            var t = 2 * Math.PI * j / radialSegments;
+            var t = (j * 2 + offset) / radialSegments * Math.PI;
             cos[j] = Math.cos(t);
             sin[j] = Math.sin(t);
         }
-        CosSinCache.set(radialSegments, { cos: cos, sin: sin });
+        CosSinCache.set(hash, { cos: cos, sin: sin });
     }
-    return CosSinCache.get(radialSegments);
+    return CosSinCache.get(hash);
 }
 export function addTube(state, controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, startCap, endCap, crossSection) {
     var currentGroup = state.currentGroup, vertices = state.vertices, normals = state.normals, indices = state.indices, groups = state.groups;
     var vertexCount = vertices.elementCount;
-    var _a = getCosSin(radialSegments), cos = _a.cos, sin = _a.sin;
-    var q1 = radialSegments / 4;
+    var _a = getCosSin(radialSegments, crossSection === 'rounded'), cos = _a.cos, sin = _a.sin;
+    var q1 = Math.round(radialSegments / 4);
     var q3 = q1 * 3;
     for (var i = 0; i <= linearSegments; ++i) {
         var i3 = i * 3;
@@ -64,7 +66,15 @@ export function addTube(state, controlPoints, normalVectors, binormalVectors, li
                     ? (j < q1 || j >= q3) ? height - width : -height + width
                     : (j >= q1 && j < q3) ? -height + width : height - width;
                 v3scaleAndAdd(surfacePoint, surfacePoint, u, h);
-                add2AndScale2(normalVector, u, v, cos[j], sin[j]);
+                if (j === q1 || j === q1 - 1) {
+                    add2AndScale2(normalVector, u, v, 0, 1);
+                }
+                else if (j === q3 || j === q3 - 1) {
+                    add2AndScale2(normalVector, u, v, 0, -1);
+                }
+                else {
+                    add2AndScale2(normalVector, u, v, cos[j], sin[j]);
+                }
             }
             else {
                 add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);

package/lib/mol-geo/geometry/mesh/builder/tube.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-geo/geometry/mesh/color-smoothing.d.ts CHANGED Viewed

@@ -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/mol-geo/geometry/mesh/color-smoothing.js CHANGED Viewed

@@ -5,11 +5,12 @@
  */
 import { createTextureImage } from '../../../mol-gl/renderable/util';
 import { Box3D } from '../../../mol-math/geometry';
+import { lerp } from '../../../mol-math/interpolate';
 import { Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
 import { getVolumeTexture2dLayout } from '../../../mol-repr/volume/util';
-import { Color } from '../../../mol-util/color';
+import { ValueCell } from '../../../mol-util';
 export 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 = Box3D.fromSphere3D(Box3D(), isInstanceType ? input.boundingSphere : input.invariantBoundingSphere);
     var scaleFactor = 1 / resolution;
@@ -21,7 +22,6 @@ export function calcMeshColorSmoothing(input, resolution, stride, webgl, texture
     var xn = gridDim[0], yn = gridDim[1];
     var _a = 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);
@@ -50,10 +50,7 @@ export 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);
@@ -75,33 +72,36 @@ export 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 = Vec2.create(width, height);
     var gridTransform = 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,
@@ -112,9 +112,14 @@ export function calcMeshColorSmoothing(input, resolution, stride, webgl, texture
 }
 export 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 = createTextureImage(Math.max(1, instanceCount * vertexCount), 3, Uint8Array);
+    var image = createTextureImage(Math.max(1, instanceCount * vertexCount), outputStride, Uint8Array);
     var array = image.array;
     var xn = gridDim[0], yn = gridDim[1];
     var width = gridTexDim[0];
@@ -145,23 +150,134 @@ export 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.fromArray(grid, getIndex(x0, y0, z0));
-            var s100 = Color.fromArray(grid, getIndex(x1, y0, z0));
-            var s001 = Color.fromArray(grid, getIndex(x0, y0, z1));
-            var s101 = Color.fromArray(grid, getIndex(x1, y0, z1));
-            var s010 = Color.fromArray(grid, getIndex(x0, y1, z0));
-            var s110 = Color.fromArray(grid, getIndex(x1, y1, z0));
-            var s011 = Color.fromArray(grid, getIndex(x0, y1, z1));
-            var s111 = Color.fromArray(grid, getIndex(x1, y1, z1));
-            var s00 = Color.interpolate(s000, s100, xd);
-            var s01 = Color.interpolate(s001, s101, xd);
-            var s10 = Color.interpolate(s010, s110, xd);
-            var s11 = Color.interpolate(s011, s111, xd);
-            var s0 = Color.interpolate(s00, s10, yd);
-            var s1 = Color.interpolate(s01, s11, yd);
-            Color.toArray(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 = lerp(s000, s100, xd);
+                var s01 = lerp(s001, s101, xd);
+                var s10 = lerp(s010, s110, xd);
+                var s11 = lerp(s011, s111, xd);
+                var s0 = lerp(s00, s10, yd);
+                var s1 = lerp(s01, s11, yd);
+                array[o + k] = lerp(s0, s1, zd);
+            }
         }
     }
     return image;
 }
+//
+function isSupportedColorType(x) {
+    return x === 'group' || x === 'groupInstance';
+}
+export 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') {
+        ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
+        ValueCell.update(values.tColorGrid, smoothingData.texture);
+        ValueCell.update(values.uColorTexDim, smoothingData.gridTexDim);
+        ValueCell.update(values.uColorGridDim, smoothingData.gridDim);
+        ValueCell.update(values.uColorGridTransform, smoothingData.gridTransform);
+    }
+    else if (smoothingData.kind === 'vertex') {
+        ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
+        ValueCell.update(values.tColor, smoothingData.texture);
+        ValueCell.update(values.uColorTexDim, smoothingData.texDim);
+    }
+}
+function isSupportedOverpaintType(x) {
+    return x === 'groupInstance';
+}
+export 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') {
+        ValueCell.updateIfChanged(values.dOverpaintType, smoothingData.type);
+        ValueCell.update(values.tOverpaintGrid, smoothingData.texture);
+        ValueCell.update(values.uOverpaintTexDim, smoothingData.gridTexDim);
+        ValueCell.update(values.uOverpaintGridDim, smoothingData.gridDim);
+        ValueCell.update(values.uOverpaintGridTransform, smoothingData.gridTransform);
+    }
+    else if (smoothingData.kind === 'vertex') {
+        ValueCell.updateIfChanged(values.dOverpaintType, smoothingData.type);
+        ValueCell.update(values.tOverpaint, smoothingData.texture);
+        ValueCell.update(values.uOverpaintTexDim, smoothingData.texDim);
+    }
+}
+function isSupportedTransparencyType(x) {
+    return x === 'groupInstance';
+}
+export 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') {
+        ValueCell.updateIfChanged(values.dTransparencyType, smoothingData.type);
+        ValueCell.update(values.tTransparencyGrid, smoothingData.texture);
+        ValueCell.update(values.uTransparencyTexDim, smoothingData.gridTexDim);
+        ValueCell.update(values.uTransparencyGridDim, smoothingData.gridDim);
+        ValueCell.update(values.uTransparencyGridTransform, smoothingData.gridTransform);
+    }
+    else if (smoothingData.kind === 'vertex') {
+        ValueCell.updateIfChanged(values.dTransparencyType, smoothingData.type);
+        ValueCell.update(values.tTransparency, smoothingData.texture);
+        ValueCell.update(values.uTransparencyTexDim, smoothingData.texDim);
+    }
+}
 //# sourceMappingURL=color-smoothing.js.map

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

	@@ -1 +1 @@
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package/lib/mol-geo/geometry/mesh/mesh.d.ts CHANGED Viewed

@@ -63,7 +63,7 @@ export declare namespace Mesh {
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
         alpha: PD.Numeric;
-        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Mesh, Params>;

package/lib/mol-geo/geometry/mesh/mesh.js CHANGED Viewed

@@ -108,7 +108,7 @@ export var Mesh;
         if (fractionDigits === void 0) { fractionDigits = 3; }
         var v = mesh.vertexBuffer.ref.value;
         var map = new Map();
-        var hash = function (v, d) { return v[0].toFixed(d) + "|" + v[1].toFixed(d) + "|" + v[2].toFixed(d); };
+        var hash = function (v, d) { return "".concat(v[0].toFixed(d), "|").concat(v[1].toFixed(d), "|").concat(v[2].toFixed(d)); };
         var duplicates = 0;
         var a = Vec3();
         for (var i = 0, il = mesh.vertexCount; i < il; ++i) {