molstar 2.3.9 → 3.0.0-dev.2

package/lib/commonjs/mol-canvas3d/passes/draw.js

@@ -18,11 +18,11 @@ var mol_util_1 = require("../../mol-util");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var quad_vert_1 = require("../../mol-gl/shader/quad.vert");
 var depth_merge_frag_1 = require("../../mol-gl/shader/depth-merge.frag");
-var copy_frag_1 = require("../../mol-gl/shader/copy.frag");
 var stereo_1 = require("../camera/stereo");
 var wboit_1 = require("./wboit");
 var postprocessing_1 = require("./postprocessing");
 var marking_1 = require("./marking");
+var util_2 = require("../../mol-gl/compute/util");
 var DepthMergeSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tDepthPrimitives: (0, schema_1.TextureSpec)('texture', 'depth', 'ushort', 'nearest'), tDepthVolumes: (0, schema_1.TextureSpec)('texture', 'depth', 'ushort', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2'), dPackedDepth: (0, schema_1.DefineSpec)('boolean') });
 var DepthMergeShaderCode = (0, shader_code_1.ShaderCode)('depth-merge', quad_vert_1.quad_vert, depth_merge_frag_1.depthMerge_frag);
 function getDepthMergeRenderable(ctx, depthTexturePrimitives, depthTextureVolumes, packedDepth) {
@@ -31,14 +31,6 @@ function getDepthMergeRenderable(ctx, depthTexturePrimitives, depthTextureVolume
     var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', DepthMergeShaderCode, schema, values);
     return (0, renderable_1.createComputeRenderable)(renderItem, values);
 }
-var CopySchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tColor: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2') });
-var CopyShaderCode = (0, shader_code_1.ShaderCode)('copy', quad_vert_1.quad_vert, copy_frag_1.copy_frag);
-function getCopyRenderable(ctx, colorTexture) {
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tColor: mol_util_1.ValueCell.create(colorTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())) });
-    var schema = (0, tslib_1.__assign)({}, CopySchema);
-    var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', CopyShaderCode, schema, values);
-    return (0, renderable_1.createComputeRenderable)(renderItem, values);
-}
 var DrawPass = /** @class */ (function () {
     function DrawPass(webgl, width, height, enableWboit) {
         this.webgl = webgl;
@@ -61,8 +53,8 @@ var DrawPass = /** @class */ (function () {
         this.marking = new marking_1.MarkingPass(webgl, width, height);
         this.postprocessing = new postprocessing_1.PostprocessingPass(webgl, this);
         this.antialiasing = new postprocessing_1.AntialiasingPass(webgl, this);
-        this.copyFboTarget = getCopyRenderable(webgl, this.colorTarget.texture);
-        this.copyFboPostprocessing = getCopyRenderable(webgl, this.postprocessing.target.texture);
+        this.copyFboTarget = (0, util_2.createCopyRenderable)(webgl, this.colorTarget.texture);
+        this.copyFboPostprocessing = (0, util_2.createCopyRenderable)(webgl, this.postprocessing.target.texture);
     }
     Object.defineProperty(DrawPass.prototype, "wboitEnabled", {
         get: function () {

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

@@ -47,7 +47,7 @@ export declare const ImageParams: {
         innerEdgeFactor: number;
     }>>;
     cameraHelper: PD.Group<PD.Normalize<{
-        axes: PD.NamedParams<PD.Normalize<{
+        axes: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             alpha: any;
             ignoreLight: any;
             colorX: any;
@@ -59,7 +59,8 @@ export declare const ImageParams: {
             flatShaded: any;
             xrayShaded: any;
             quality: any;
-        }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">;
+            material: any;
+        }>, "on">;
     }>>;
 };
 export declare type ImageProps = PD.Values<typeof ImageParams>;

package/lib/commonjs/mol-data/int/impl/sorted-array.d.ts

@@ -9,7 +9,7 @@ export declare const Empty: Nums;
 export declare function ofSingleton(v: number): number[];
 export declare function ofSortedArray(xs: Nums): Nums;
 export declare function ofUnsortedArray(xs: Nums): Nums;
-export declare function ofRange(min: number, max: number): Int32Array | never[];
+export declare function ofRange(min: number, max: number): never[] | Int32Array;
 export declare function is(xs: any): xs is Nums;
 export declare function isRange(xs: Nums): boolean;
 export declare function start(xs: Nums): number;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -22,16 +22,33 @@ export declare const VisualQualityInfo: {
     lowest: {};
 };
 export declare type VisualQuality = keyof typeof VisualQualityInfo;
-export declare const VisualQualityNames: ("custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest")[];
-export declare const VisualQualityOptions: ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string][];
+export declare const VisualQualityNames: ("auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest")[];
+export declare const VisualQualityOptions: ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string][];
+export declare const ColorSmoothingParams: {
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+        resolutionFactor: number;
+        sampleStride: number;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+};
+export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
+export declare function hasColorSmoothingProp(props: PD.Values<any>): props is PD.Values<ColorSmoothingParams>;
+export declare function getColorSmoothingProps(smoothColors: PD.Values<ColorSmoothingParams>['smoothColors'], preferSmoothing?: boolean, resolution?: number): {
+    resolution: number;
+    stride: number;
+} | undefined;
 export declare namespace BaseGeometry {
+    const MaterialCategory: PD.Info;
+    const ShadingCategory: PD.Info;
+    const CustomQualityParamInfo: PD.Info;
     const Params: {
         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">;
+        material: PD.Group<PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>>;
     };
     type Params = typeof Params;
-    const ShadingCategory: PD.Info;
-    const CustomQualityParamInfo: PD.Info;
     type Counts = {
         drawCount: number;
         vertexCount: number;
@@ -49,6 +66,9 @@ export declare namespace BaseGeometry {
         uVertexCount: ValueCell<number, never>;
         uGroupCount: ValueCell<number, never>;
         drawCount: ValueCell<number, never>;
+        uMetalness: ValueCell<number, never>;
+        uRoughness: ValueCell<number, never>;
+        dLightCount: ValueCell<number, never>;
     };
     function updateValues(values: BaseValues, props: PD.Values<Params>): void;
     function createRenderableState(props?: Partial<PD.Values<Params>>): RenderableState;

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

@@ -1,11 +1,11 @@
 "use strict";
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.BaseGeometry = exports.VisualQualityOptions = exports.VisualQualityNames = exports.VisualQualityInfo = void 0;
+exports.BaseGeometry = exports.getColorSmoothingProps = exports.hasColorSmoothingProp = exports.ColorSmoothingParams = exports.VisualQualityOptions = exports.VisualQualityNames = exports.VisualQualityInfo = void 0;
 var mol_util_1 = require("../../mol-util");
 var location_iterator_1 = require("../util/location-iterator");
 var param_definition_1 = require("../../mol-util/param-definition");
@@ -14,6 +14,8 @@ var names_1 = require("../../mol-util/color/names");
 var location_1 = require("../../mol-model/location");
 var uniform_1 = require("../../mol-theme/color/uniform");
 var uniform_2 = require("../../mol-theme/size/uniform");
+var interpolate_1 = require("../../mol-math/interpolate");
+var material_1 = require("../../mol-util/material");
 exports.VisualQualityInfo = {
     'custom': {},
     'auto': {},
@@ -28,17 +30,53 @@ exports.VisualQualityInfo = {
 exports.VisualQualityNames = Object.keys(exports.VisualQualityInfo);
 exports.VisualQualityOptions = param_definition_1.ParamDefinition.arrayToOptions(exports.VisualQualityNames);
 //
+exports.ColorSmoothingParams = {
+    smoothColors: param_definition_1.ParamDefinition.MappedStatic('auto', {
+        auto: param_definition_1.ParamDefinition.Group({}),
+        on: param_definition_1.ParamDefinition.Group({
+            resolutionFactor: param_definition_1.ParamDefinition.Numeric(2, { min: 0.5, max: 6, step: 0.1 }),
+            sampleStride: param_definition_1.ParamDefinition.Numeric(3, { min: 1, max: 12, step: 1 }),
+        }),
+        off: param_definition_1.ParamDefinition.Group({})
+    }),
+};
+function hasColorSmoothingProp(props) {
+    return !!props.smoothColors;
+}
+exports.hasColorSmoothingProp = hasColorSmoothingProp;
+function getColorSmoothingProps(smoothColors, preferSmoothing, resolution) {
+    if ((smoothColors.name === 'on' || (smoothColors.name === 'auto' && preferSmoothing)) && resolution && resolution < 3) {
+        var stride = 3;
+        if (smoothColors.name === 'on') {
+            resolution *= smoothColors.params.resolutionFactor;
+            stride = smoothColors.params.sampleStride;
+        }
+        else {
+            // https://graphtoy.com/?f1(x,t)=(2-smoothstep(0,1.1,x))*x&coords=0.7,0.6,1.8
+            resolution *= 2 - (0, interpolate_1.smoothstep)(0, 1.1, resolution);
+            resolution = Math.max(0.5, resolution);
+            if (resolution > 1.2)
+                stride = 2;
+        }
+        return { resolution: resolution, stride: stride };
+    }
+    ;
+}
+exports.getColorSmoothingProps = getColorSmoothingProps;
+//
 var BaseGeometry;
 (function (BaseGeometry) {
-    BaseGeometry.Params = {
-        alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity', isEssential: true, description: 'How opaque/transparent the representation is rendered.' }),
-        quality: param_definition_1.ParamDefinition.Select('auto', exports.VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }),
-    };
+    BaseGeometry.MaterialCategory = { category: 'Material' };
     BaseGeometry.ShadingCategory = { category: 'Shading' };
     BaseGeometry.CustomQualityParamInfo = {
         category: 'Custom Quality',
         hideIf: function (params) { return typeof params.quality !== 'undefined' && params.quality !== 'custom'; }
     };
+    BaseGeometry.Params = {
+        alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity', isEssential: true, description: 'How opaque/transparent the representation is rendered.' }),
+        quality: param_definition_1.ParamDefinition.Select('auto', exports.VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }),
+        material: material_1.Material.getParam(),
+    };
     function createSimple(colorValue, sizeValue, transform) {
         if (colorValue === void 0) { colorValue = names_1.ColorNames.grey; }
         if (sizeValue === void 0) { sizeValue = 1; }
@@ -59,11 +97,16 @@ var BaseGeometry;
             uVertexCount: mol_util_1.ValueCell.create(counts.vertexCount),
             uGroupCount: mol_util_1.ValueCell.create(counts.groupCount),
             drawCount: mol_util_1.ValueCell.create(counts.drawCount),
+            uMetalness: mol_util_1.ValueCell.create(props.material.metalness),
+            uRoughness: mol_util_1.ValueCell.create(props.material.roughness),
+            dLightCount: mol_util_1.ValueCell.create(1),
         };
     }
     BaseGeometry.createValues = createValues;
     function updateValues(values, props) {
         mol_util_1.ValueCell.updateIfChanged(values.alpha, props.alpha); // `uAlpha` is set in renderable.render
+        mol_util_1.ValueCell.updateIfChanged(values.uMetalness, props.material.metalness);
+        mol_util_1.ValueCell.updateIfChanged(values.uRoughness, props.material.roughness);
     }
     BaseGeometry.updateValues = updateValues;
     function createRenderableState(props) {

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

@@ -44,7 +44,11 @@ export declare namespace Cylinders {
         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">;
+        material: PD.Group<PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>>;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Cylinders, Params>;

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

@@ -22,6 +22,7 @@ var overpaint_data_1 = require("../overpaint-data");
 var transparency_data_1 = require("../transparency-data");
 var util_3 = require("../../../mol-data/util");
 var clipping_data_1 = require("../clipping-data");
+var substance_data_1 = require("../substance-data");
 var Cylinders;
 (function (Cylinders) {
     function create(mappings, indices, groups, starts, ends, scales, caps, cylinderCount, cylinders) {
@@ -149,12 +150,13 @@ var Cylinders;
         var marker = (0, marker_data_1.createMarkers)(instanceCount * groupCount);
         var overpaint = (0, overpaint_data_1.createEmptyOverpaint)();
         var transparency = (0, transparency_data_1.createEmptyTransparency)();
+        var material = (0, substance_data_1.createEmptySubstance)();
         var clipping = (0, clipping_data_1.createEmptyClipping)();
         var counts = { drawCount: cylinders.cylinderCount * 4 * 3, vertexCount: cylinders.cylinderCount * 6, groupCount: groupCount, instanceCount: instanceCount };
         var padding = (0, size_data_1.getMaxSize)(size) * props.sizeFactor;
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
     }
     function createValuesSimple(cylinders, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

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<{
@@ -72,7 +72,11 @@ 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">;
+        material: PD.Group<PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>>;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<DirectVolume, Params>;

package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js

@@ -25,6 +25,7 @@ var transfer_function_1 = require("./transfer-function");
 var clipping_data_1 = require("../clipping-data");
 var volume_1 = require("../../../mol-model/volume");
 var names_1 = require("../../../mol-util/color/names");
+var substance_data_1 = require("../substance-data");
 var VolumeBox = (0, box_1.Box)();
 var DirectVolume;
 (function (DirectVolume) {
@@ -192,6 +193,7 @@ var DirectVolume;
         var marker = (0, marker_data_1.createMarkers)(instanceCount * groupCount);
         var overpaint = (0, overpaint_data_1.createEmptyOverpaint)();
         var transparency = (0, transparency_data_1.createEmptyTransparency)();
+        var material = (0, substance_data_1.createEmptySubstance)();
         var clipping = (0, clipping_data_1.createEmptyClipping)();
         var _a = gridDimension.ref.value, x = _a[0], y = _a[1], z = _a[2];
         var counts = { drawCount: VolumeBox.indices.length, vertexCount: x * y * z, groupCount: groupCount, instanceCount: instanceCount };
@@ -205,7 +207,7 @@ var DirectVolume;
         var singleLayer = props.renderMode.name === 'isosurface'
             ? props.renderMode.params.singleLayer
             : false;
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, color), marker), overpaint), transparency), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: mol_util_1.ValueCell.create(VolumeBox.vertices), elements: mol_util_1.ValueCell.create(VolumeBox.indices), boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)), uIsoValue: mol_util_1.ValueCell.create(getNormalizedIsoValue((0, linear_algebra_1.Vec2)(), isoValue, directVolume.gridStats.ref.value)), uBboxMin: bboxMin, uBboxMax: bboxMax, uBboxSize: bboxSize, uMaxSteps: mol_util_1.ValueCell.create(getMaxSteps(gridDimension.ref.value, props.stepsPerCell)), uStepScale: mol_util_1.ValueCell.create(getStepScale(directVolume.cellDim.ref.value, props.stepsPerCell)), uJumpLength: mol_util_1.ValueCell.create(props.jumpLength), uTransform: gridTransform, uGridDim: gridDimension, dRenderMode: mol_util_1.ValueCell.create(props.renderMode.name), tTransferTex: transferTex, uTransferScale: mol_util_1.ValueCell.create(getTransferScale(props.stepsPerCell)), dGridTexType: mol_util_1.ValueCell.create(gridTexture.ref.value.getDepth() > 0 ? '3d' : '2d'), uGridTexDim: gridTextureDim, tGridTex: gridTexture, uGridStats: gridStats, uCellDim: directVolume.cellDim, uCartnToUnit: directVolume.cartnToUnit, uUnitToCartn: directVolume.unitToCartn, dPackedGroup: directVolume.packedGroup, dSingleLayer: mol_util_1.ValueCell.create(singleLayer), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: mol_util_1.ValueCell.create(VolumeBox.vertices), elements: mol_util_1.ValueCell.create(VolumeBox.indices), boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)), uIsoValue: mol_util_1.ValueCell.create(getNormalizedIsoValue((0, linear_algebra_1.Vec2)(), isoValue, directVolume.gridStats.ref.value)), uBboxMin: bboxMin, uBboxMax: bboxMax, uBboxSize: bboxSize, uMaxSteps: mol_util_1.ValueCell.create(getMaxSteps(gridDimension.ref.value, props.stepsPerCell)), uStepScale: mol_util_1.ValueCell.create(getStepScale(directVolume.cellDim.ref.value, props.stepsPerCell)), uJumpLength: mol_util_1.ValueCell.create(props.jumpLength), uTransform: gridTransform, uGridDim: gridDimension, dRenderMode: mol_util_1.ValueCell.create(props.renderMode.name), tTransferTex: transferTex, uTransferScale: mol_util_1.ValueCell.create(getTransferScale(props.stepsPerCell)), dGridTexType: mol_util_1.ValueCell.create(gridTexture.ref.value.getDepth() > 0 ? '3d' : '2d'), uGridTexDim: gridTextureDim, tGridTex: gridTexture, uGridStats: gridStats, uCellDim: directVolume.cellDim, uCartnToUnit: directVolume.cartnToUnit, uUnitToCartn: directVolume.unitToCartn, dPackedGroup: directVolume.packedGroup, dSingleLayer: mol_util_1.ValueCell.create(singleLayer), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
     }
     function createValuesSimple(directVolume, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -213,8 +215,7 @@ var DirectVolume;
         return createValues(directVolume, s.transform, s.locationIterator, s.theme, p);
     }
     function updateValues(values, props) {
-        mol_util_1.ValueCell.updateIfChanged(values.alpha, props.alpha);
-        mol_util_1.ValueCell.updateIfChanged(values.uAlpha, props.alpha);
+        base_1.BaseGeometry.updateValues(values, props);
         mol_util_1.ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
         mol_util_1.ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded);
         mol_util_1.ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);

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

@@ -33,7 +33,11 @@ declare namespace Image {
     const Params: {
         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">;
+        material: PD.Group<PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>>;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Image, Params>;

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

@@ -23,6 +23,7 @@ var array_1 = require("../../../mol-util/array");
 var clipping_data_1 = require("../clipping-data");
 var location_1 = require("../../../mol-model/location");
 var util_3 = require("../../../mol-gl/compute/util");
+var substance_data_1 = require("../substance-data");
 var QuadIndices = new Uint32Array([
     0, 1, 2,
     1, 3, 2
@@ -111,11 +112,12 @@ var Image;
         var marker = (0, marker_data_1.createMarkers)(instanceCount * groupCount);
         var overpaint = (0, overpaint_data_1.createEmptyOverpaint)();
         var transparency = (0, transparency_data_1.createEmptyTransparency)();
+        var material = (0, substance_data_1.createEmptySubstance)();
         var clipping = (0, clipping_data_1.createEmptyClipping)();
         var counts = { drawCount: QuadIndices.length, vertexCount: util_3.QuadPositions.length / 3, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(image.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, color), marker), overpaint), transparency), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: image.cornerBuffer, aUv: mol_util_1.ValueCell.create(QuadUvs), elements: mol_util_1.ValueCell.create(QuadIndices), 
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: image.cornerBuffer, aUv: mol_util_1.ValueCell.create(QuadUvs), elements: mol_util_1.ValueCell.create(QuadIndices), 
             // aGroup is used as a vertex index here, group id is in tGroupTex
             aGroup: mol_util_1.ValueCell.create((0, array_1.fillSerial)(new Float32Array(4))), boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)), dInterpolation: mol_util_1.ValueCell.create(props.interpolation), uImageTexDim: image.imageTextureDim, tImageTex: image.imageTexture, tGroupTex: image.groupTexture });
     }

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

@@ -40,7 +40,11 @@ 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">;
+        material: PD.Group<PD.Normalize<{
+            metalness: number;
+            roughness: number;
+        }>>;
     };
     type Params = typeof Params;
     const Utils: GeometryUtils<Lines, Params>;

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

@@ -23,6 +23,7 @@ var overpaint_data_1 = require("../overpaint-data");
 var transparency_data_1 = require("../transparency-data");
 var util_3 = require("../../../mol-data/util");
 var clipping_data_1 = require("../clipping-data");
+var substance_data_1 = require("../substance-data");
 var Lines;
 (function (Lines) {
     function create(mappings, indices, groups, starts, ends, lineCount, lines) {
@@ -162,11 +163,12 @@ var Lines;
         var marker = (0, marker_data_1.createMarkers)(instanceCount * groupCount);
         var overpaint = (0, overpaint_data_1.createEmptyOverpaint)();
         var transparency = (0, transparency_data_1.createEmptyTransparency)();
+        var material = (0, substance_data_1.createEmptySubstance)();
         var clipping = (0, clipping_data_1.createEmptyClipping)();
         var counts = { drawCount: lines.lineCount * 2 * 3, vertexCount: lines.lineCount * 4, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(lines.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: lines.mappingBuffer, aGroup: lines.groupBuffer, aStart: lines.startBuffer, aEnd: lines.endBuffer, elements: lines.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dLineSizeAttenuation: mol_util_1.ValueCell.create(props.lineSizeAttenuation), dDoubleSided: mol_util_1.ValueCell.create(true), dFlipSided: mol_util_1.ValueCell.create(false) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: lines.mappingBuffer, aGroup: lines.groupBuffer, aStart: lines.startBuffer, aEnd: lines.endBuffer, elements: lines.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dLineSizeAttenuation: mol_util_1.ValueCell.create(props.lineSizeAttenuation), dDoubleSided: mol_util_1.ValueCell.create(true), dFlipSided: mol_util_1.ValueCell.create(false) });
     }
     function createValuesSimple(lines, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

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

@@ -33,24 +33,26 @@ var v3dot = linear_algebra_1.Vec3.dot;
 var v3unitX = linear_algebra_1.Vec3.unitX;
 var caAdd3 = util_1.ChunkedArray.add3;
 var CosSinCache = new Map();
-function getCosSin(radialSegments) {
-    if (!CosSinCache.has(radialSegments)) {
+function getCosSin(radialSegments, shift) {
+    var offset = shift ? 1 : 0;
+    var hash = (0, util_1.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);
 }
 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;
@@ -67,7 +69,15 @@ function addTube(state, controlPoints, normalVectors, binormalVectors, linearSeg
                     ? (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/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 +50,14 @@ 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 declare function applyMeshSubstanceSmoothing(values: MeshValues, resolution: number, stride: number, webgl?: WebGLContext, colorTexture?: Texture): void;
 export {};