molstar 2.3.9 → 3.0.0-dev.10

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

@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.PickHelper = exports.PickPass = void 0;
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var misc_1 = require("../../mol-math/misc");
-var float_packing_1 = require("../../mol-util/float-packing");
+var number_packing_1 = require("../../mol-util/number-packing");
 var stereo_1 = require("../camera/stereo");
 var util_1 = require("../camera/util");
 var util_2 = require("../camera/util");
@@ -46,29 +46,29 @@ var PickPass = /** @class */ (function () {
             this.depthPickTarget.setSize(this.pickWidth, this.pickHeight);
         }
     };
-    PickPass.prototype.renderVariant = function (renderer, camera, scene, helper, variant) {
+    PickPass.prototype.renderVariant = function (renderer, camera, scene, helper, variant, pickType) {
         var depth = this.drawPass.depthTexturePrimitives;
         renderer.clear(false);
         renderer.update(camera);
-        renderer.renderPick(scene.primitives, camera, variant, null);
-        renderer.renderPick(scene.volumes, camera, variant, depth);
-        renderer.renderPick(helper.handle.scene, camera, variant, null);
+        renderer.renderPick(scene.primitives, camera, variant, null, pickType);
+        renderer.renderPick(scene.volumes, camera, variant, depth, pickType);
+        renderer.renderPick(helper.handle.scene, camera, variant, null, pickType);
         if (helper.camera.isEnabled) {
             helper.camera.update(camera);
             renderer.update(helper.camera.camera);
-            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null);
+            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null, pickType);
         }
     };
     PickPass.prototype.render = function (renderer, camera, scene, helper) {
         this.objectPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pickObject');
+        this.renderVariant(renderer, camera, scene, helper, 'pick', 1 /* Object */);
         this.instancePickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pickInstance');
+        this.renderVariant(renderer, camera, scene, helper, 'pick', 2 /* Instance */);
         this.groupPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pickGroup');
+        this.renderVariant(renderer, camera, scene, helper, 'pick', 3 /* Group */);
         // printTexture(this.webgl, this.groupPickTarget.texture, { id: 'group' })
         this.depthPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'depth');
+        this.renderVariant(renderer, camera, scene, helper, 'depth', 0 /* None */);
     };
     return PickPass;
 }());
@@ -127,11 +127,11 @@ var PickHelper = /** @class */ (function () {
     PickHelper.prototype.getDepth = function (x, y) {
         var idx = this.getBufferIdx(x, y);
         var b = this.depthBuffer;
-        return (0, float_packing_1.unpackRGBAToDepth)(b[idx], b[idx + 1], b[idx + 2], b[idx + 3]);
+        return (0, number_packing_1.unpackRGBAToDepth)(b[idx], b[idx + 1], b[idx + 2], b[idx + 3]);
     };
     PickHelper.prototype.getId = function (x, y, buffer) {
         var idx = this.getBufferIdx(x, y);
-        return (0, float_packing_1.decodeFloatRGB)(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
+        return (0, number_packing_1.unpackRGBToInt)(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
     };
     PickHelper.prototype.render = function (camera) {
         var _a = this, pickX = _a.pickX, pickY = _a.pickY, pickWidth = _a.pickWidth, pickHeight = _a.pickHeight, halfPickWidth = _a.halfPickWidth;

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

@@ -20,6 +20,7 @@ export declare const PostprocessingParams: {
     outline: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         scale: number;
         threshold: number;
+        color: Color;
     }>, "on">>;
     antialiasing: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         edgeThreshold: number;

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

@@ -34,7 +34,7 @@ function getOutlinesRenderable(ctx, depthTexture) {
 }
 var SsaoSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uSamples: (0, schema_1.UniformSpec)('v3[]'), dNSamples: (0, schema_1.DefineSpec)('number'), uProjection: (0, schema_1.UniformSpec)('m4'), uInvProjection: (0, schema_1.UniformSpec)('m4'), uBounds: (0, schema_1.UniformSpec)('v4'), uTexSize: (0, schema_1.UniformSpec)('v2'), uRadius: (0, schema_1.UniformSpec)('f'), uBias: (0, schema_1.UniformSpec)('f') });
 function getSsaoRenderable(ctx, depthTexture) {
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tDepth: mol_util_1.ValueCell.create(depthTexture), uSamples: mol_util_1.ValueCell.create([0.0, 0.0, 1.0]), dNSamples: mol_util_1.ValueCell.create(1), uProjection: mol_util_1.ValueCell.create(linear_algebra_1.Mat4.identity()), uInvProjection: mol_util_1.ValueCell.create(linear_algebra_1.Mat4.identity()), uBounds: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec4)()), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)), uRadius: mol_util_1.ValueCell.create(8.0), uBias: mol_util_1.ValueCell.create(0.025) });
+    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tDepth: mol_util_1.ValueCell.create(depthTexture), uSamples: mol_util_1.ValueCell.create([0.0, 0.0, 1.0]), dNSamples: mol_util_1.ValueCell.create(32), uProjection: mol_util_1.ValueCell.create(linear_algebra_1.Mat4.identity()), uInvProjection: mol_util_1.ValueCell.create(linear_algebra_1.Mat4.identity()), uBounds: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec4)()), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)), uRadius: mol_util_1.ValueCell.create(8.0), uBias: mol_util_1.ValueCell.create(0.025) });
     var schema = (0, tslib_1.__assign)({}, SsaoSchema);
     var shaderCode = (0, shader_code_1.ShaderCode)('ssao', quad_vert_1.quad_vert, ssao_frag_1.ssao_frag);
     var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
@@ -42,7 +42,7 @@ function getSsaoRenderable(ctx, depthTexture) {
 }
 var SsaoBlurSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tSsaoDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2'), uKernel: (0, schema_1.UniformSpec)('f[]'), dOcclusionKernelSize: (0, schema_1.DefineSpec)('number'), uBlurDirectionX: (0, schema_1.UniformSpec)('f'), uBlurDirectionY: (0, schema_1.UniformSpec)('f'), uMaxPossibleViewZDiff: (0, schema_1.UniformSpec)('f'), uNear: (0, schema_1.UniformSpec)('f'), uFar: (0, schema_1.UniformSpec)('f'), uBounds: (0, schema_1.UniformSpec)('v4'), dOrthographic: (0, schema_1.DefineSpec)('number') });
 function getSsaoBlurRenderable(ctx, ssaoDepthTexture, direction) {
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tSsaoDepth: mol_util_1.ValueCell.create(ssaoDepthTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())), uKernel: mol_util_1.ValueCell.create([0.0]), dOcclusionKernelSize: mol_util_1.ValueCell.create(1), uBlurDirectionX: mol_util_1.ValueCell.create(direction === 'horizontal' ? 1 : 0), uBlurDirectionY: mol_util_1.ValueCell.create(direction === 'vertical' ? 1 : 0), uMaxPossibleViewZDiff: mol_util_1.ValueCell.create(0.5), uNear: mol_util_1.ValueCell.create(0.0), uFar: mol_util_1.ValueCell.create(10000.0), uBounds: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec4)()), dOrthographic: mol_util_1.ValueCell.create(0) });
+    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tSsaoDepth: mol_util_1.ValueCell.create(ssaoDepthTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())), uKernel: mol_util_1.ValueCell.create([0.0]), dOcclusionKernelSize: mol_util_1.ValueCell.create(15), uBlurDirectionX: mol_util_1.ValueCell.create(direction === 'horizontal' ? 1 : 0), uBlurDirectionY: mol_util_1.ValueCell.create(direction === 'vertical' ? 1 : 0), uMaxPossibleViewZDiff: mol_util_1.ValueCell.create(0.5), uNear: mol_util_1.ValueCell.create(0.0), uFar: mol_util_1.ValueCell.create(10000.0), uBounds: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec4)()), dOrthographic: mol_util_1.ValueCell.create(0) });
     var schema = (0, tslib_1.__assign)({}, SsaoBlurSchema);
     var shaderCode = (0, shader_code_1.ShaderCode)('ssao_blur', quad_vert_1.quad_vert, ssao_blur_frag_1.ssaoBlur_frag);
     var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
@@ -68,9 +68,9 @@ function getSamples(vectorSamples, nSamples) {
     }
     return samples;
 }
-var PostprocessingSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tSsaoDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tColor: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tOutlines: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2'), dOrthographic: (0, schema_1.DefineSpec)('number'), uNear: (0, schema_1.UniformSpec)('f'), uFar: (0, schema_1.UniformSpec)('f'), uFogNear: (0, schema_1.UniformSpec)('f'), uFogFar: (0, schema_1.UniformSpec)('f'), uFogColor: (0, schema_1.UniformSpec)('v3'), uTransparentBackground: (0, schema_1.UniformSpec)('b'), uMaxPossibleViewZDiff: (0, schema_1.UniformSpec)('f'), dOcclusionEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineScale: (0, schema_1.DefineSpec)('number'), uOutlineThreshold: (0, schema_1.UniformSpec)('f') });
+var PostprocessingSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tSsaoDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tColor: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tOutlines: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2'), dOrthographic: (0, schema_1.DefineSpec)('number'), uNear: (0, schema_1.UniformSpec)('f'), uFar: (0, schema_1.UniformSpec)('f'), uFogNear: (0, schema_1.UniformSpec)('f'), uFogFar: (0, schema_1.UniformSpec)('f'), uFogColor: (0, schema_1.UniformSpec)('v3'), uOutlineColor: (0, schema_1.UniformSpec)('v3'), uTransparentBackground: (0, schema_1.UniformSpec)('b'), uMaxPossibleViewZDiff: (0, schema_1.UniformSpec)('f'), dOcclusionEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineScale: (0, schema_1.DefineSpec)('number'), uOutlineThreshold: (0, schema_1.UniformSpec)('f') });
 function getPostprocessingRenderable(ctx, colorTexture, depthTexture, outlinesTexture, ssaoDepthTexture) {
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tSsaoDepth: mol_util_1.ValueCell.create(ssaoDepthTexture), tColor: mol_util_1.ValueCell.create(colorTexture), tDepth: mol_util_1.ValueCell.create(depthTexture), tOutlines: mol_util_1.ValueCell.create(outlinesTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())), dOrthographic: mol_util_1.ValueCell.create(0), uNear: mol_util_1.ValueCell.create(1), uFar: mol_util_1.ValueCell.create(10000), uFogNear: mol_util_1.ValueCell.create(10000), uFogFar: mol_util_1.ValueCell.create(10000), uFogColor: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)), uTransparentBackground: mol_util_1.ValueCell.create(false), uMaxPossibleViewZDiff: mol_util_1.ValueCell.create(0.5), dOcclusionEnable: mol_util_1.ValueCell.create(false), dOutlineEnable: mol_util_1.ValueCell.create(false), dOutlineScale: mol_util_1.ValueCell.create(1), uOutlineThreshold: mol_util_1.ValueCell.create(0.33) });
+    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tSsaoDepth: mol_util_1.ValueCell.create(ssaoDepthTexture), tColor: mol_util_1.ValueCell.create(colorTexture), tDepth: mol_util_1.ValueCell.create(depthTexture), tOutlines: mol_util_1.ValueCell.create(outlinesTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())), dOrthographic: mol_util_1.ValueCell.create(0), uNear: mol_util_1.ValueCell.create(1), uFar: mol_util_1.ValueCell.create(10000), uFogNear: mol_util_1.ValueCell.create(10000), uFogFar: mol_util_1.ValueCell.create(10000), uFogColor: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)), uOutlineColor: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(0, 0, 0)), uTransparentBackground: mol_util_1.ValueCell.create(false), uMaxPossibleViewZDiff: mol_util_1.ValueCell.create(0.5), dOcclusionEnable: mol_util_1.ValueCell.create(true), dOutlineEnable: mol_util_1.ValueCell.create(false), dOutlineScale: mol_util_1.ValueCell.create(1), uOutlineThreshold: mol_util_1.ValueCell.create(0.33) });
     var schema = (0, tslib_1.__assign)({}, PostprocessingSchema);
     var shaderCode = (0, shader_code_1.ShaderCode)('postprocessing', quad_vert_1.quad_vert, postprocessing_frag_1.postprocessing_frag);
     var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
@@ -90,6 +90,7 @@ exports.PostprocessingParams = {
         on: param_definition_1.ParamDefinition.Group({
             scale: param_definition_1.ParamDefinition.Numeric(1, { min: 1, max: 5, step: 1 }),
             threshold: param_definition_1.ParamDefinition.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
+            color: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0x000000)),
         }),
         off: param_definition_1.ParamDefinition.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' }),
@@ -223,6 +224,7 @@ var PostprocessingPass = /** @class */ (function () {
             mol_util_1.ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
             mol_util_1.ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
             mol_util_1.ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
+            mol_util_1.ValueCell.update(this.renderable.values.uOutlineColor, color_1.Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, props.outline.params.color));
             mol_util_1.ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) {
                 needsUpdateMain = true;

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

@@ -138,7 +138,7 @@ function getWeightsRenderable(ctx, edgesTexture) {
     var height = edgesTexture.getHeight();
     var areaTexture = (0, texture_1.createTexture)(ctx.gl, ctx.extensions, 'image-uint8', 'rgb', 'ubyte', 'linear');
     var searchTexture = (0, texture_1.createTexture)(ctx.gl, ctx.extensions, 'image-uint8', 'rgba', 'ubyte', 'nearest');
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tEdges: mol_util_1.ValueCell.create(edgesTexture), tArea: mol_util_1.ValueCell.create(areaTexture), tSearch: mol_util_1.ValueCell.create(searchTexture), uTexSizeInv: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(1 / width, 1 / height)), uViewport: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec4)()), dMaxSearchSteps: mol_util_1.ValueCell.create(8) });
+    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tEdges: mol_util_1.ValueCell.create(edgesTexture), tArea: mol_util_1.ValueCell.create(areaTexture), tSearch: mol_util_1.ValueCell.create(searchTexture), uTexSizeInv: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(1 / width, 1 / height)), uViewport: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec4)()), dMaxSearchSteps: mol_util_1.ValueCell.create(16) });
     // Note: loading image textures requires `HTMLImageElement` to be available
     (0, texture_1.loadImageTexture)(getAreaTexture(), values.tArea, areaTexture);
     (0, texture_1.loadImageTexture)(getSearchTexture(), values.tSearch, searchTexture);

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>
  */
@@ -10,6 +10,7 @@ import { LocationIterator } from '../util/location-iterator';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { TransformData } from './transform-data';
 import { Theme } from '../../mol-theme/theme';
+import { Clip } from '../../mol-util/clip';
 export declare const VisualQualityInfo: {
     custom: {};
     auto: {};
@@ -22,16 +23,44 @@ 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;
+            bumpiness: number;
+        }>>;
+        clip: PD.Group<PD.Normalize<{
+            variant: Clip.Variant;
+            objects: PD.Normalize<{
+                type: any;
+                invert: any;
+                position: any;
+                rotation: any;
+                scale: any;
+            }>[];
+        }>>;
     };
     type Params = typeof Params;
-    const ShadingCategory: PD.Info;
-    const CustomQualityParamInfo: PD.Info;
     type Counts = {
         drawCount: number;
         vertexCount: number;
@@ -49,6 +78,17 @@ export declare namespace BaseGeometry {
         uVertexCount: ValueCell<number, never>;
         uGroupCount: ValueCell<number, never>;
         drawCount: ValueCell<number, never>;
+        uMetalness: ValueCell<number, never>;
+        uRoughness: ValueCell<number, never>;
+        uBumpiness: ValueCell<number, never>;
+        dLightCount: ValueCell<number, never>;
+        dClipObjectCount: ValueCell<number, never>;
+        dClipVariant: ValueCell<Clip.Variant, never>;
+        uClipObjectType: ValueCell<number[], never>;
+        uClipObjectInvert: ValueCell<boolean[], never>;
+        uClipObjectPosition: ValueCell<number[], never>;
+        uClipObjectRotation: ValueCell<number[], never>;
+        uClipObjectScale: 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 +14,9 @@ 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");
+var clip_1 = require("../../mol-util/clip");
 exports.VisualQualityInfo = {
     'custom': {},
     'auto': {},
@@ -28,17 +31,54 @@ 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(),
+        clip: param_definition_1.ParamDefinition.Group(clip_1.Clip.Params),
+    };
     function createSimple(colorValue, sizeValue, transform) {
         if (colorValue === void 0) { colorValue = names_1.ColorNames.grey; }
         if (sizeValue === void 0) { sizeValue = 1; }
@@ -53,17 +93,40 @@ var BaseGeometry;
     }
     BaseGeometry.createSimple = createSimple;
     function createValues(props, counts) {
+        var clip = clip_1.Clip.getClip(props.clip);
         return {
             alpha: mol_util_1.ValueCell.create(props.alpha),
             uAlpha: mol_util_1.ValueCell.create(props.alpha),
             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),
+            uBumpiness: mol_util_1.ValueCell.create(props.material.bumpiness),
+            dLightCount: mol_util_1.ValueCell.create(1),
+            dClipObjectCount: mol_util_1.ValueCell.create(clip.objects.count),
+            dClipVariant: mol_util_1.ValueCell.create(clip.variant),
+            uClipObjectType: mol_util_1.ValueCell.create(clip.objects.type),
+            uClipObjectInvert: mol_util_1.ValueCell.create(clip.objects.invert),
+            uClipObjectPosition: mol_util_1.ValueCell.create(clip.objects.position),
+            uClipObjectRotation: mol_util_1.ValueCell.create(clip.objects.rotation),
+            uClipObjectScale: mol_util_1.ValueCell.create(clip.objects.scale),
         };
     }
     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);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpiness, props.material.bumpiness);
+        var clip = clip_1.Clip.getClip(props.clip);
+        mol_util_1.ValueCell.update(values.dClipObjectCount, clip.objects.count);
+        mol_util_1.ValueCell.update(values.dClipVariant, clip.variant);
+        mol_util_1.ValueCell.update(values.uClipObjectType, clip.objects.type);
+        mol_util_1.ValueCell.update(values.uClipObjectInvert, clip.objects.invert);
+        mol_util_1.ValueCell.update(values.uClipObjectPosition, clip.objects.position);
+        mol_util_1.ValueCell.update(values.uClipObjectRotation, clip.objects.rotation);
+        mol_util_1.ValueCell.update(values.uClipObjectScale, clip.objects.scale);
     }
     BaseGeometry.updateValues = updateValues;
     function createRenderableState(props) {
@@ -77,7 +140,6 @@ var BaseGeometry;
             colorOnly: false,
             opaque: opaque,
             writeDepth: opaque,
-            noClip: false,
         };
     }
     BaseGeometry.createRenderableState = createRenderableState;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,8 +8,6 @@ import { Vec2 } from '../../mol-math/linear-algebra';
 import { TextureImage } from '../../mol-gl/renderable/util';
 import { Clipping } from '../../mol-theme/clipping';
 export declare type ClippingData = {
-    dClipObjectCount: ValueCell<number>;
-    dClipVariant: ValueCell<string>;
     tClipping: ValueCell<TextureImage<Uint8Array>>;
     uClippingTexDim: ValueCell<Vec2>;
     dClipping: ValueCell<boolean>;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,9 +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");
 function applyClippingGroups(array, start, end, groups) {
-    for (var i = start; i < end; ++i) {
-        array[i] = groups;
-    }
+    array.fill(groups, start, end);
     return true;
 }
 exports.applyClippingGroups = applyClippingGroups;
@@ -30,8 +28,6 @@ function createClipping(count, clippingData) {
     }
     else {
         return {
-            dClipObjectCount: value_cell_1.ValueCell.create(0),
-            dClipVariant: value_cell_1.ValueCell.create('instance'),
             tClipping: value_cell_1.ValueCell.create(clipping),
             uClippingTexDim: value_cell_1.ValueCell.create(linear_algebra_1.Vec2.create(clipping.width, clipping.height)),
             dClipping: value_cell_1.ValueCell.create(count > 0),
@@ -44,12 +40,11 @@ function createEmptyClipping(clippingData) {
     if (clippingData) {
         value_cell_1.ValueCell.update(clippingData.tClipping, emptyClippingTexture);
         value_cell_1.ValueCell.update(clippingData.uClippingTexDim, linear_algebra_1.Vec2.create(1, 1));
+        value_cell_1.ValueCell.updateIfChanged(clippingData.dClipping, false);
         return clippingData;
     }
     else {
         return {
-            dClipObjectCount: value_cell_1.ValueCell.create(0),
-            dClipVariant: value_cell_1.ValueCell.create('instance'),
             tClipping: value_cell_1.ValueCell.create(emptyClippingTexture),
             uClippingTexDim: value_cell_1.ValueCell.create(linear_algebra_1.Vec2.create(1, 1)),
             dClipping: value_cell_1.ValueCell.create(false),

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

@@ -11,7 +11,7 @@ import { Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
 import { LocationIterator } from '../util/location-iterator';
 import { ColorTheme } from '../../mol-theme/color';
 import { Texture } from '../../mol-gl/webgl/texture';
-export declare type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance' | 'volume' | 'volumeInstance';
+export declare type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance' | 'volume' | 'volumeInstance' | 'direct';
 export declare type ColorData = {
     uColor: ValueCell<Vec3>;
     tColor: ValueCell<TextureImage<Uint8Array>>;

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

@@ -36,6 +36,7 @@ function _createColors(locationIt, positionIt, colorTheme, colorData) {
         case 'vertexInstance': return createVertexInstanceColor(positionIt, colorTheme.color, colorData);
         case 'volume': return createGridColor(colorTheme.grid, 'volume', colorData);
         case 'volumeInstance': return createGridColor(colorTheme.grid, 'volumeInstance', colorData);
+        case 'direct': return createDirectColor(colorData);
     }
 }
 function updatePaletteTexture(palette, cell) {
@@ -210,4 +211,25 @@ function createGridColor(grid, type, colorData) {
     }
 }
 exports.createGridColor = createGridColor;
+//
+/** Creates direct color */
+function createDirectColor(colorData) {
+    if (colorData) {
+        mol_util_1.ValueCell.updateIfChanged(colorData.dColorType, 'direct');
+        return colorData;
+    }
+    else {
+        return {
+            uColor: mol_util_1.ValueCell.create((0, linear_algebra_1.Vec3)()),
+            tColor: mol_util_1.ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            tColorGrid: mol_util_1.ValueCell.create((0, texture_1.createNullTexture)()),
+            tPalette: mol_util_1.ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            uColorTexDim: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(1, 1)),
+            uColorGridDim: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)),
+            uColorGridTransform: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.create(0, 0, 0, 1)),
+            dColorType: mol_util_1.ValueCell.create('direct'),
+            dUsePalette: mol_util_1.ValueCell.create(false),
+        };
+    }
+}
 //# sourceMappingURL=color-data.js.map

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

@@ -43,8 +43,25 @@ export declare namespace Cylinders {
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
+        bumpFrequency: PD.Numeric;
+        bumpAmplitude: 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; /** Number of cylinders */
+            roughness: number;
+            bumpiness: number;
+        }>>;
+        clip: PD.Group<PD.Normalize<{
+            variant: import("../../../mol-util/clip").Clip.Variant;
+            objects: PD.Normalize<{
+                type: any;
+                invert: any;
+                position: any;
+                rotation: any;
+                scale: any;
+            }>[];
+        }>>;
     };
     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) {
@@ -109,7 +110,7 @@ var Cylinders;
     }
     Cylinders.transform = transform;
     //
-    Cylinders.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory) });
+    Cylinders.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
     Cylinders.Utils = {
         Params: Cylinders.Params,
         createEmpty: createEmpty,
@@ -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)({ dGeometryType: mol_util_1.ValueCell.create('cylinders'), aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
     }
     function createValuesSimple(cylinders, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -164,9 +166,11 @@ var Cylinders;
     function updateValues(values, props) {
         base_1.BaseGeometry.updateValues(values, props);
         mol_util_1.ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor * props.sizeAspectRatio);
-        mol_util_1.ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
+        mol_util_1.ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
     function updateBoundingSphere(values, cylinders) {
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);