molstar 3.0.0-dev.6 → 3.0.0

package/lib/mol-canvas3d/passes/multi-sample.d.ts

@@ -23,6 +23,13 @@ declare type Props = {
     multiSample: MultiSampleProps;
     postprocessing: PostprocessingProps;
     marking: MarkingProps;
+    transparentBackground: boolean;
+};
+declare type RenderContext = {
+    renderer: Renderer;
+    camera: Camera | StereoCamera;
+    scene: Scene;
+    helper: Helper;
 };
 export declare class MultiSamplePass {
     private webgl;
@@ -34,7 +41,7 @@ export declare class MultiSamplePass {
     private compose;
     constructor(webgl: WebGLContext, drawPass: DrawPass);
     syncSize(): void;
-    render(sampleIndex: number, renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props): number;
+    render(sampleIndex: number, ctx: RenderContext, props: Props, toDrawingBuffer: boolean, forceOn: boolean): number;
     private bindOutputTarget;
     private renderMultiSample;
     private renderTemporalMultiSample;
@@ -44,7 +51,7 @@ export declare class MultiSampleHelper {
     private sampleIndex;
     update(changed: boolean, props: MultiSampleProps): boolean;
     /** Return `true` while more samples are needed */
-    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props): boolean;
+    render(ctx: RenderContext, props: Props, toDrawingBuffer: boolean, forceOn?: boolean): boolean;
     constructor(multiSamplePass: MultiSamplePass);
 }
 export {};

package/lib/mol-canvas3d/passes/multi-sample.js

@@ -55,13 +55,13 @@ var MultiSamplePass = /** @class */ (function () {
             ValueCell.update(this.compose.values.uTexSize, Vec2.set(this.compose.values.uTexSize.ref.value, width, height));
         }
     };
-    MultiSamplePass.prototype.render = function (sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props) {
-        if (props.multiSample.mode === 'temporal') {
-            return this.renderTemporalMultiSample(sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+    MultiSamplePass.prototype.render = function (sampleIndex, ctx, props, toDrawingBuffer, forceOn) {
+        if (props.multiSample.mode === 'temporal' && !forceOn) {
+            return this.renderTemporalMultiSample(sampleIndex, ctx, props, toDrawingBuffer);
         }
         else {
-            this.renderMultiSample(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
-            return sampleIndex;
+            this.renderMultiSample(ctx, toDrawingBuffer, props);
+            return -2;
         }
     };
     MultiSamplePass.prototype.bindOutputTarget = function (toDrawingBuffer) {
@@ -72,7 +72,8 @@ var MultiSamplePass = /** @class */ (function () {
             this.colorTarget.bind();
         }
     };
-    MultiSamplePass.prototype.renderMultiSample = function (renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props) {
+    MultiSamplePass.prototype.renderMultiSample = function (ctx, toDrawingBuffer, props) {
+        var camera = ctx.camera;
         var _a = this, compose = _a.compose, composeTarget = _a.composeTarget, drawPass = _a.drawPass, webgl = _a.webgl;
         var gl = webgl.gl, state = webgl.state;
         // based on the Multisample Anti-Aliasing Render Pass
@@ -100,7 +101,7 @@ var MultiSamplePass = /** @class */ (function () {
             var sampleWeight = baseSampleWeight + roundingRange * uniformCenteredDistribution;
             ValueCell.update(compose.values.uWeight, sampleWeight);
             // render scene
-            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
+            drawPass.render(ctx, props, false);
             // compose rendered scene with compose target
             composeTarget.bind();
             state.enable(gl.BLEND);
@@ -127,7 +128,8 @@ var MultiSamplePass = /** @class */ (function () {
         camera.viewOffset.enabled = false;
         camera.update();
     };
-    MultiSamplePass.prototype.renderTemporalMultiSample = function (sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props) {
+    MultiSamplePass.prototype.renderTemporalMultiSample = function (sampleIndex, ctx, props, toDrawingBuffer) {
+        var camera = ctx.camera;
         var _a = this, compose = _a.compose, composeTarget = _a.composeTarget, holdTarget = _a.holdTarget, drawPass = _a.drawPass, webgl = _a.webgl;
         var gl = webgl.gl, state = webgl.state;
         // based on the Multisample Anti-Aliasing Render Pass
@@ -141,7 +143,7 @@ var MultiSamplePass = /** @class */ (function () {
         var _b = camera.viewport, x = _b.x, y = _b.y, width = _b.width, height = _b.height;
         var sampleWeight = 1.0 / offsetList.length;
         if (sampleIndex === -1) {
-            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
+            drawPass.render(ctx, props, false);
             ValueCell.update(compose.values.uWeight, 1.0);
             ValueCell.update(compose.values.tColor, drawPass.getColorTarget(props.postprocessing).texture);
             compose.update();
@@ -167,7 +169,7 @@ var MultiSamplePass = /** @class */ (function () {
                 Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height);
                 camera.update();
                 // render scene
-                drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
+                drawPass.render(ctx, props, false);
                 // compose rendered scene with compose target
                 composeTarget.bind();
                 state.enable(gl.BLEND);
@@ -264,8 +266,8 @@ var MultiSampleHelper = /** @class */ (function () {
         return props.mode === 'temporal' ? this.sampleIndex !== -2 : false;
     };
     /** Return `true` while more samples are needed */
-    MultiSampleHelper.prototype.render = function (renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props) {
-        this.sampleIndex = this.multiSamplePass.render(this.sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+    MultiSampleHelper.prototype.render = function (ctx, props, toDrawingBuffer, forceOn) {
+        this.sampleIndex = this.multiSamplePass.render(this.sampleIndex, ctx, props, toDrawingBuffer, !!forceOn);
         return this.sampleIndex < 0;
     };
     return MultiSampleHelper;

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

@@ -5,7 +5,7 @@
  */
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { spiral2d } from '../../mol-math/misc';
-import { decodeFloatRGB, unpackRGBAToDepth } from '../../mol-util/float-packing';
+import { unpackRGBToInt, unpackRGBAToDepth } from '../../mol-util/number-packing';
 import { StereoCamera } from '../camera/stereo';
 import { cameraUnproject } from '../camera/util';
 import { Viewport } from '../camera/util';
@@ -43,29 +43,29 @@ 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;
 }());
@@ -128,7 +128,7 @@ var PickHelper = /** @class */ (function () {
     };
     PickHelper.prototype.getId = function (x, y, buffer) {
         var idx = this.getBufferIdx(x, y);
-        return decodeFloatRGB(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
+        return 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/mol-canvas3d/passes/postprocessing.js

@@ -31,7 +31,7 @@ function getOutlinesRenderable(ctx, depthTexture) {
 }
 var SsaoSchema = __assign(__assign({}, QuadSchema), { tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'), uSamples: UniformSpec('v3[]'), dNSamples: DefineSpec('number'), uProjection: UniformSpec('m4'), uInvProjection: UniformSpec('m4'), uBounds: UniformSpec('v4'), uTexSize: UniformSpec('v2'), uRadius: UniformSpec('f'), uBias: UniformSpec('f') });
 function getSsaoRenderable(ctx, depthTexture) {
-    var values = __assign(__assign({}, QuadValues), { tDepth: ValueCell.create(depthTexture), uSamples: ValueCell.create([0.0, 0.0, 1.0]), dNSamples: ValueCell.create(1), uProjection: ValueCell.create(Mat4.identity()), uInvProjection: ValueCell.create(Mat4.identity()), uBounds: ValueCell.create(Vec4()), uTexSize: ValueCell.create(Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)), uRadius: ValueCell.create(8.0), uBias: ValueCell.create(0.025) });
+    var values = __assign(__assign({}, QuadValues), { tDepth: ValueCell.create(depthTexture), uSamples: ValueCell.create([0.0, 0.0, 1.0]), dNSamples: ValueCell.create(32), uProjection: ValueCell.create(Mat4.identity()), uInvProjection: ValueCell.create(Mat4.identity()), uBounds: ValueCell.create(Vec4()), uTexSize: ValueCell.create(Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)), uRadius: ValueCell.create(8.0), uBias: ValueCell.create(0.025) });
     var schema = __assign({}, SsaoSchema);
     var shaderCode = ShaderCode('ssao', quad_vert, ssao_frag);
     var renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
@@ -39,7 +39,7 @@ function getSsaoRenderable(ctx, depthTexture) {
 }
 var SsaoBlurSchema = __assign(__assign({}, QuadSchema), { tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: UniformSpec('v2'), uKernel: UniformSpec('f[]'), dOcclusionKernelSize: DefineSpec('number'), uBlurDirectionX: UniformSpec('f'), uBlurDirectionY: UniformSpec('f'), uMaxPossibleViewZDiff: UniformSpec('f'), uNear: UniformSpec('f'), uFar: UniformSpec('f'), uBounds: UniformSpec('v4'), dOrthographic: DefineSpec('number') });
 function getSsaoBlurRenderable(ctx, ssaoDepthTexture, direction) {
-    var values = __assign(__assign({}, QuadValues), { tSsaoDepth: ValueCell.create(ssaoDepthTexture), uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())), uKernel: ValueCell.create([0.0]), dOcclusionKernelSize: ValueCell.create(1), uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0), uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0), uMaxPossibleViewZDiff: ValueCell.create(0.5), uNear: ValueCell.create(0.0), uFar: ValueCell.create(10000.0), uBounds: ValueCell.create(Vec4()), dOrthographic: ValueCell.create(0) });
+    var values = __assign(__assign({}, QuadValues), { tSsaoDepth: ValueCell.create(ssaoDepthTexture), uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())), uKernel: ValueCell.create([0.0]), dOcclusionKernelSize: ValueCell.create(15), uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0), uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0), uMaxPossibleViewZDiff: ValueCell.create(0.5), uNear: ValueCell.create(0.0), uFar: ValueCell.create(10000.0), uBounds: ValueCell.create(Vec4()), dOrthographic: ValueCell.create(0) });
     var schema = __assign({}, SsaoBlurSchema);
     var shaderCode = ShaderCode('ssao_blur', quad_vert, ssaoBlur_frag);
     var renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
@@ -67,7 +67,7 @@ function getSamples(vectorSamples, nSamples) {
 }
 var PostprocessingSchema = __assign(__assign({}, QuadSchema), { tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'), tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'), tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'), tOutlines: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: UniformSpec('v2'), dOrthographic: DefineSpec('number'), uNear: UniformSpec('f'), uFar: UniformSpec('f'), uFogNear: UniformSpec('f'), uFogFar: UniformSpec('f'), uFogColor: UniformSpec('v3'), uOutlineColor: UniformSpec('v3'), uTransparentBackground: UniformSpec('b'), uMaxPossibleViewZDiff: UniformSpec('f'), dOcclusionEnable: DefineSpec('boolean'), dOutlineEnable: DefineSpec('boolean'), dOutlineScale: DefineSpec('number'), uOutlineThreshold: UniformSpec('f') });
 function getPostprocessingRenderable(ctx, colorTexture, depthTexture, outlinesTexture, ssaoDepthTexture) {
-    var values = __assign(__assign({}, QuadValues), { tSsaoDepth: ValueCell.create(ssaoDepthTexture), tColor: ValueCell.create(colorTexture), tDepth: ValueCell.create(depthTexture), tOutlines: ValueCell.create(outlinesTexture), uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())), dOrthographic: ValueCell.create(0), uNear: ValueCell.create(1), uFar: ValueCell.create(10000), uFogNear: ValueCell.create(10000), uFogFar: ValueCell.create(10000), uFogColor: ValueCell.create(Vec3.create(1, 1, 1)), uOutlineColor: ValueCell.create(Vec3.create(0, 0, 0)), uTransparentBackground: ValueCell.create(false), uMaxPossibleViewZDiff: ValueCell.create(0.5), dOcclusionEnable: ValueCell.create(false), dOutlineEnable: ValueCell.create(false), dOutlineScale: ValueCell.create(1), uOutlineThreshold: ValueCell.create(0.33) });
+    var values = __assign(__assign({}, QuadValues), { tSsaoDepth: ValueCell.create(ssaoDepthTexture), tColor: ValueCell.create(colorTexture), tDepth: ValueCell.create(depthTexture), tOutlines: ValueCell.create(outlinesTexture), uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())), dOrthographic: ValueCell.create(0), uNear: ValueCell.create(1), uFar: ValueCell.create(10000), uFogNear: ValueCell.create(10000), uFogFar: ValueCell.create(10000), uFogColor: ValueCell.create(Vec3.create(1, 1, 1)), uOutlineColor: ValueCell.create(Vec3.create(0, 0, 0)), uTransparentBackground: ValueCell.create(false), uMaxPossibleViewZDiff: ValueCell.create(0.5), dOcclusionEnable: ValueCell.create(true), dOutlineEnable: ValueCell.create(false), dOutlineScale: ValueCell.create(1), uOutlineThreshold: ValueCell.create(0.33) });
     var schema = __assign({}, PostprocessingSchema);
     var shaderCode = ShaderCode('postprocessing', quad_vert, postprocessing_frag);
     var renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);

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

@@ -135,7 +135,7 @@ function getWeightsRenderable(ctx, edgesTexture) {
     var height = edgesTexture.getHeight();
     var areaTexture = createTexture(ctx.gl, ctx.extensions, 'image-uint8', 'rgb', 'ubyte', 'linear');
     var searchTexture = createTexture(ctx.gl, ctx.extensions, 'image-uint8', 'rgba', 'ubyte', 'nearest');
-    var values = __assign(__assign({}, QuadValues), { tEdges: ValueCell.create(edgesTexture), tArea: ValueCell.create(areaTexture), tSearch: ValueCell.create(searchTexture), uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)), uViewport: ValueCell.create(Vec4()), dMaxSearchSteps: ValueCell.create(8) });
+    var values = __assign(__assign({}, QuadValues), { tEdges: ValueCell.create(edgesTexture), tArea: ValueCell.create(areaTexture), tSearch: ValueCell.create(searchTexture), uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)), uViewport: ValueCell.create(Vec4()), dMaxSearchSteps: ValueCell.create(16) });
     // Note: loading image textures requires `HTMLImageElement` to be available
     loadImageTexture(getAreaTexture(), values.tArea, areaTexture);
     loadImageTexture(getSearchTexture(), values.tSearch, searchTexture);

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

@@ -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: {};
@@ -48,6 +49,16 @@ export declare namespace BaseGeometry {
             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;
     type Counts = {
@@ -71,6 +82,13 @@ export declare namespace BaseGeometry {
         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/mol-geo/geometry/base.js

@@ -13,6 +13,7 @@ import { UniformColorTheme } from '../../mol-theme/color/uniform';
 import { UniformSizeTheme } from '../../mol-theme/size/uniform';
 import { smoothstep } from '../../mol-math/interpolate';
 import { Material } from '../../mol-util/material';
+import { Clip } from '../../mol-util/clip';
 export var VisualQualityInfo = {
     'custom': {},
     'auto': {},
@@ -71,6 +72,7 @@ export var BaseGeometry;
         alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity', isEssential: true, description: 'How opaque/transparent the representation is rendered.' }),
         quality: PD.Select('auto', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }),
         material: Material.getParam(),
+        clip: PD.Group(Clip.Params),
     };
     function createSimple(colorValue, sizeValue, transform) {
         if (colorValue === void 0) { colorValue = ColorNames.grey; }
@@ -86,6 +88,7 @@ export var BaseGeometry;
     }
     BaseGeometry.createSimple = createSimple;
     function createValues(props, counts) {
+        var clip = Clip.getClip(props.clip);
         return {
             alpha: ValueCell.create(props.alpha),
             uAlpha: ValueCell.create(props.alpha),
@@ -96,6 +99,13 @@ export var BaseGeometry;
             uRoughness: ValueCell.create(props.material.roughness),
             uBumpiness: ValueCell.create(props.material.bumpiness),
             dLightCount: ValueCell.create(1),
+            dClipObjectCount: ValueCell.create(clip.objects.count),
+            dClipVariant: ValueCell.create(clip.variant),
+            uClipObjectType: ValueCell.create(clip.objects.type),
+            uClipObjectInvert: ValueCell.create(clip.objects.invert),
+            uClipObjectPosition: ValueCell.create(clip.objects.position),
+            uClipObjectRotation: ValueCell.create(clip.objects.rotation),
+            uClipObjectScale: ValueCell.create(clip.objects.scale),
         };
     }
     BaseGeometry.createValues = createValues;
@@ -104,6 +114,14 @@ export var BaseGeometry;
         ValueCell.updateIfChanged(values.uMetalness, props.material.metalness);
         ValueCell.updateIfChanged(values.uRoughness, props.material.roughness);
         ValueCell.updateIfChanged(values.uBumpiness, props.material.bumpiness);
+        var clip = Clip.getClip(props.clip);
+        ValueCell.update(values.dClipObjectCount, clip.objects.count);
+        ValueCell.update(values.dClipVariant, clip.variant);
+        ValueCell.update(values.uClipObjectType, clip.objects.type);
+        ValueCell.update(values.uClipObjectInvert, clip.objects.invert);
+        ValueCell.update(values.uClipObjectPosition, clip.objects.position);
+        ValueCell.update(values.uClipObjectRotation, clip.objects.rotation);
+        ValueCell.update(values.uClipObjectScale, clip.objects.scale);
     }
     BaseGeometry.updateValues = updateValues;
     function createRenderableState(props) {
@@ -117,7 +135,6 @@ export var BaseGeometry;
             colorOnly: false,
             opaque: opaque,
             writeDepth: opaque,
-            noClip: false,
         };
     }
     BaseGeometry.createRenderableState = createRenderableState;

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

@@ -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>
  */
@@ -7,9 +7,7 @@ import { ValueCell } from '../../mol-util/value-cell';
 import { Vec2 } from '../../mol-math/linear-algebra';
 import { createTextureImage } from '../../mol-gl/renderable/util';
 export function applyClippingGroups(array, start, end, groups) {
-    for (var i = start; i < end; ++i) {
-        array[i] = groups;
-    }
+    array.fill(groups, start, end);
     return true;
 }
 export function clearClipping(array, start, end) {
@@ -25,8 +23,6 @@ export function createClipping(count, clippingData) {
     }
     else {
         return {
-            dClipObjectCount: ValueCell.create(0),
-            dClipVariant: ValueCell.create('instance'),
             tClipping: ValueCell.create(clipping),
             uClippingTexDim: ValueCell.create(Vec2.create(clipping.width, clipping.height)),
             dClipping: ValueCell.create(count > 0),
@@ -38,12 +34,11 @@ export function createEmptyClipping(clippingData) {
     if (clippingData) {
         ValueCell.update(clippingData.tClipping, emptyClippingTexture);
         ValueCell.update(clippingData.uClippingTexDim, Vec2.create(1, 1));
+        ValueCell.updateIfChanged(clippingData.dClipping, false);
         return clippingData;
     }
     else {
         return {
-            dClipObjectCount: ValueCell.create(0),
-            dClipVariant: ValueCell.create('instance'),
             tClipping: ValueCell.create(emptyClippingTexture),
             uClippingTexDim: ValueCell.create(Vec2.create(1, 1)),
             dClipping: ValueCell.create(false),

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

@@ -32,6 +32,7 @@ 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) {
@@ -203,4 +204,25 @@ export function createGridColor(grid, type, colorData) {
         };
     }
 }
+//
+/** Creates direct color */
+function createDirectColor(colorData) {
+    if (colorData) {
+        ValueCell.updateIfChanged(colorData.dColorType, 'direct');
+        return colorData;
+    }
+    else {
+        return {
+            uColor: ValueCell.create(Vec3()),
+            tColor: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            tColorGrid: ValueCell.create(createNullTexture()),
+            tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            uColorTexDim: ValueCell.create(Vec2.create(1, 1)),
+            uColorGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
+            uColorGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
+            dColorType: ValueCell.create('direct'),
+            dUsePalette: ValueCell.create(false),
+        };
+    }
+}
 //# sourceMappingURL=color-data.js.map

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

@@ -52,6 +52,16 @@ export declare namespace 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/mol-geo/geometry/cylinders/cylinders.js

@@ -153,7 +153,7 @@ export var Cylinders;
         var padding = getMaxSize(size) * props.sizeFactor;
         var invariantBoundingSphere = Sphere3D.clone(cylinders.boundingSphere);
         var boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return __assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign({ aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: ValueCell.create(boundingSphere), invariantBoundingSphere: ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: ValueCell.create(Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: ValueCell.create(padding) }), BaseGeometry.createValues(props, counts)), { uSizeFactor: ValueCell.create(props.sizeFactor * props.sizeAspectRatio), dDoubleSided: ValueCell.create(props.doubleSided), dIgnoreLight: ValueCell.create(props.ignoreLight), dXrayShaded: ValueCell.create(props.xrayShaded), uBumpFrequency: ValueCell.create(props.bumpFrequency), uBumpAmplitude: ValueCell.create(props.bumpAmplitude) });
+        return __assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign({ dGeometryType: 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: ValueCell.create(boundingSphere), invariantBoundingSphere: ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: ValueCell.create(Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: ValueCell.create(padding) }), BaseGeometry.createValues(props, counts)), { uSizeFactor: ValueCell.create(props.sizeFactor * props.sizeAspectRatio), uDoubleSided: ValueCell.create(props.doubleSided), dIgnoreLight: ValueCell.create(props.ignoreLight), dXrayShaded: ValueCell.create(props.xrayShaded), uBumpFrequency: ValueCell.create(props.bumpFrequency), uBumpAmplitude: ValueCell.create(props.bumpAmplitude) });
     }
     function createValuesSimple(cylinders, props, colorValue, sizeValue, transform) {
         var s = BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -163,7 +163,7 @@ export var Cylinders;
     function updateValues(values, props) {
         BaseGeometry.updateValues(values, props);
         ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor * props.sizeAspectRatio);
-        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
+        ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
         ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);

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

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2018-2020 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>
  */
 import { Texture } from '../../../mol-gl/webgl/texture';
 import { Box3D, Sphere3D } from '../../../mol-math/geometry';
-import { Mat4, Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
+import { Mat4, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
 import { ValueCell } from '../../../mol-util';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { GeometryUtils } from '../geometry';
@@ -24,51 +24,18 @@ export interface DirectVolume {
     readonly unitToCartn: ValueCell<Mat4>;
     readonly cartnToUnit: ValueCell<Mat4>;
     readonly packedGroup: ValueCell<boolean>;
+    readonly axisOrder: ValueCell<Vec3>;
     /** Bounding sphere of the volume */
     readonly boundingSphere: Sphere3D;
     setBoundingSphere(boundingSphere: Sphere3D): void;
 }
 export declare namespace DirectVolume {
-    function create(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, directVolume?: DirectVolume): DirectVolume;
+    function create(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, axisOrder: Vec3, directVolume?: DirectVolume): DirectVolume;
     function createEmpty(directVolume?: DirectVolume): DirectVolume;
-    function createRenderModeParam(stats?: Grid['stats']): PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
     const Params: {
-        doubleSided: PD.BooleanParam;
-        flipSided: PD.BooleanParam;
-        flatShaded: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
-        renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            controlPoints: Vec2[];
-            list: {
-                kind: "set" | "interpolate";
-                colors: import("../../../mol-util/color/color").ColorListEntry[];
-            };
-        }>, "volume"> | PD.NamedParams<PD.Normalize<{
-            isoValue: Readonly<{
-                kind: "absolute";
-                absoluteValue: number;
-            }> | Readonly<{
-                kind: "relative";
-                relativeValue: number;
-            }>;
-            singleLayer: boolean;
-        }>, "isosurface">>;
+        controlPoints: PD.LineGraph;
         stepsPerCell: PD.Numeric;
         jumpLength: PD.Numeric;
         alpha: PD.Numeric;
@@ -78,6 +45,16 @@ export declare namespace DirectVolume {
             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<DirectVolume, Params>;