1.2.4

GPU grid 3d computation wrapper

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.2.1",
+  "version": "1.2.4",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.2.1",
+  "version": "1.2.4",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/cli/state-docs/pd-to-md.ts

@@ -26,7 +26,8 @@ function paramInfo(param: PD.Any, offset: number): string {
         case 'file': return `JavaScript File Handle`;
         case 'file-list': return `JavaScript FileList Handle`;
         case 'select': return `One of ${oToS(param.options)}`;
-        case 'value-ref': return `Reference to a state object.`;
+        case 'value-ref': return `Reference to a runtime defined value.`;
+        case 'data-ref': return `Reference to a computed data value.`;
         case 'text': return 'String';
         case 'interval': return `Interval [min, max]`;
         case 'group': return `Object with:\n${getParams(param.params, offset + 2)}`;

src/examples/alpha-orbitals/index.ts

@@ -20,8 +20,8 @@ import { BehaviorSubject } from 'rxjs';
 import { debounceTime, skip } from 'rxjs/operators';
 import './index.html';
 import { Basis, AlphaOrbital } from '../../extensions/alpha-orbitals/data-model';
-import { canComputeAlphaOrbitalsOnGPU } from '../../extensions/alpha-orbitals/gpu/compute';
 import { PluginCommands } from '../../mol-plugin/commands';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 require('mol-plugin-ui/skin/light.scss');
 
 interface DemoInput {
@@ -71,7 +71,7 @@ export class AlphaOrbitalsExample {
 
         this.plugin.managers.interactivity.setProps({ granularity: 'element' });
 
-        if (!canComputeAlphaOrbitalsOnGPU(this.plugin.canvas3d?.webgl)) {
+        if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
             PluginCommands.Toast.Show(this.plugin, {
                 title: 'Error',
                 message: `Browser/device does not support required WebGL extension (OES_texture_float).`

src/extensions/alpha-orbitals/data-model.ts

@@ -7,8 +7,8 @@
 import { Mat4, Tensor, Vec3 } from '../../mol-math/linear-algebra';
 import { Grid } from '../../mol-model/volume';
 import { SphericalBasisOrder } from './spherical-functions';
-import { Box3D } from '../../mol-math/geometry';
-import { arrayMin, arrayMax, arrayRms } from '../../mol-util/array';
+import { Box3D, RegularGrid3d } from '../../mol-math/geometry';
+import { arrayMin, arrayMax, arrayRms, arrayMean } from '../../mol-util/array';
 
 // Note: generally contracted gaussians are currently not supported.
 export interface SphericalElectronShell {
@@ -95,7 +95,7 @@ export function initCubeGrid(params: CubeGridComputationParams): CubeGridInfo {
 
 const BohrToAngstromFactor = 0.529177210859;
 
-export function createGrid(gridInfo: CubeGridInfo, values: Float32Array, axisOrder: number[]) {
+export function createGrid(gridInfo: RegularGrid3d, values: Float32Array, axisOrder: number[]) {
     const boxSize = Box3D.size(Vec3(), gridInfo.box);
     const boxOrigin = Vec3.clone(gridInfo.box.min);
 
@@ -122,7 +122,7 @@ export function createGrid(gridInfo: CubeGridInfo, values: Float32Array, axisOrd
         stats: {
             min: arrayMin(values),
             max: arrayMax(values),
-            mean: arrayMax(values),
+            mean: arrayMean(values),
             sigma: arrayRms(values),
         },
     };

src/extensions/alpha-orbitals/density.ts

@@ -5,10 +5,11 @@
  */
 
 import { sortArray } from '../../mol-data/util';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Task } from '../../mol-task';
 import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
-import { canComputeAlphaOrbitalsOnGPU, gpuComputeAlphaOrbitalsDensityGridValues } from './gpu/compute';
+import { gpuComputeAlphaOrbitalsDensityGridValues } from './gpu/compute';
 
 export function createSphericalCollocationDensityGrid(
     params: CubeGridComputationParams, orbitals: AlphaOrbital[], webgl?: WebGLContext
@@ -17,9 +18,9 @@ export function createSphericalCollocationDensityGrid(
         const cubeGrid = initCubeGrid(params);
 
         let matrix: Float32Array;
-        if (canComputeAlphaOrbitalsOnGPU(webgl)) {
+        if (canComputeGrid3dOnGPU(webgl)) {
             // console.time('gpu');
-            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(webgl!, cubeGrid, orbitals, ctx);
+            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl!, cubeGrid, orbitals);
             // console.timeEnd('gpu');
         } else {
             throw new Error('Missing OES_texture_float WebGL extension.');

src/extensions/alpha-orbitals/gpu/compute.ts

@@ -4,46 +4,72 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { QuadSchema, QuadValues } from '../../../mol-gl/compute/util';
-import { ComputeRenderable, createComputeRenderable } from '../../../mol-gl/renderable';
-import { DefineSpec, TextureSpec, UniformSpec, Values } from '../../../mol-gl/renderable/schema';
-import { ShaderCode } from '../../../mol-gl/shader-code';
-import quad_vert from '../../../mol-gl/shader/quad.vert';
+import { createGrid3dComputeRenderable } from '../../../mol-gl/compute/grid3d';
+import { TextureSpec, UnboxedValues, UniformSpec } from '../../../mol-gl/renderable/schema';
 import { WebGLContext } from '../../../mol-gl/webgl/context';
-import { createComputeRenderItem } from '../../../mol-gl/webgl/render-item';
 import { RuntimeContext } from '../../../mol-task';
 import { ValueCell } from '../../../mol-util';
 import { arrayMin } from '../../../mol-util/array';
-import { isLittleEndian } from '../../../mol-util/is-little-endian';
 import { AlphaOrbital, Basis, CubeGridInfo } from '../data-model';
 import { normalizeBasicOrder, SphericalBasisOrder } from '../spherical-functions';
-import shader_frag from './shader.frag';
+import { MAIN, UTILS } from './shader.frag';
 
-const AlphaOrbitalsSchema = {
-    ...QuadSchema,
-    uDimensions: UniformSpec('v3'),
-    uMin: UniformSpec('v3'),
-    uDelta: UniformSpec('v3'),
+const Schema = {
     tCenters: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
     tInfo: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
     tCoeff: TextureSpec('image-float32', 'rgb', 'float', 'nearest'),
     tAlpha: TextureSpec('image-float32', 'alpha', 'float', 'nearest'),
-    uWidth: UniformSpec('f'),
     uNCenters: UniformSpec('i'),
     uNAlpha: UniformSpec('i'),
     uNCoeff: UniformSpec('i'),
     uMaxCoeffs: UniformSpec('i'),
-    uLittleEndian: UniformSpec('b'),
-    uDensity: UniformSpec('b'),
-    uOccupancy: UniformSpec('f'),
-    tCumulativeSum: TextureSpec('texture', 'rgba', 'ubyte', 'nearest')
 };
-type AlphaOrbitalsSchema = Values<typeof AlphaOrbitalsSchema>
-const AlphaOrbitalsName = 'alpha-orbitals';
-const AlphaOrbitalsTex0 = 'alpha-orbitals-0';
-const AlphaOrbitalsTex1 = 'alpha-orbitals-1';
-const AlphaOrbitalsShaderCode = ShaderCode(AlphaOrbitalsName, quad_vert, shader_frag);
-type AlphaOrbitalsRenderable = ComputeRenderable<AlphaOrbitalsSchema>
+
+const Orbitals = createGrid3dComputeRenderable({
+    schema: Schema,
+    loopBounds: ['uNCenters', 'uMaxCoeffs'],
+    mainCode: MAIN,
+    utilCode: UTILS,
+    returnCode: 'v',
+    values(params: { grid: CubeGridInfo, orbital: AlphaOrbital }) {
+        return createTextureData(params.grid, params.orbital);
+    }
+});
+
+const Density = createGrid3dComputeRenderable({
+    schema: {
+        ...Schema,
+        uOccupancy: UniformSpec('f'),
+    },
+    loopBounds: ['uNCenters', 'uMaxCoeffs'],
+    mainCode: MAIN,
+    utilCode: UTILS,
+    returnCode: 'current + uOccupancy * v * v',
+    values(params: { grid: CubeGridInfo, orbitals: AlphaOrbital[] }) {
+        return {
+            ...createTextureData(params.grid, params.orbitals[0]),
+            uOccupancy: 0
+        };
+    },
+    cumulative: {
+        states(params: { grid: CubeGridInfo, orbitals: AlphaOrbital[] }) {
+            return params.orbitals.filter(o => o.occupancy !== 0);
+        },
+        update({ grid }, state: AlphaOrbital, values) {
+            const alpha = getNormalizedAlpha(grid.params.basis, state.alpha, grid.params.sphericalOrder);
+            ValueCell.updateIfChanged(values.uOccupancy, state.occupancy);
+            ValueCell.update(values.tAlpha, { width: alpha.length, height: 1, array: alpha });
+        }
+    }
+});
+
+export function gpuComputeAlphaOrbitalsGridValues(ctx: RuntimeContext, webgl: WebGLContext, grid: CubeGridInfo, orbital: AlphaOrbital) {
+    return Orbitals(ctx, webgl, grid, { grid, orbital });
+}
+
+export function gpuComputeAlphaOrbitalsDensityGridValues(ctx: RuntimeContext, webgl: WebGLContext, grid: CubeGridInfo, orbitals: AlphaOrbital[]) {
+    return Density(ctx, webgl, grid, { grid, orbitals });
+}
 
 function getNormalizedAlpha(basis: Basis, alphaOrbitals: number[], sphericalOrder: SphericalBasisOrder) {
     const alpha = new Float32Array(alphaOrbitals.length);
@@ -62,7 +88,7 @@ function getNormalizedAlpha(basis: Basis, alphaOrbitals: number[], sphericalOrde
     return alpha;
 }
 
-function createTextureData(grid: CubeGridInfo, orbital: AlphaOrbital) {
+function createTextureData(grid: CubeGridInfo, orbital: AlphaOrbital): UnboxedValues<typeof Schema> {
     const { basis, sphericalOrder, cutoffThreshold } = grid.params;
 
     let centerCount = 0;
@@ -131,179 +157,14 @@ function createTextureData(grid: CubeGridInfo, orbital: AlphaOrbital) {
         }
     }
 
-    return { nCenters: centerCount, nAlpha: baseCount, nCoeff: coeffCount, maxCoeffs, centers, info, alpha, coeff };
-}
-
-function createAlphaOrbitalsRenderable(ctx: WebGLContext, grid: CubeGridInfo, orbital: AlphaOrbital): AlphaOrbitalsRenderable {
-    const data = createTextureData(grid, orbital);
-
-    const [nx, ny, nz] = grid.dimensions;
-    const width = Math.ceil(Math.sqrt(nx * ny * nz));
-
-    if (!ctx.namedFramebuffers[AlphaOrbitalsName]) {
-        ctx.namedFramebuffers[AlphaOrbitalsName] = ctx.resources.framebuffer();
-    }
-    if (!ctx.namedTextures[AlphaOrbitalsTex0]) {
-        ctx.namedTextures[AlphaOrbitalsTex0] = ctx.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
-    }
-    if (!ctx.namedTextures[AlphaOrbitalsTex1]) {
-        ctx.namedTextures[AlphaOrbitalsTex1] = ctx.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
-    }
-
-    const values: AlphaOrbitalsSchema = {
-        ...QuadValues,
-        uDimensions: ValueCell.create(grid.dimensions),
-        uMin: ValueCell.create(grid.box.min),
-        uDelta: ValueCell.create(grid.delta),
-        uWidth: ValueCell.create(width),
-        uNCenters: ValueCell.create(data.nCenters),
-        uNAlpha: ValueCell.create(data.nAlpha),
-        uNCoeff: ValueCell.create(data.nCoeff),
-        uMaxCoeffs: ValueCell.create(data.maxCoeffs),
-        tCenters: ValueCell.create({ width: data.nCenters, height: 1, array: data.centers }),
-        tInfo: ValueCell.create({ width: data.nCenters, height: 1, array: data.info }),
-        tCoeff: ValueCell.create({ width: data.nCoeff, height: 1, array: data.coeff }),
-        tAlpha: ValueCell.create({ width: data.nAlpha, height: 1, array: data.alpha }),
-        uLittleEndian: ValueCell.create(isLittleEndian()),
-        uDensity: ValueCell.create(false),
-        uOccupancy: ValueCell.create(0),
-        tCumulativeSum: ValueCell.create(ctx.namedTextures[AlphaOrbitalsTex1])
+    return {
+        uNCenters: centerCount,
+        uNAlpha: baseCount,
+        uNCoeff: coeffCount,
+        uMaxCoeffs: maxCoeffs,
+        tCenters: { width: centerCount, height: 1, array: centers },
+        tInfo: { width: centerCount, height: 1, array: info },
+        tCoeff: { width: coeffCount, height: 1, array: coeff },
+        tAlpha: { width: baseCount, height: 1, array: alpha },
     };
-
-    const schema = { ...AlphaOrbitalsSchema };
-    if (!ctx.isWebGL2) {
-        // workaround for webgl1 limitation that loop counters need to be `const`
-        (schema.uNCenters as any) = DefineSpec('number');
-        (schema.uMaxCoeffs as any) = DefineSpec('number');
-    }
-
-    const renderItem = createComputeRenderItem(ctx, 'triangles', AlphaOrbitalsShaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
-
-function getAlphaOrbitalsRenderable(ctx: WebGLContext, grid: CubeGridInfo, orbital: AlphaOrbital): AlphaOrbitalsRenderable {
-    if (ctx.namedComputeRenderables[AlphaOrbitalsName]) {
-        const v = ctx.namedComputeRenderables[AlphaOrbitalsName].values as AlphaOrbitalsSchema;
-
-        const data = createTextureData(grid, orbital);
-
-        const [nx, ny, nz] = grid.dimensions;
-        const width = Math.ceil(Math.sqrt(nx * ny * nz));
-
-        ValueCell.update(v.uDimensions, grid.dimensions);
-        ValueCell.update(v.uMin, grid.box.min);
-        ValueCell.update(v.uDelta, grid.delta);
-        ValueCell.updateIfChanged(v.uWidth, width);
-        ValueCell.updateIfChanged(v.uNCenters, data.nCenters);
-        ValueCell.updateIfChanged(v.uNAlpha, data.nAlpha);
-        ValueCell.updateIfChanged(v.uNCoeff, data.nCoeff);
-        ValueCell.updateIfChanged(v.uMaxCoeffs, data.maxCoeffs);
-        ValueCell.update(v.tCenters, { width: data.nCenters, height: 1, array: data.centers });
-        ValueCell.update(v.tInfo, { width: data.nCenters, height: 1, array: data.info });
-        ValueCell.update(v.tCoeff, { width: data.nCoeff, height: 1, array: data.coeff });
-        ValueCell.update(v.tAlpha, { width: data.nAlpha, height: 1, array: data.alpha });
-        ValueCell.updateIfChanged(v.uLittleEndian, isLittleEndian());
-        ValueCell.updateIfChanged(v.uDensity, false);
-        ValueCell.updateIfChanged(v.uOccupancy, 0);
-        ValueCell.updateIfChanged(v.tCumulativeSum, ctx.namedTextures[AlphaOrbitalsTex1]);
-
-        ctx.namedComputeRenderables[AlphaOrbitalsName].update();
-    } else {
-        ctx.namedComputeRenderables[AlphaOrbitalsName] = createAlphaOrbitalsRenderable(ctx, grid, orbital);
-    }
-    return ctx.namedComputeRenderables[AlphaOrbitalsName];
-}
-
-export function gpuComputeAlphaOrbitalsGridValues(webgl: WebGLContext, grid: CubeGridInfo, orbital: AlphaOrbital) {
-    const [nx, ny, nz] = grid.dimensions;
-    const renderable = getAlphaOrbitalsRenderable(webgl, grid, orbital);
-    const width = renderable.values.uWidth.ref.value;
-
-    const framebuffer = webgl.namedFramebuffers[AlphaOrbitalsName];
-    webgl.namedTextures[AlphaOrbitalsTex0].define(width, width);
-    webgl.namedTextures[AlphaOrbitalsTex0].attachFramebuffer(framebuffer, 'color0');
-
-    const { gl, state } = webgl;
-    framebuffer.bind();
-    gl.viewport(0, 0, width, width);
-    gl.scissor(0, 0, width, width);
-    state.disable(gl.SCISSOR_TEST);
-    state.disable(gl.BLEND);
-    state.disable(gl.DEPTH_TEST);
-    state.depthMask(false);
-    renderable.render();
-
-    const array = new Uint8Array(width * width * 4);
-    webgl.readPixels(0, 0, width, width, array);
-    return new Float32Array(array.buffer, array.byteOffset, nx * ny * nz);
-}
-
-export function canComputeAlphaOrbitalsOnGPU(webgl?: WebGLContext) {
-    return !!webgl?.extensions.textureFloat;
-}
-
-export async function gpuComputeAlphaOrbitalsDensityGridValues(webgl: WebGLContext, grid: CubeGridInfo, orbitals: AlphaOrbital[], ctx: RuntimeContext) {
-    await ctx.update({ message: 'Initializing...', isIndeterminate: true });
-
-    const [nx, ny, nz] = grid.dimensions;
-    const renderable = getAlphaOrbitalsRenderable(webgl, grid, orbitals[0]);
-    const width = renderable.values.uWidth.ref.value;
-
-    if (!webgl.namedFramebuffers[AlphaOrbitalsName]) {
-        webgl.namedFramebuffers[AlphaOrbitalsName] = webgl.resources.framebuffer();
-    }
-    const framebuffer = webgl.namedFramebuffers[AlphaOrbitalsName];
-    const tex = [webgl.namedTextures[AlphaOrbitalsTex0], webgl.namedTextures[AlphaOrbitalsTex1]];
-
-    tex[0].define(width, width);
-    tex[1].define(width, width);
-
-    const values = renderable.values as AlphaOrbitalsSchema;
-    const { gl, state } = webgl;
-
-    gl.viewport(0, 0, width, width);
-    gl.scissor(0, 0, width, width);
-    state.disable(gl.SCISSOR_TEST);
-    state.disable(gl.BLEND);
-    state.disable(gl.DEPTH_TEST);
-    state.depthMask(false);
-
-    gl.clearColor(0, 0, 0, 0);
-
-    tex[0].attachFramebuffer(framebuffer, 'color0');
-    gl.clear(gl.COLOR_BUFFER_BIT);
-
-    tex[1].attachFramebuffer(framebuffer, 'color0');
-    gl.clear(gl.COLOR_BUFFER_BIT);
-
-    ValueCell.update(values.uDensity, true);
-
-    const nonZero = orbitals.filter(o => o.occupancy !== 0);
-    await ctx.update({ message: 'Computing...', isIndeterminate: false, current: 0, max: nonZero.length });
-    for (let i = 0; i < nonZero.length; i++) {
-        const alpha = getNormalizedAlpha(grid.params.basis, nonZero[i].alpha, grid.params.sphericalOrder);
-
-        ValueCell.update(values.uOccupancy, nonZero[i].occupancy);
-        ValueCell.update(values.tCumulativeSum, tex[(i + 1) % 2]);
-        ValueCell.update(values.tAlpha, { width: alpha.length, height: 1, array: alpha });
-        tex[i % 2].attachFramebuffer(framebuffer, 'color0');
-        gl.viewport(0, 0, width, width);
-        gl.scissor(0, 0, width, width);
-        state.disable(gl.SCISSOR_TEST);
-        state.disable(gl.BLEND);
-        state.disable(gl.DEPTH_TEST);
-        state.depthMask(false);
-        renderable.update();
-        renderable.render();
-
-        if (i !== nonZero.length - 1 && ctx.shouldUpdate) {
-            await ctx.update({ current: i + 1 });
-        }
-    }
-
-    const array = new Uint8Array(width * width * 4);
-    webgl.readPixels(0, 0, width, width, array);
-
-    return new Float32Array(array.buffer, array.byteOffset, nx * ny * nz);
 }

src/extensions/alpha-orbitals/gpu/shader.frag.ts

@@ -4,145 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export default `
-precision highp float;
-precision highp int;
-precision highp sampler2D;
-
-uniform vec2 uQuadShift;
-uniform vec3 uDimensions;
-uniform vec3 uMin;
-uniform vec3 uDelta;
-
-uniform sampler2D tCenters;
-uniform sampler2D tInfo;
-uniform sampler2D tCoeff;
-uniform sampler2D tAlpha;
-
-uniform float uWidth;
-
-#ifndef uNCenters
-    uniform int uNCenters;
-#endif
-
-uniform int uNCoeff;
-uniform int uNAlpha;
-
-uniform bool uDensity;
-uniform float uOccupancy;
-uniform sampler2D tCumulativeSum;
-
-uniform bool uLittleEndian;
-
-float shiftRight (float v, float amt) {
-  v = floor(v) + 0.5;
-  return floor(v / exp2(amt));
-}
-float shiftLeft (float v, float amt) {
-    return floor(v * exp2(amt) + 0.5);
-}
-float maskLast (float v, float bits) {
-    return mod(v, shiftLeft(1.0, bits));
-}
-float extractBits (float num, float from, float to) {
-    from = floor(from + 0.5); to = floor(to + 0.5);
-    return maskLast(shiftRight(num, from), to - from);
-}
-// Adapted from https://github.com/equinor/glsl-float-to-rgba
-// MIT License, Copyright (c) 2020 Equinor
-vec4 floatToRgba(float texelFloat) {
-    if (texelFloat == 0.0) return vec4(0, 0, 0, 0);
-    float sign = texelFloat > 0.0 ? 0.0 : 1.0;
-    texelFloat = abs(texelFloat);
-    float exponent = floor(log2(texelFloat));
-    float biased_exponent = exponent + 127.0;
-    float fraction = ((texelFloat / exp2(exponent)) - 1.0) * 8388608.0;
-    float t = biased_exponent / 2.0;
-    float last_bit_of_biased_exponent = fract(t) * 2.0;
-    float remaining_bits_of_biased_exponent = floor(t);
-    float byte4 = extractBits(fraction, 0.0, 8.0) / 255.0;
-    float byte3 = extractBits(fraction, 8.0, 16.0) / 255.0;
-    float byte2 = (last_bit_of_biased_exponent * 128.0 + extractBits(fraction, 16.0, 23.0)) / 255.0;
-    float byte1 = (sign * 128.0 + remaining_bits_of_biased_exponent) / 255.0;
-    return (
-        uLittleEndian
-            ? vec4(byte4, byte3, byte2, byte1)
-            : vec4(byte1, byte2, byte3, byte4)
-    );
-}
-
-///////////////////////////////////////////////////////
-
-ivec4 floatsToBytes(vec4 inputFloats) {
-  ivec4 bytes = ivec4(inputFloats * 255.0);
-  return (
-    uLittleEndian
-    ? bytes.abgr
-    : bytes
-  );
-}
-
-// Break the four bytes down into an array of 32 bits.
-void bytesToBits(const in ivec4 bytes, out bool bits[32]) {
-  for (int channelIndex = 0; channelIndex < 4; ++channelIndex) {
-    float acc = float(bytes[channelIndex]);
-    for (int indexInByte = 7; indexInByte >= 0; --indexInByte) {
-      float powerOfTwo = exp2(float(indexInByte));
-      bool bit = acc >= powerOfTwo;
-      bits[channelIndex * 8 + (7 - indexInByte)] = bit;
-      acc = mod(acc, powerOfTwo);
-    }
-  }
-}
-
-// Compute the exponent of the 32-bit float.
-float getExponent(bool bits[32]) {
-  const int startIndex = 1;
-  const int bitStringLength = 8;
-  const int endBeforeIndex = startIndex + bitStringLength;
-  float acc = 0.0;
-  int pow2 = bitStringLength - 1;
-  for (int bitIndex = startIndex; bitIndex < endBeforeIndex; ++bitIndex) {
-    acc += float(bits[bitIndex]) * exp2(float(pow2--));
-  }
-  return acc;
-}
-
-// Compute the mantissa of the 32-bit float.
-float getMantissa(bool bits[32], bool subnormal) {
-  const int startIndex = 9;
-  const int bitStringLength = 23;
-  const int endBeforeIndex = startIndex + bitStringLength;
-  // Leading/implicit/hidden bit convention:
-  // If the number is not subnormal (with exponent 0), we add a leading 1 digit.
-  float acc = float(!subnormal) * exp2(float(bitStringLength));
-  int pow2 = bitStringLength - 1;
-  for (int bitIndex = startIndex; bitIndex < endBeforeIndex; ++bitIndex) {
-    acc += float(bits[bitIndex]) * exp2(float(pow2--));
-  }
-  return acc;
-}
-
-// Parse the float from its 32 bits.
-float bitsToFloat(bool bits[32]) {
-  float signBit = float(bits[0]) * -2.0 + 1.0;
-  float exponent = getExponent(bits);
-  bool subnormal = abs(exponent - 0.0) < 0.01;
-  float mantissa = getMantissa(bits, subnormal);
-  float exponentBias = 127.0;
-  return signBit * mantissa * exp2(exponent - exponentBias - 23.0);
-}
-
-// Decode a 32-bit float from the RGBA color channels of a texel.
-float rgbaToFloat(vec4 texelRGBA) {
-  ivec4 rgbaBytes = floatsToBytes(texelRGBA);
-  bool bits[32];
-  bytesToBits(rgbaBytes, bits);
-  return bitsToFloat(bits);
-}
-
-///////////////////////////////////////////////////////
-
+export const UTILS = `
 float L1(vec3 p, float a0, float a1, float a2) {
     return a0 * p.z + a1 * p.x + a2 * p.y;
 }
@@ -193,12 +55,10 @@ float L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, flo
 }
 
 float alpha(float offset, float f) {
-    #ifdef uMaxCoeffs
+    #ifdef WEBGL1
         // in webgl1, the value is in the alpha channel!
         return texture2D(tAlpha, vec2(offset * f, 0.5)).a;
-    #endif
-
-    #ifndef uMaxCoeffs
+    #else
         return texture2D(tAlpha, vec2(offset * f, 0.5)).x;
     #endif
 }
@@ -229,7 +89,7 @@ float Y(int L, vec3 X, float aO, float fA) {
     return 0.0;
 }
 
-#ifndef uMaxCoeffs
+#ifndef WEBGL1
     float R(float R2, int start, int end, float fCoeff) {
         float gauss = 0.0;
         for (int i = start; i < end; i++) {
@@ -238,9 +98,7 @@ float Y(int L, vec3 X, float aO, float fA) {
         }
         return gauss;
     }
-#endif
-
-#ifdef uMaxCoeffs
+#else
     float R(float R2, int start, int end, float fCoeff) {
         float gauss = 0.0;
         int o = start;
@@ -254,28 +112,13 @@ float Y(int L, vec3 X, float aO, float fA) {
         return gauss;
     }
 #endif
+`;
 
-float intDiv(float a, float b) { return float(int(a) / int(b)); }
-float intMod(float a, float b) { return a - b * float(int(a) / int(b)); }
-
-void main(void) {
-    float offset = floor(gl_FragCoord.x) + floor(gl_FragCoord.y) * uWidth;
-
-    // axis order fast to slow Z, Y, X
-    // TODO: support arbitrary axis orders?
-    float k = intMod(offset, uDimensions.z), kk = intDiv(offset, uDimensions.z);
-    float j = intMod(kk, uDimensions.y);
-    float i = intDiv(kk, uDimensions.y);
-
-    vec3 xyz = uMin + uDelta * vec3(i, j, k);
-
+export const MAIN = `
     float fCenter = 1.0 / float(uNCenters - 1);
     float fCoeff = 1.0 / float(uNCoeff - 1);
     float fA = 1.0 / float(uNAlpha - 1);
 
-    // gl_FragColor = floatToRgba(offset);
-    // return;
-
     float v = 0.0;
 
     for (int i = 0; i < uNCenters; i++) {
@@ -299,13 +142,4 @@ void main(void) {
 
         v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
     }
-
-    
-    if (uDensity) {
-        float current = rgbaToFloat(texture2D(tCumulativeSum, gl_FragCoord.xy / vec2(uWidth, uWidth)));
-        gl_FragColor = floatToRgba(current + uOccupancy * v * v);
-    } else {
-         gl_FragColor = floatToRgba(v);
-    }
-}
 `;

src/extensions/alpha-orbitals/orbitals.ts

@@ -7,11 +7,14 @@
  */
 
 import { sortArray } from '../../mol-data/util';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Task } from '../../mol-task';
 import { sphericalCollocation } from './collocation';
 import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
-import { canComputeAlphaOrbitalsOnGPU, gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
+import { gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
+
+// setDebugMode(true);
 
 export function createSphericalCollocationGrid(
     params: CubeGridComputationParams, orbital: AlphaOrbital, webgl?: WebGLContext
@@ -20,9 +23,9 @@ export function createSphericalCollocationGrid(
         const cubeGrid = initCubeGrid(params);
 
         let matrix: Float32Array;
-        if (canComputeAlphaOrbitalsOnGPU(webgl)) {
+        if (canComputeGrid3dOnGPU(webgl)) {
             // console.time('gpu');
-            matrix = gpuComputeAlphaOrbitalsGridValues(webgl!, cubeGrid, orbital);
+            matrix = await gpuComputeAlphaOrbitalsGridValues(ctx, webgl!, cubeGrid, orbital);
             // console.timeEnd('gpu');
         } else {
             // console.time('cpu');

src/mol-canvas3d/canvas3d.ts

@@ -150,9 +150,10 @@ namespace Canvas3D {
     export interface ClickEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
 
     export function fromCanvas(canvas: HTMLCanvasElement, props: Partial<Canvas3DProps> = {}, attribs: Partial<{ antialias: boolean, pixelScale: number, pickScale: number, enableWboit: boolean }> = {}) {
+        const antialias = (attribs.antialias ?? true) && !attribs.enableWboit;
         const gl = getGLContext(canvas, {
             alpha: true,
-            antialias: (attribs.antialias ?? true) && !attribs.enableWboit,
+            antialias,
             depth: true,
             preserveDrawingBuffer: true,
             premultipliedAlpha: true,
@@ -197,6 +198,14 @@ namespace Canvas3D {
             if (isDebugMode) console.log('context restored');
         }, false);
 
+        // disable postprocessing anti-aliasing if canvas anti-aliasing is enabled
+        if (antialias && !props.postprocessing?.antialiasing) {
+            props.postprocessing = {
+                ...DefaultCanvas3DParams.postprocessing,
+                antialiasing: { name: 'off', params: {} }
+            };
+        }
+
         return create(webgl, input, passes, props, { pixelScale });
     }
 

src/mol-canvas3d/passes/draw.ts

@@ -75,7 +75,7 @@ export class DrawPass {
 
         this.drawTarget = createNullRenderTarget(webgl.gl);
 
-        this.colorTarget = webgl.createRenderTarget(width, height);
+        this.colorTarget = webgl.createRenderTarget(width, height, true, 'uint8', 'linear');
         this.packedDepth = !extensions.depthTexture;
 
         this.depthTarget = webgl.createRenderTarget(width, height);

src/mol-canvas3d/passes/postprocessing.ts

@@ -48,11 +48,14 @@ const PostprocessingShaderCode = ShaderCode('postprocessing', quad_vert, postpro
 type PostprocessingRenderable = ComputeRenderable<Values<typeof PostprocessingSchema>>
 
 function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTexture: Texture): PostprocessingRenderable {
+    const width = colorTexture.getWidth();
+    const height = colorTexture.getHeight();
+
     const values: Values<typeof PostprocessingSchema> = {
         ...QuadValues,
         tColor: ValueCell.create(colorTexture),
         tPackedDepth: ValueCell.create(depthTexture),
-        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
 
         dOrthographic: ValueCell.create(0),
         uNear: ValueCell.create(1),
@@ -93,13 +96,21 @@ export const PostprocessingParams = {
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' }),
-    antialiasing: PD.Boolean(true, { description: 'Fast Approximate Anti-Aliasing (FXAA)' })
+    antialiasing: PD.MappedStatic('on', {
+        on: PD.Group({
+            edgeThresholdMin:PD.Numeric(0.0312, { min: 0.0312, max: 0.0833, step: 0.0001 }, { description: 'Trims the algorithm from processing darks.' }),
+            edgeThresholdMax: PD.Numeric(0.063, { min: 0.063, max: 0.333, step: 0.001 }, { description: 'The minimum amount of local contrast required to apply algorithm.' }),
+            iterations: PD.Numeric(12, { min: 0, max: 32, step: 1 }, { description: 'Number of edge exploration steps.' }),
+            subpixelQuality: PD.Numeric(1.00, { min: 0.00, max: 1.00, step: 0.01 }, { description: 'Choose the amount of sub-pixel aliasing removal.' }),
+        }),
+        off: PD.Group({})
+    }, { cycle: true, description: 'Fast Approximate Anti-Aliasing (FXAA)' }),
 };
 export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
 
 export class PostprocessingPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.occlusion.name === 'on' || props.outline.name === 'on';
+        return props.occlusion.name === 'on' || props.outline.name === 'on' || props.antialiasing.name === 'on';
     }
 
     readonly target: RenderTarget
@@ -114,7 +125,7 @@ export class PostprocessingPass {
         const height = colorTarget.getHeight();
 
         this.target = webgl.createRenderTarget(width, height, false);
-        this.tmpTarget = webgl.createRenderTarget(width, height, false);
+        this.tmpTarget = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
         this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture);
         this.fxaa = getFxaaRenderable(webgl, this.tmpTarget.texture);
     }
@@ -128,14 +139,14 @@ export class PostprocessingPass {
             this.target.setSize(width, height);
             this.tmpTarget.setSize(width, height);
             ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
-            ValueCell.update(this.fxaa.values.uTexSize, Vec2.set(this.fxaa.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.fxaa.values.uTexSizeInv, Vec2.set(this.fxaa.values.uTexSizeInv.ref.value, 1 / width, 1 / height));
         }
     }
 
     private updateState(camera: ICamera) {
         const { gl, state } = this.webgl;
 
-        state.disable(gl.SCISSOR_TEST);
+        state.enable(gl.SCISSOR_TEST);
         state.disable(gl.BLEND);
         state.disable(gl.DEPTH_TEST);
         state.depthMask(false);
@@ -185,7 +196,7 @@ export class PostprocessingPass {
             this.renderable.update();
         }
 
-        if (props.antialiasing) {
+        if (props.antialiasing.name === 'on') {
             this.tmpTarget.bind();
         } else if (toDrawingBuffer) {
             this.webgl.unbindFramebuffer();
@@ -198,10 +209,30 @@ export class PostprocessingPass {
     }
 
     private _renderFxaa(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
+        if (props.antialiasing.name === 'off') return;
+
+        const { values } = this.fxaa;
+
+        let needsUpdate = false;
+
         const input = (props.occlusion.name === 'on' || props.outline.name === 'on')
             ? this.tmpTarget.texture : this.drawPass.colorTarget.texture;
-        if (this.fxaa.values.tColor.ref.value !== input) {
+        if (values.tColor.ref.value !== input) {
             ValueCell.update(this.fxaa.values.tColor, input);
+            needsUpdate = true;
+        }
+
+        const { edgeThresholdMin, edgeThresholdMax, iterations, subpixelQuality } = props.antialiasing.params;
+        if (values.dEdgeThresholdMin.ref.value !== edgeThresholdMin) needsUpdate = true;
+        ValueCell.updateIfChanged(values.dEdgeThresholdMin, edgeThresholdMin);
+        if (values.dEdgeThresholdMax.ref.value !== edgeThresholdMax) needsUpdate = true;
+        ValueCell.updateIfChanged(values.dEdgeThresholdMax, edgeThresholdMax);
+        if (values.dIterations.ref.value !== iterations) needsUpdate = true;
+        ValueCell.updateIfChanged(values.dIterations, iterations);
+        if (values.dSubpixelQuality.ref.value !== subpixelQuality) needsUpdate = true;
+        ValueCell.updateIfChanged(values.dSubpixelQuality, subpixelQuality);
+
+        if (needsUpdate) {
             this.fxaa.update();
         }
 
@@ -216,11 +247,11 @@ export class PostprocessingPass {
     }
 
     private _render(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
-        if (props.occlusion.name === 'on' || props.outline.name === 'on' || !props.antialiasing) {
+        if (props.occlusion.name === 'on' || props.outline.name === 'on' || props.antialiasing.name === 'off') {
             this._renderPostprocessing(camera, toDrawingBuffer, props);
         }
 
-        if (props.antialiasing) {
+        if (props.antialiasing.name === 'on') {
             this._renderFxaa(camera, toDrawingBuffer, props);
         }
     }
@@ -240,16 +271,29 @@ export class PostprocessingPass {
 const FxaaSchema = {
     ...QuadSchema,
     tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    uTexSize: UniformSpec('v2'),
+    uTexSizeInv: UniformSpec('v2'),
+
+    dEdgeThresholdMin: DefineSpec('number'),
+    dEdgeThresholdMax: DefineSpec('number'),
+    dIterations: DefineSpec('number'),
+    dSubpixelQuality: DefineSpec('number'),
 };
 const FxaaShaderCode = ShaderCode('fxaa', quad_vert, fxaa_frag);
 type FxaaRenderable = ComputeRenderable<Values<typeof FxaaSchema>>
 
 function getFxaaRenderable(ctx: WebGLContext, colorTexture: Texture): FxaaRenderable {
+    const width = colorTexture.getWidth();
+    const height = colorTexture.getHeight();
+
     const values: Values<typeof FxaaSchema> = {
         ...QuadValues,
         tColor: ValueCell.create(colorTexture),
-        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+        uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)),
+
+        dEdgeThresholdMin: ValueCell.create(0.0312),
+        dEdgeThresholdMax: ValueCell.create(0.125),
+        dIterations: ValueCell.create(12),
+        dSubpixelQuality: ValueCell.create(0.75),
     };
 
     const schema = { ...FxaaSchema };

src/mol-gl/compute/grid3d.ts

@@ -0,0 +1,223 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { RenderableSchema, Values, UnboxedValues, UniformSpec, TextureSpec, DefineSpec, RenderableValues } from '../renderable/schema';
+import { WebGLContext } from '../webgl/context';
+import { getRegularGrid3dDelta, RegularGrid3d } from '../../mol-math/geometry/common';
+import shader_template from '../shader/util/grid3d-template.frag';
+import quad_vert from '../shader/quad.vert';
+import { ShaderCode } from '../shader-code';
+import { UUID, ValueCell } from '../../mol-util';
+import { objectForEach } from '../../mol-util/object';
+import { getUniformGlslType, isUniformValueScalar } from '../webgl/uniform';
+import { QuadSchema, QuadValues } from './util';
+import { createComputeRenderItem } from '../webgl/render-item';
+import { createComputeRenderable } from '../renderable';
+import { isLittleEndian } from '../../mol-util/is-little-endian';
+import { RuntimeContext } from '../../mol-task';
+
+export function canComputeGrid3dOnGPU(webgl?: WebGLContext) {
+    return !!webgl?.extensions.textureFloat;
+}
+
+export interface Grid3DComputeRenderableSpec<S extends RenderableSchema, P, CS> {
+    schema: S,
+    // indicate which params are loop bounds for WebGL1 compat
+    loopBounds?: (keyof S)[]
+    utilCode?: string,
+    mainCode: string,
+    returnCode: string,
+
+    values(params: P, grid: RegularGrid3d): UnboxedValues<S>,
+
+    cumulative?: {
+        states(params: P): CS[],
+        update(params: P, state: CS, values: Values<S>): void,
+        // call gl.readPixes every 'yieldPeriod' states to split the computation
+        // into multiple parts, if not set, the computation will be synchronous
+        yieldPeriod?: number
+    }
+}
+
+const FrameBufferName = 'grid3d-computable' as const;
+const Texture0Name = 'grid3d-computable-0' as const;
+const Texture1Name = 'grid3d-computable-1' as const;
+
+const SchemaBase = {
+    ...QuadSchema,
+    uDimensions: UniformSpec('v3'),
+    uMin: UniformSpec('v3'),
+    uDelta: UniformSpec('v3'),
+    uWidth: UniformSpec('f'),
+    uLittleEndian: UniformSpec('b'),
+};
+
+const CumulativeSumSchema = {
+    tCumulativeSum: TextureSpec('texture', 'rgba', 'ubyte', 'nearest')
+};
+
+export function createGrid3dComputeRenderable<S extends RenderableSchema, P, CS>(spec: Grid3DComputeRenderableSpec<S, P, CS>) {
+    const id = UUID.create22();
+
+    const uniforms: string[] = [];
+
+    objectForEach(spec.schema, (u, k) => {
+        if (u.type === 'define') return;
+        if (u.kind.indexOf('[]') >= 0) throw new Error('array uniforms are not supported');
+        const isBound = (spec.loopBounds?.indexOf(k) ?? -1) >= 0;
+        if (isBound) uniforms.push(`#ifndef ${k}`);
+        if (u.type === 'uniform') uniforms.push(`uniform ${getUniformGlslType(u.kind as any)} ${k};`);
+        else if (u.type === 'texture') uniforms.push(`uniform sampler2D ${k};`);
+        if (isBound) uniforms.push(`#endif`);
+    });
+
+    const code = shader_template
+        .replace('{UNIFORMS}', uniforms.join('\n'))
+        .replace('{UTILS}', spec.utilCode ?? '')
+        .replace('{MAIN}', spec.mainCode)
+        .replace('{RETURN}', spec.returnCode);
+
+    const shader = ShaderCode(id, quad_vert, code);
+
+    return async (ctx: RuntimeContext, webgl: WebGLContext, grid: RegularGrid3d, params: P) => {
+        const schema: RenderableSchema = {
+            ...SchemaBase,
+            ...(spec.cumulative ? CumulativeSumSchema : {}),
+            ...spec.schema,
+        };
+
+        if (!webgl.isWebGL2) {
+            if (spec.loopBounds) {
+                for (const b of spec.loopBounds) {
+                    (schema as any)[b] = DefineSpec('number');
+                }
+            }
+            (schema as any)['WEBGL1'] = DefineSpec('boolean');
+        }
+
+        if (spec.cumulative) {
+            (schema as any)['CUMULATIVE'] = DefineSpec('boolean');
+        }
+
+        if (!webgl.namedFramebuffers[FrameBufferName]) {
+            webgl.namedFramebuffers[FrameBufferName] = webgl.resources.framebuffer();
+        }
+        const framebuffer = webgl.namedFramebuffers[FrameBufferName];
+
+        if (!webgl.namedTextures[Texture0Name]) {
+            webgl.namedTextures[Texture0Name] = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        }
+        if (spec.cumulative && !webgl.namedTextures[Texture1Name]) {
+            webgl.namedTextures[Texture1Name] = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        }
+
+        const tex = [webgl.namedTextures[Texture0Name], webgl.namedTextures[Texture1Name]];
+
+        const [nx, ny, nz] = grid.dimensions;
+        const uWidth = Math.ceil(Math.sqrt(nx * ny * nz));
+
+        const values: UnboxedValues<S & typeof SchemaBase> = {
+            uDimensions: grid.dimensions,
+            uMin: grid.box.min,
+            uDelta: getRegularGrid3dDelta(grid),
+            uWidth,
+            uLittleEndian: isLittleEndian(),
+            ...spec.values(params, grid)
+        } as any;
+
+        if (!webgl.isWebGL2) {
+            (values as any).WEBGL1 = true;
+        }
+        if (spec.cumulative) {
+            (values as any).tCumulativeSum = tex[0];
+            (values as any).CUMULATIVE = true;
+        }
+
+        let renderable = webgl.namedComputeRenderables[id];
+        let cells: RenderableValues;
+        if (renderable) {
+            cells = renderable.values as RenderableValues;
+            objectForEach(values, (c, k) => {
+                const s = schema[k];
+                if (s?.type === 'value' || s?.type === 'attribute') return;
+
+                if (!s || !isUniformValueScalar(s.kind as any)) {
+                    ValueCell.update(cells[k], c);
+                } else {
+                    ValueCell.updateIfChanged(cells[k], c);
+                }
+            });
+        } else {
+            cells = {} as any;
+            objectForEach(QuadValues, (v, k) => (cells as any)[k] = v);
+            objectForEach(values, (v, k) => (cells as any)[k] = ValueCell.create(v));
+            renderable = createComputeRenderable(createComputeRenderItem(webgl, 'triangles', shader, schema, cells), cells);
+        }
+
+        const array = new Uint8Array(uWidth * uWidth * 4);
+        if (spec.cumulative) {
+            const { gl } = webgl;
+
+            const states = spec.cumulative.states(params);
+
+            tex[0].define(uWidth, uWidth);
+            tex[1].define(uWidth, uWidth);
+
+            resetGl(webgl, uWidth);
+            gl.clearColor(0, 0, 0, 0);
+
+            tex[0].attachFramebuffer(framebuffer, 'color0');
+            gl.clear(gl.COLOR_BUFFER_BIT);
+
+            tex[1].attachFramebuffer(framebuffer, 'color0');
+            gl.clear(gl.COLOR_BUFFER_BIT);
+
+            if (spec.cumulative.yieldPeriod) {
+                await ctx.update({ message: 'Computing...', isIndeterminate: false, current: 0, max: states.length });
+            }
+
+            const yieldPeriod = Math.max(1, spec.cumulative.yieldPeriod ?? 1 | 0);
+
+            for (let i = 0; i < states.length; i++) {
+                ValueCell.update(cells.tCumulativeSum, tex[(i + 1) % 2]);
+                tex[i % 2].attachFramebuffer(framebuffer, 'color0');
+                resetGl(webgl, uWidth);
+                spec.cumulative.update(params, states[i], cells as any);
+                renderable.update();
+                renderable.render();
+
+                if (spec.cumulative.yieldPeriod && i !== states.length - 1) {
+                    if (i % yieldPeriod === yieldPeriod - 1) {
+                        webgl.readPixels(0, 0, 1, 1, array);
+                    }
+                    if (ctx.shouldUpdate) {
+                        await ctx.update({ current: i + 1 });
+                    }
+                }
+            }
+        } else {
+            tex[0].define(uWidth, uWidth);
+            tex[0].attachFramebuffer(framebuffer, 'color0');
+            framebuffer.bind();
+            resetGl(webgl, uWidth);
+            renderable.update();
+            renderable.render();
+        }
+
+        webgl.readPixels(0, 0, uWidth, uWidth, array);
+        return new Float32Array(array.buffer, array.byteOffset, nx * ny * nz);
+    };
+}
+
+function resetGl(webgl: WebGLContext, w: number) {
+    const { gl, state } = webgl;
+    gl.viewport(0, 0, w, w);
+    gl.scissor(0, 0, w, w);
+    state.disable(gl.SCISSOR_TEST);
+    state.disable(gl.BLEND);
+    state.disable(gl.DEPTH_TEST);
+    state.depthMask(false);
+}

src/mol-gl/renderable/schema.ts

@@ -29,6 +29,7 @@ export type ValueKind = keyof ValueKindType
 export type KindValue = UniformKindValue & DataTypeArrayType & TextureKindValue & ValueKindType
 
 export type Values<S extends RenderableSchema> = { readonly [k in keyof S]: ValueCell<KindValue[S[k]['kind']]> }
+export type UnboxedValues<S extends RenderableSchema> = { readonly [k in keyof S]: KindValue[S[k]['kind']] }
 
 export function splitValues(schema: RenderableSchema, values: RenderableValues) {
     const attributeValues: AttributeValues = {};
@@ -102,6 +103,7 @@ export type RenderableSchema = {
 }
 export type RenderableValues = { readonly [k: string]: ValueCell<any> }
 
+
 //
 
 export const GlobalUniformSchema = {

src/mol-gl/shader-code.ts

@@ -151,7 +151,7 @@ export type ShaderDefines = {
     [k: string]: ValueCell<DefineType>
 }
 
-function getDefinesCode (defines: ShaderDefines) {
+function getDefinesCode(defines: ShaderDefines) {
     if (defines === undefined) return '';
     const lines = [];
     for (const name in defines) {

src/mol-gl/shader/fxaa.frag.ts

@@ -4,104 +4,226 @@ precision highp int;
 precision highp sampler2D;
 
 uniform sampler2D tColor;
-uniform vec2 uTexSize;
+uniform vec2 uTexSizeInv;
 
-// Basic FXAA implementation based on the code on geeks3d.com with the
-// modification that the texture2DLod stuff was removed since it's
-// unsupported by WebGL.
-// --
-// From:
-// https://github.com/mitsuhiko/webgl-meincraft
-// Copyright (c) 2011 by Armin Ronacher.
-// Some rights reserved.
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above
-//       copyright notice, this list of conditions and the following
-//       disclaimer in the documentation and/or other materials provided
-//       with the distribution.
-//     * The names of the contributors may not be used to endorse or
-//       promote products derived from this software without specific
-//       prior written permission.
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-// */
+// adapted from https://github.com/kosua20/Rendu
+// MIT License Copyright (c) 2017 Simon Rodriguez
 
-#ifndef FXAA_REDUCE_MIN
-    #define FXAA_REDUCE_MIN   (1.0/ 128.0)
-#endif
-#ifndef FXAA_REDUCE_MUL
-    #define FXAA_REDUCE_MUL   (1.0 / 8.0)
-#endif
-#ifndef FXAA_SPAN_MAX
-    #define FXAA_SPAN_MAX     8.0
-#endif
+#define QUALITY(q) ((q) < 5 ? 1.0 : ((q) > 5 ? ((q) < 10 ? 2.0 : ((q) < 11 ? 4.0 : 8.0)) : 1.5))
 
-vec4 fxaa(sampler2D tex, const in vec2 fragCoord, const in vec2 resolution) {
-    vec2 inverseVP = 1.0 / resolution;
-    vec2 v_rgbNW = (fragCoord + vec2(-1.0, -1.0)) * inverseVP;
-    vec2 v_rgbNE = (fragCoord + vec2(1.0, -1.0)) * inverseVP;
-    vec2 v_rgbSW = (fragCoord + vec2(-1.0, 1.0)) * inverseVP;
-    vec2 v_rgbSE = (fragCoord + vec2(1.0, 1.0)) * inverseVP;
-    vec2 v_rgbM = vec2(fragCoord * inverseVP);
+float rgb2luma(vec3 rgb){
+    return sqrt(dot(rgb, vec3(0.299, 0.587, 0.114)));
+}
 
-    vec4 col = vec4(0.0);
-    vec3 rgbNW = texture2D(tex, v_rgbNW).xyz;
-    vec3 rgbNE = texture2D(tex, v_rgbNE).xyz;
-    vec3 rgbSW = texture2D(tex, v_rgbSW).xyz;
-    vec3 rgbSE = texture2D(tex, v_rgbSE).xyz;
-    vec4 texColor = texture2D(tex, v_rgbM);
-    vec3 rgbM  = texColor.xyz;
-    vec3 luma = vec3(0.299, 0.587, 0.114);
-    float lumaNW = dot(rgbNW, luma);
-    float lumaNE = dot(rgbNE, luma);
-    float lumaSW = dot(rgbSW, luma);
-    float lumaSE = dot(rgbSE, luma);
-    float lumaM  = dot(rgbM,  luma);
-    float lumaMin = min(lumaM, min(min(lumaNW, lumaNE), min(lumaSW, lumaSE)));
-    float lumaMax = max(lumaM, max(max(lumaNW, lumaNE), max(lumaSW, lumaSE)));
+float sampleLuma(vec2 uv) {
+    return rgb2luma(texture2D(tColor, uv).rgb);
+}
 
-    vec2 dir;
-    dir.x = -((lumaNW + lumaNE) - (lumaSW + lumaSE));
-    dir.y =  ((lumaNW + lumaSW) - (lumaNE + lumaSE));
-
-    float dirReduce = max((lumaNW + lumaNE + lumaSW + lumaSE) *
-                          (0.25 * FXAA_REDUCE_MUL), FXAA_REDUCE_MIN);
-
-    float rcpDirMin = 1.0 / (min(abs(dir.x), abs(dir.y)) + dirReduce);
-    dir = min(vec2(FXAA_SPAN_MAX, FXAA_SPAN_MAX),
-              max(vec2(-FXAA_SPAN_MAX, -FXAA_SPAN_MAX),
-              dir * rcpDirMin)) * inverseVP;
-
-    vec4 rgbA1 = texture2D(tex, fragCoord * inverseVP + dir * (1.0 / 3.0 - 0.5));
-    vec4 rgbA2 = texture2D(tex, fragCoord * inverseVP + dir * (2.0 / 3.0 - 0.5));
-    vec4 rgbA = 0.5 * (rgbA1 + rgbA2);
-
-    vec4 rgbB1 = texture2D(tex, fragCoord * inverseVP + dir * -0.5);
-    vec4 rgbB2 = texture2D(tex, fragCoord * inverseVP + dir * 0.5);
-    vec4 rgbB = rgbA * 0.5 + 0.25 * (rgbB1 + rgbB2);
-
-    float lumaB = dot(rgbB.rgb, luma);
-    if ((lumaB < lumaMin) || (lumaB > lumaMax))
-        col = vec4(rgbA.rgb, rgbA.a);
-    else
-        col = vec4(rgbB.rgb, rgbB.a);
-    return col;
+float sampleLuma(vec2 uv, float uOffset, float vOffset) {
+    uv += uTexSizeInv * vec2(uOffset, vOffset);
+    return sampleLuma(uv);
 }
 
 void main(void) {
-    gl_FragColor = fxaa(tColor, gl_FragCoord.xy, uTexSize);
+    vec2 coords = gl_FragCoord.xy * uTexSizeInv;
+    vec2 inverseScreenSize = uTexSizeInv;
+
+    vec4 colorCenter = texture2D(tColor, coords);
+
+    // Luma at the current fragment
+    float lumaCenter = rgb2luma(colorCenter.rgb);
+
+    // Luma at the four direct neighbours of the current fragment.
+    float lumaDown = sampleLuma(coords, 0.0, -1.0);
+    float lumaUp = sampleLuma(coords, 0.0, 1.0);
+    float lumaLeft = sampleLuma(coords, -1.0, 0.0);
+    float lumaRight = sampleLuma(coords, 1.0, 0.0);
+
+    // Find the maximum and minimum luma around the current fragment.
+    float lumaMin = min(lumaCenter, min(min(lumaDown, lumaUp), min(lumaLeft, lumaRight)));
+    float lumaMax = max(lumaCenter, max(max(lumaDown, lumaUp), max(lumaLeft, lumaRight)));
+
+    // Compute the delta.
+    float lumaRange = lumaMax - lumaMin;
+
+    // If the luma variation is lower that a threshold (or if we are in a really dark area),
+    // we are not on an edge, don't perform any AA.
+    if (lumaRange < max(dEdgeThresholdMin, lumaMax * dEdgeThresholdMax)) {
+        gl_FragColor = colorCenter;
+        return;
+    }
+
+    // Query the 4 remaining corners lumas.
+    float lumaDownLeft = sampleLuma(coords, -1.0, -1.0);
+    float lumaUpRight = sampleLuma(coords, 1.0, 1.0);
+    float lumaUpLeft = sampleLuma(coords, -1.0, 1.0);
+    float lumaDownRight = sampleLuma(coords, 1.0, -1.0);
+
+    // Combine the four edges lumas (using intermediary variables for future computations
+    // with the same values).
+    float lumaDownUp = lumaDown + lumaUp;
+    float lumaLeftRight = lumaLeft + lumaRight;
+
+    // Same for corners
+    float lumaLeftCorners = lumaDownLeft + lumaUpLeft;
+    float lumaDownCorners = lumaDownLeft + lumaDownRight;
+    float lumaRightCorners = lumaDownRight + lumaUpRight;
+    float lumaUpCorners = lumaUpRight + lumaUpLeft;
+
+    // Compute an estimation of the gradient along the horizontal and vertical axis.
+    float edgeHorizontal = abs(-2.0 * lumaLeft + lumaLeftCorners) + abs(-2.0 * lumaCenter + lumaDownUp) * 2.0 + abs(-2.0 * lumaRight + lumaRightCorners);
+    float edgeVertical = abs(-2.0 * lumaUp + lumaUpCorners) + abs(-2.0 * lumaCenter + lumaLeftRight) * 2.0 + abs(-2.0 * lumaDown + lumaDownCorners);
+
+    // Is the local edge horizontal or vertical ?
+    bool isHorizontal = (edgeHorizontal >= edgeVertical);
+
+    // Choose the step size (one pixel) accordingly.
+    float stepLength = isHorizontal ? inverseScreenSize.y : inverseScreenSize.x;
+
+    // Select the two neighboring texels lumas in the opposite direction to the local edge.
+    float luma1 = isHorizontal ? lumaDown : lumaLeft;
+    float luma2 = isHorizontal ? lumaUp : lumaRight;
+    // Compute gradients in this direction.
+    float gradient1 = luma1 - lumaCenter;
+    float gradient2 = luma2 - lumaCenter;
+
+    // Which direction is the steepest ?
+    bool is1Steepest = abs(gradient1) >= abs(gradient2);
+
+    // Gradient in the corresponding direction, normalized.
+    float gradientScaled = 0.25 * max(abs(gradient1), abs(gradient2));
+
+    // Average luma in the correct direction.
+    float lumaLocalAverage = 0.0;
+    if(is1Steepest){
+        // Switch the direction
+        stepLength = -stepLength;
+        lumaLocalAverage = 0.5 * (luma1 + lumaCenter);
+    } else {
+        lumaLocalAverage = 0.5 * (luma2 + lumaCenter);
+    }
+
+    // Shift UV in the correct direction by half a pixel.
+    vec2 currentUv = coords;
+    if(isHorizontal){
+        currentUv.y += stepLength * 0.5;
+    } else {
+        currentUv.x += stepLength * 0.5;
+    }
+
+    // Compute offset (for each iteration step) in the right direction.
+    vec2 offset = isHorizontal ? vec2(inverseScreenSize.x, 0.0) : vec2(0.0, inverseScreenSize.y);
+    // Compute UVs to explore on each side of the edge, orthogonally.
+    // The QUALITY allows us to step faster.
+    vec2 uv1 = currentUv - offset * QUALITY(0);
+    vec2 uv2 = currentUv + offset * QUALITY(0);
+
+    // Read the lumas at both current extremities of the exploration segment,
+    // and compute the delta wrt to the local average luma.
+    float lumaEnd1 = sampleLuma(uv1);
+    float lumaEnd2 = sampleLuma(uv2);
+    lumaEnd1 -= lumaLocalAverage;
+    lumaEnd2 -= lumaLocalAverage;
+
+    // If the luma deltas at the current extremities is larger than the local gradient,
+    // we have reached the side of the edge.
+    bool reached1 = abs(lumaEnd1) >= gradientScaled;
+    bool reached2 = abs(lumaEnd2) >= gradientScaled;
+    bool reachedBoth = reached1 && reached2;
+
+    // If the side is not reached, we continue to explore in this direction.
+    if(!reached1){
+        uv1 -= offset * QUALITY(1);
+    }
+    if(!reached2){
+        uv2 += offset * QUALITY(1);
+    }
+
+    // If both sides have not been reached, continue to explore.
+    if(!reachedBoth){
+        for(int i = 2; i < dIterations; i++){
+            // If needed, read luma in 1st direction, compute delta.
+            if(!reached1){
+                lumaEnd1 = sampleLuma(uv1);
+                lumaEnd1 = lumaEnd1 - lumaLocalAverage;
+            }
+            // If needed, read luma in opposite direction, compute delta.
+            if(!reached2){
+                lumaEnd2 = sampleLuma(uv2);
+                lumaEnd2 = lumaEnd2 - lumaLocalAverage;
+            }
+            // If the luma deltas at the current extremities is larger than the local gradient,
+            // we have reached the side of the edge.
+            reached1 = abs(lumaEnd1) >= gradientScaled;
+            reached2 = abs(lumaEnd2) >= gradientScaled;
+            reachedBoth = reached1 && reached2;
+
+            // If the side is not reached, we continue to explore in this direction,
+            // with a variable quality.
+            if(!reached1){
+                uv1 -= offset * QUALITY(i);
+            }
+            if(!reached2){
+                uv2 += offset * QUALITY(i);
+            }
+
+            // If both sides have been reached, stop the exploration.
+            if(reachedBoth){
+                break;
+            }
+        }
+    }
+
+    // Compute the distances to each side edge of the edge (!).
+    float distance1 = isHorizontal ? (coords.x - uv1.x) : (coords.y - uv1.y);
+    float distance2 = isHorizontal ? (uv2.x - coords.x) : (uv2.y - coords.y);
+
+    // In which direction is the side of the edge closer ?
+    bool isDirection1 = distance1 < distance2;
+    float distanceFinal = min(distance1, distance2);
+
+    // Thickness of the edge.
+    float edgeThickness = (distance1 + distance2);
+
+    // Is the luma at center smaller than the local average ?
+    bool isLumaCenterSmaller = lumaCenter < lumaLocalAverage;
+
+    // If the luma at center is smaller than at its neighbour,
+    // the delta luma at each end should be positive (same variation).
+    bool correctVariation1 = (lumaEnd1 < 0.0) != isLumaCenterSmaller;
+    bool correctVariation2 = (lumaEnd2 < 0.0) != isLumaCenterSmaller;
+
+    // Only keep the result in the direction of the closer side of the edge.
+    bool correctVariation = isDirection1 ? correctVariation1 : correctVariation2;
+
+    // UV offset: read in the direction of the closest side of the edge.
+    float pixelOffset = - distanceFinal / edgeThickness + 0.5;
+
+    // If the luma variation is incorrect, do not offset.
+    float finalOffset = correctVariation ? pixelOffset : 0.0;
+
+    // Sub-pixel shifting
+    // Full weighted average of the luma over the 3x3 neighborhood.
+    float lumaAverage = (1.0 / 12.0) * (2.0 * (lumaDownUp + lumaLeftRight) + lumaLeftCorners + lumaRightCorners);
+    // Ratio of the delta between the global average and the center luma,
+    // over the luma range in the 3x3 neighborhood.
+    float subPixelOffset1 = clamp(abs(lumaAverage - lumaCenter) / lumaRange, 0.0, 1.0);
+    float subPixelOffset2 = (-2.0 * subPixelOffset1 + 3.0) * subPixelOffset1 * subPixelOffset1;
+    // Compute a sub-pixel offset based on this delta.
+    float subPixelOffsetFinal = subPixelOffset2 * subPixelOffset2 * float(dSubpixelQuality);
+
+    // Pick the biggest of the two offsets.
+    finalOffset = max(finalOffset, subPixelOffsetFinal);
+
+    // Compute the final UV coordinates.
+    vec2 finalUv = coords;
+    if(isHorizontal){
+        finalUv.y += finalOffset * stepLength;
+    } else {
+        finalUv.x += finalOffset * stepLength;
+    }
+
+    // Read the color at the new UV coordinates, and use it.
+    gl_FragColor = texture2D(tColor, finalUv);
 }
 `;

src/mol-gl/shader/util/grid3d-template.frag.ts

@@ -0,0 +1,181 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export default `
+precision highp float;
+precision highp int;
+precision highp sampler2D;
+
+uniform vec2 uQuadShift;
+uniform vec3 uDimensions;
+uniform vec3 uMin;
+uniform vec3 uDelta;
+uniform bool uLittleEndian;
+uniform float uWidth;
+
+#ifdef CUMULATIVE
+uniform sampler2D tCumulativeSum;
+#endif
+
+{UNIFORMS}
+
+{UTILS}
+
+//////////////////////////////////////////////////////////
+
+// floatToRgba adapted from https://github.com/equinor/glsl-float-to-rgba
+// MIT License, Copyright (c) 2020 Equinor
+
+float shiftRight (float v, float amt) {
+  v = floor(v) + 0.5;
+  return floor(v / exp2(amt));
+}
+float shiftLeft (float v, float amt) {
+    return floor(v * exp2(amt) + 0.5);
+}
+float maskLast (float v, float bits) {
+    return mod(v, shiftLeft(1.0, bits));
+}
+float extractBits (float num, float from, float to) {
+    from = floor(from + 0.5); to = floor(to + 0.5);
+    return maskLast(shiftRight(num, from), to - from);
+}
+
+vec4 floatToRgba(float texelFloat) {
+    if (texelFloat == 0.0) return vec4(0, 0, 0, 0);
+    float sign = texelFloat > 0.0 ? 0.0 : 1.0;
+    texelFloat = abs(texelFloat);
+    float exponent = floor(log2(texelFloat));
+    float biased_exponent = exponent + 127.0;
+    float fraction = ((texelFloat / exp2(exponent)) - 1.0) * 8388608.0;
+    float t = biased_exponent / 2.0;
+    float last_bit_of_biased_exponent = fract(t) * 2.0;
+    float remaining_bits_of_biased_exponent = floor(t);
+    float byte4 = extractBits(fraction, 0.0, 8.0) / 255.0;
+    float byte3 = extractBits(fraction, 8.0, 16.0) / 255.0;
+    float byte2 = (last_bit_of_biased_exponent * 128.0 + extractBits(fraction, 16.0, 23.0)) / 255.0;
+    float byte1 = (sign * 128.0 + remaining_bits_of_biased_exponent) / 255.0;
+    return (
+        uLittleEndian
+            ? vec4(byte4, byte3, byte2, byte1)
+            : vec4(byte1, byte2, byte3, byte4)
+    );
+}
+
+///////////////////////////////////////////////////////
+
+// rgbaToFloat adapted from https://github.com/ihmeuw/glsl-rgba-to-float
+// BSD 3-Clause License
+//
+// Copyright (c) 2019, Institute for Health Metrics and Evaluation All rights reserved.
+// Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+//  - Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+//  - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+//  - Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+// INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+// IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
+// OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
+// OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+// OF THE POSSIBILITY OF SUCH DAMAGE.
+
+#ifdef CUMULATIVE
+
+ivec4 floatsToBytes(vec4 inputFloats) {
+  ivec4 bytes = ivec4(inputFloats * 255.0);
+  return (
+    uLittleEndian
+    ? bytes.abgr
+    : bytes
+  );
+}
+
+// Break the four bytes down into an array of 32 bits.
+void bytesToBits(const in ivec4 bytes, out bool bits[32]) {
+  for (int channelIndex = 0; channelIndex < 4; ++channelIndex) {
+    float acc = float(bytes[channelIndex]);
+    for (int indexInByte = 7; indexInByte >= 0; --indexInByte) {
+      float powerOfTwo = exp2(float(indexInByte));
+      bool bit = acc >= powerOfTwo;
+      bits[channelIndex * 8 + (7 - indexInByte)] = bit;
+      acc = mod(acc, powerOfTwo);
+    }
+  }
+}
+
+// Compute the exponent of the 32-bit float.
+float getExponent(bool bits[32]) {
+  const int startIndex = 1;
+  const int bitStringLength = 8;
+  const int endBeforeIndex = startIndex + bitStringLength;
+  float acc = 0.0;
+  int pow2 = bitStringLength - 1;
+  for (int bitIndex = startIndex; bitIndex < endBeforeIndex; ++bitIndex) {
+    acc += float(bits[bitIndex]) * exp2(float(pow2--));
+  }
+  return acc;
+}
+
+// Compute the mantissa of the 32-bit float.
+float getMantissa(bool bits[32], bool subnormal) {
+  const int startIndex = 9;
+  const int bitStringLength = 23;
+  const int endBeforeIndex = startIndex + bitStringLength;
+  // Leading/implicit/hidden bit convention:
+  // If the number is not subnormal (with exponent 0), we add a leading 1 digit.
+  float acc = float(!subnormal) * exp2(float(bitStringLength));
+  int pow2 = bitStringLength - 1;
+  for (int bitIndex = startIndex; bitIndex < endBeforeIndex; ++bitIndex) {
+    acc += float(bits[bitIndex]) * exp2(float(pow2--));
+  }
+  return acc;
+}
+
+// Parse the float from its 32 bits.
+float bitsToFloat(bool bits[32]) {
+  float signBit = float(bits[0]) * -2.0 + 1.0;
+  float exponent = getExponent(bits);
+  bool subnormal = abs(exponent - 0.0) < 0.01;
+  float mantissa = getMantissa(bits, subnormal);
+  float exponentBias = 127.0;
+  return signBit * mantissa * exp2(exponent - exponentBias - 23.0);
+}
+
+float rgbaToFloat(vec4 texelRGBA) {
+  ivec4 rgbaBytes = floatsToBytes(texelRGBA);
+  bool bits[32];
+  bytesToBits(rgbaBytes, bits);
+  return bitsToFloat(bits);
+}
+
+#endif
+
+///////////////////////////////////////////////////////
+
+float intDiv(float a, float b) { return float(int(a) / int(b)); }
+float intMod(float a, float b) { return a - b * float(int(a) / int(b)); }
+
+void main(void) {
+    float offset = floor(gl_FragCoord.x) + floor(gl_FragCoord.y) * uWidth;
+
+    // axis order fast to slow Z, Y, X
+    // TODO: support arbitrary axis orders?
+    float k = intMod(offset, uDimensions.z), kk = intDiv(offset, uDimensions.z);
+    float j = intMod(kk, uDimensions.y);
+    float i = intDiv(kk, uDimensions.y);
+
+    vec3 xyz = uMin + uDelta * vec3(i, j, k);
+
+    {MAIN}
+
+    #ifdef CUMULATIVE
+        float current = rgbaToFloat(texture2D(tCumulativeSum, gl_FragCoord.xy / vec2(uWidth, uWidth)));
+    #endif
+    gl_FragColor = floatToRgba({RETURN});
+}
+`;

src/mol-gl/webgl/resources.ts

@@ -22,7 +22,7 @@ import { VertexArray, createVertexArray } from './vertex-array';
 
 function defineValueHash(v: boolean | number | string): number {
     return typeof v === 'boolean' ? (v ? 1 : 0) :
-        typeof v === 'number' ? v : hashString(v);
+        typeof v === 'number' ? (v * 10000) : hashString(v);
 }
 
 function wrapCached<T extends Resource>(resourceItem: ReferenceItem<T>) {

src/mol-gl/webgl/uniform.ts

@@ -79,4 +79,30 @@ export function getUniformSetters(schema: RenderableSchema) {
         }
     });
     return setters;
+}
+
+export function getUniformGlslType(kind: UniformKind): string {
+    switch (kind) {
+        case 'f': return 'float';
+        case 'i': return 'int';
+        case 't': return 'sampler2D';
+        case 'b': return 'bool';
+        case 'v2': return 'vec2';
+        case 'v3': return 'vec3';
+        case 'v4': return 'vec4';
+        case 'm3': return 'mat3';
+        case 'm4': return 'mat4';
+    }
+    throw new Error(`${kind} has no primitive GLSL type.`);
+}
+
+export function isUniformValueScalar(kind: UniformKind): boolean {
+    switch (kind) {
+        case 'f':
+        case 'i':
+        case 'b':
+            return true;
+        default:
+            return false;
+    }
 }

src/mol-math/geometry/common.ts

@@ -37,6 +37,15 @@ export type DensityTextureData = {
     gridTexScale: Vec2
 }
 
+export interface RegularGrid3d {
+    box: Box3D,
+    dimensions: Vec3
+}
+
+export function getRegularGrid3dDelta({ box, dimensions }: RegularGrid3d) {
+    return Vec3.div(Vec3(), Box3D.size(Vec3(), box), Vec3.subScalar(Vec3(), dimensions, 1));
+}
+
 export function fillGridDim(length: number, start: number, step: number) {
     const a = new Float32Array(length);
     for (let i = 0; i < a.length; i++) {

src/mol-model-formats/structure/mmcif.ts

@@ -18,6 +18,7 @@ import { AtomSiteAnisotrop } from './property/anisotropic';
 import { ComponentBond } from './property/bonds/chem_comp';
 import { StructConn } from './property/bonds/struct_conn';
 import { Trajectory } from '../../mol-model/structure';
+import { GlobalModelTransformInfo } from '../../mol-model/structure/model/properties/global-transform';
 
 function modelSymmetryFromMmcif(model: Model) {
     if (!MmcifFormat.is(model.sourceData)) return;
@@ -69,6 +70,8 @@ function structConnFromMmcif(model: Model) {
 }
 StructConn.Provider.formatRegistry.add('mmCIF', structConnFromMmcif);
 
+GlobalModelTransformInfo.Provider.formatRegistry.add('mmCIF', GlobalModelTransformInfo.fromMmCif, GlobalModelTransformInfo.hasData);
+
 //
 
 export { MmcifFormat };

src/mol-model/structure/export/mmcif.ts

@@ -132,7 +132,8 @@ function getCustomPropCategories(customProp: CustomPropertyDescriptor, ctx: CifE
 type encode_mmCIF_categories_Params = {
     skipCategoryNames?: Set<string>,
     exportCtx?: CifExportContext,
-    copyAllCategories?: boolean
+    copyAllCategories?: boolean,
+    customProperties?: CustomPropertyDescriptor[]
 }
 
 /** Doesn't start a data block */
@@ -144,7 +145,7 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures:
     const ctx: CifExportContext = params?.exportCtx || CifExportContext.create(structures);
 
     if (params?.copyAllCategories && MmcifFormat.is(models[0].sourceData)) {
-        encode_mmCIF_categories_copyAll(encoder, ctx);
+        encode_mmCIF_categories_copyAll(encoder, ctx, params);
     } else {
         encode_mmCIF_categories_default(encoder, ctx, params);
     }
@@ -168,6 +169,14 @@ function encode_mmCIF_categories_default(encoder: CifWriter.Encoder, ctx: CifExp
         }
     }
 
+    if (params?.customProperties) {
+        for (const customProp of params?.customProperties) {
+            for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
+                encoder.writeCategory(cat, propCtx);
+            }
+        }
+    }
+
     for (const s of ctx.structures) {
         if (!s.hasCustomProperties) continue;
         for (const customProp of s.customPropertyDescriptors.all) {
@@ -178,7 +187,7 @@ function encode_mmCIF_categories_default(encoder: CifWriter.Encoder, ctx: CifExp
     }
 }
 
-function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExportContext) {
+function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExportContext, params?: encode_mmCIF_categories_Params) {
     const providedCategories = new Map<string, CifExportCategoryInfo>();
 
     for (const cat of Categories) {
@@ -188,12 +197,21 @@ function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExp
     const mapping = atom_site_operator_mapping(ctx);
     if (mapping) providedCategories.set(mapping[0].name, mapping);
 
+    const _params = params || { };
     for (const customProp of ctx.firstModel.customProperties.all) {
-        for (const info of getCustomPropCategories(customProp, ctx)) {
+        for (const info of getCustomPropCategories(customProp, ctx, _params)) {
             providedCategories.set(info[0].name, info);
         }
     }
 
+    if (params?.customProperties) {
+        for (const customProp of params?.customProperties) {
+            for (const info of getCustomPropCategories(customProp, ctx, _params)) {
+                providedCategories.set(info[0].name, info);
+            }
+        }
+    }
+
     for (const s of ctx.structures) {
         if (!s.hasCustomProperties) continue;
         for (const customProp of s.customPropertyDescriptors.all) {

src/mol-model/structure/model/properties/format-specific.ts

@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-// TODO add access to things like MOL2 charge ...

src/mol-model/structure/model/properties/global-transform.ts

@@ -0,0 +1,80 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Mat4, Tensor } from '../../../../mol-math/linear-algebra';
+import { FormatPropertyProvider } from '../../../../mol-model-formats/structure/common/property';
+import { CustomPropertyDescriptor } from '../../../custom-property';
+import { CifExportContext } from '../../structure';
+import { Model } from '../model';
+import { Column, Table } from '../../../../mol-data/db';
+import { CifWriter } from '../../../../mol-io/writer/cif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { toTable } from '../../../../mol-io/reader/cif/schema';
+
+export namespace GlobalModelTransformInfo {
+    const CategoryName = 'molstar_global_model_transform_info' as const;
+    export const Schema = {
+        [CategoryName]: {
+            matrix: Column.Schema.Matrix(4, 4, Column.Schema.float)
+        }
+    };
+    export type Schema = typeof Schema
+
+    export const Descriptor = CustomPropertyDescriptor({
+        name: CategoryName,
+        cifExport: {
+            categories: [{
+                name: CategoryName,
+                instance(ctx: CifExportContext) {
+                    const mat = get(ctx.firstModel);
+                    if (!mat) return CifWriter.Category.Empty;
+                    const table = Table.ofRows(Schema.molstar_global_model_transform_info, [{ matrix: mat as unknown as Tensor.Data }]);
+                    return CifWriter.Category.ofTable(table);
+                }
+            }],
+            prefix: 'molstar'
+        }
+    });
+
+    export const Provider = FormatPropertyProvider.create<Mat4>(Descriptor);
+
+    export function attach(model: Model, matrix: Mat4) {
+        if (!model.customProperties.has(Descriptor)) {
+            model.customProperties.add(Descriptor);
+        }
+        Provider.set(model, matrix);
+    }
+
+    export function get(model: Model): Mat4 | undefined {
+        return Provider.get(model);
+    }
+
+    export function fromMmCif(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) return;
+
+        const cat = model.sourceData.data.frame.categories[CategoryName];
+        if (!cat) return;
+        const table = toTable(Schema[CategoryName], cat);
+        if (table._rowCount === 0) return;
+        return table.matrix.value(0) as unknown as Mat4;
+    }
+
+    export function hasData(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const cat = model.sourceData.data.frame.categories[CategoryName];
+        return !!cat && cat.rowCount > 0;
+    }
+
+    export function writeMmCif(encoder: CifWriter.Encoder, matrix: Mat4) {
+        encoder.writeCategory({
+            name: CategoryName,
+            instance() {
+                const table = Table.ofRows(Schema.molstar_global_model_transform_info, [{ matrix: matrix as unknown as Tensor.Data }]);
+                return CifWriter.Category.ofTable(table);
+            }
+        });
+    }
+}

src/mol-model/structure/structure/element/loci.ts

@@ -7,7 +7,7 @@
 
 import { UniqueArray } from '../../../../mol-data/generic';
 import { OrderedSet, SortedArray, Interval } from '../../../../mol-data/int';
-import { Vec3 } from '../../../../mol-math/linear-algebra';
+import { Mat4, Vec3 } from '../../../../mol-math/linear-algebra';
 import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
 import Structure from '../structure';
 import Unit from '../unit';
@@ -489,7 +489,7 @@ export namespace Loci {
 
     const boundaryHelper = new BoundaryHelper('98');
     const tempPosBoundary = Vec3();
-    export function getBoundary(loci: Loci): Boundary {
+    export function getBoundary(loci: Loci, transform?: Mat4): Boundary {
         boundaryHelper.reset();
 
         for (const e of loci.elements) {
@@ -499,6 +499,7 @@ export namespace Loci {
             for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
                 const eI = elements[OrderedSet.getAt(indices, i)];
                 pos(eI, tempPosBoundary);
+                if (transform) Vec3.transformMat4(tempPosBoundary, tempPosBoundary, transform);
                 boundaryHelper.includePositionRadius(tempPosBoundary, r(eI));
             }
         }
@@ -510,6 +511,7 @@ export namespace Loci {
             for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
                 const eI = elements[OrderedSet.getAt(indices, i)];
                 pos(eI, tempPosBoundary);
+                if (transform) Vec3.transformMat4(tempPosBoundary, tempPosBoundary, transform);
                 boundaryHelper.radiusPositionRadius(tempPosBoundary, r(eI));
             }
         }

src/mol-plugin-state/transforms/representation.ts

@@ -131,7 +131,6 @@ const StructureRepresentation3D = PluginStateTransform.BuiltIn({
             await Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: a.data }, params);
             repr.setTheme(Theme.create(plugin.representation.structure.themes, { structure: a.data }, params));
 
-            // TODO set initial state, repr.setState({})
             const props = params.type.params || {};
             await repr.createOrUpdate(props, a.data).runInContext(ctx);
             return new SO.Molecule.Structure.Representation3D({ repr, source: a }, { label: provider.label });
@@ -205,6 +204,8 @@ const UnwindStructureAssemblyRepresentation3D = PluginStateTransform.BuiltIn({
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
         if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
         const unitTransforms = b.data.state.unitTransforms!;
         unwindStructureAssembly(structure, unitTransforms, newParams.t);
@@ -240,6 +241,8 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
     update({ a, b, newParams, oldParams }) {
         const structure = a.data.source.data;
         if (b.data.info !== structure.root) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
         const unitTransforms = b.data.state.unitTransforms!;
         explodeStructure(structure.root, unitTransforms, newParams.t);
@@ -287,6 +290,8 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
         const oldStructure = b.data.info as Structure;
         const newStructure = a.data.source.data;
         if (newStructure !== oldStructure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         const oldOverpaint = b.data.state.overpaint!;
         const newOverpaint = Overpaint.ofScript(newParams.layers, newStructure);
         if (Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged;
@@ -337,6 +342,8 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
         const oldStructure = b.data.info as Structure;
         const newStructure = a.data.source.data;
         if (newStructure !== oldStructure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         const oldOverpaint = b.data.state.overpaint!;
         const newOverpaint = Overpaint.ofBundle(newParams.layers, newStructure);
         if (Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged;
@@ -383,6 +390,8 @@ const TransparencyStructureRepresentation3DFromScript = PluginStateTransform.Bui
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
         if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         const oldTransparency = b.data.state.transparency!;
         const newTransparency = Transparency.ofScript(newParams.layers, structure);
         if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged;
@@ -430,6 +439,8 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
         if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         const oldTransparency = b.data.state.transparency!;
         const newTransparency = Transparency.ofBundle(newParams.layers, structure);
         if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged;
@@ -476,6 +487,8 @@ const ClippingStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
         if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         const oldClipping = b.data.state.clipping!;
         const newClipping = Clipping.ofScript(newParams.layers, structure);
         if (Clipping.areEqual(oldClipping, newClipping)) return StateTransformer.UpdateResult.Unchanged;
@@ -523,6 +536,8 @@ const ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
         if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+
         const oldClipping = b.data.state.clipping!;
         const newClipping = Clipping.ofBundle(newParams.layers, structure);
         if (Clipping.areEqual(oldClipping, newClipping)) return StateTransformer.UpdateResult.Unchanged;
@@ -619,7 +634,6 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
     }
 })({
     canAutoUpdate({ oldParams, newParams }) {
-        // TODO: allow for small molecules
         return oldParams.type.name === newParams.type.name;
     },
     apply({ a, params }, plugin: PluginContext) {
@@ -627,10 +641,10 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
             const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
             const provider = plugin.representation.volume.registry.get(params.type.name);
             if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
-            const props = params.type.params || {};
             const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.volume.themes }, provider.getParams);
             repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
-            // TODO set initial state, repr.setState({})
+
+            const props = params.type.params || {};
             await repr.createOrUpdate(props, a.data).runInContext(ctx);
             return new SO.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
         });
@@ -673,7 +687,6 @@ const ShapeRepresentation3D = PluginStateTransform.BuiltIn({
         return Task.create('Shape Representation', async ctx => {
             const props = { ...PD.getDefaultValues(a.data.params), ...params };
             const repr = ShapeRepresentation(a.data.getShape, a.data.geometryUtils);
-            // TODO set initial state, repr.setState({})
             await repr.createOrUpdate(props, a.data.data).runInContext(ctx);
             return new SO.Shape.Representation3D({ repr, source: a }, { label: a.data.label });
         });

src/mol-plugin-ui/controls/parameters.tsx

@@ -186,6 +186,7 @@ function controlFor(param: PD.Any): ParamControl | undefined {
         case 'file-list': return FileListControl;
         case 'select': return SelectControl;
         case 'value-ref': return ValueRefControl;
+        case 'data-ref': return void 0;
         case 'text': return TextControl;
         case 'interval': return typeof param.min !== 'undefined' && typeof param.max !== 'undefined'
             ? BoundedIntervalControl : IntervalControl;

src/mol-plugin/behavior/dynamic/representation.ts

@@ -44,7 +44,7 @@ export const HighlightLoci = PluginBehavior.create({
     ctor: class extends PluginBehavior.Handler<HighlightLociProps> {
         private lociMarkProvider = (interactionLoci: Representation.Loci, action: MarkerAction) => {
             if (!this.ctx.canvas3d || !this.params.mark) return;
-            this.ctx.canvas3d.mark({ loci: interactionLoci.loci }, action);
+            this.ctx.canvas3d.mark(interactionLoci, action);
         }
         register() {
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, ({ current, buttons, modifiers }) => {
@@ -57,12 +57,14 @@ export const HighlightLoci = PluginBehavior.create({
                 let matched = false;
 
                 if (Binding.match(this.params.bindings.hoverHighlightOnly, buttons, modifiers)) {
-                    this.ctx.managers.interactivity.lociHighlights.highlightOnly(current);
+                    // remove repr to highlight loci everywhere on hover
+                    this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci: current.loci });
                     matched = true;
                 }
 
                 if (Binding.match(this.params.bindings.hoverHighlightOnlyExtend, buttons, modifiers)) {
-                    this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend(current);
+                    // remove repr to highlight loci everywhere on hover
+                    this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci: current.loci });
                     matched = true;
                 }
 

src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts

@@ -10,7 +10,7 @@ import { PluginStateObject } from '../../../../mol-plugin-state/objects';
 import { Volume, Grid } from '../../../../mol-model/volume';
 import { VolumeServerHeader, VolumeServerInfo } from './model';
 import { Box3D } from '../../../../mol-math/geometry';
-import { Vec3 } from '../../../../mol-math/linear-algebra';
+import { Mat4, Vec3 } from '../../../../mol-math/linear-algebra';
 import { Color } from '../../../../mol-util/color';
 import { PluginBehavior } from '../../behavior';
 import { LRUCache } from '../../../../mol-util/lru-cache';
@@ -23,6 +23,7 @@ import { StructureElement, Structure } from '../../../../mol-model/structure';
 import { PluginContext } from '../../../context';
 import { EmptyLoci, Loci, isEmptyLoci } from '../../../../mol-model/loci';
 import { Asset } from '../../../../mol-util/assets';
+import { GlobalModelTransformInfo } from '../../../../mol-model/structure/model/properties/global-transform';
 
 export class VolumeStreaming extends PluginStateObject.CreateBehavior<VolumeStreaming.Behavior>({ name: 'Volume Streaming' }) { }
 
@@ -302,6 +303,7 @@ export namespace VolumeStreaming {
             }
         }
 
+        private _invTransform: Mat4 = Mat4();
         private getBoxFromLoci(loci: StructureElement.Loci | EmptyLoci): Box3D {
             if (Loci.isEmpty(loci)) {
                 return Box3D();
@@ -312,11 +314,16 @@ export namespace VolumeStreaming {
             const root = this.getStructureRoot();
             if (!root || root.obj?.data !== parent.obj?.data) return Box3D();
 
+            const transform = GlobalModelTransformInfo.get(root.obj?.data.models[0]!);
+            if (transform) Mat4.invert(this._invTransform, transform);
+
             const extendedLoci = StructureElement.Loci.extendToWholeResidues(loci);
-            const box = StructureElement.Loci.getBoundary(extendedLoci).box;
+            const box = StructureElement.Loci.getBoundary(extendedLoci, transform && !Number.isNaN(this._invTransform[0]) ? this._invTransform : void 0).box;
+
             if (StructureElement.Loci.size(extendedLoci) === 1) {
                 Box3D.expand(box, box, Vec3.create(1, 1, 1));
             }
+
             return box;
         }
 
@@ -360,7 +367,6 @@ export namespace VolumeStreaming {
             const switchedToSelection = params.entry.params.view.name === 'selection-box' && this.params && this.params.entry && this.params.entry.params && this.params.entry.params.view && this.params.entry.params.view.name !== 'selection-box';
 
             this.params = params;
-
             let box: Box3D | undefined = void 0, emptyData = false;
 
             switch (params.entry.params.view.name) {

src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts

@@ -22,6 +22,7 @@ import { Box3D } from '../../../../mol-math/geometry';
 import { Vec3 } from '../../../../mol-math/linear-algebra';
 import { PluginConfig } from '../../../config';
 import { Model } from '../../../../mol-model/structure';
+import { GlobalModelTransformInfo } from '../../../../mol-model/structure/model/properties/global-transform';
 
 function addEntry(entries: InfoEntryProps[], method: VolumeServerInfo.Kind, dataId: string, emDefaultContourLevel: number) {
     entries.push({
@@ -253,20 +254,22 @@ const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
         channel: PD.Select<VolumeStreaming.ChannelType>('em', VolumeStreaming.ChannelTypeOptions, { isHidden: true })
     }
 })({
-    apply: ({ a, params: srcParams }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
+    apply: ({ a, params: srcParams, spine }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
         const channel = a.data.channels[srcParams.channel];
         if (!channel) return StateObject.Null;
 
         const params = createVolumeProps(a.data, srcParams.channel);
-
         const provider = VolumeRepresentationRegistry.BuiltIn.isosurface;
         const props = params.type.params || {};
         const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.volume.themes }, provider.getParams);
         repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
+        const structure = spine.getAncestorOfType(SO.Molecule.Structure)?.data;
+        const transform = structure?.models.length === 0 ? void 0 : GlobalModelTransformInfo.get(structure?.models[0]!);
         await repr.createOrUpdate(props, channel.data).runInContext(ctx);
+        if (transform) repr.setState({ transform });
         return new SO.Volume.Representation3D({ repr, source: a }, { label: `${Math.round(channel.isoValue.relativeValue * 100) / 100} σ [${srcParams.channel}]` });
     }),
-    update: ({ a, b, oldParams, newParams }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
+    update: ({ a, b, newParams, spine }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
         // TODO : check if params/underlying data/etc have changed; maybe will need to export "data" or some other "tag" in the Representation for this to work
 
         const channel = a.data.channels[newParams.channel];
@@ -277,6 +280,13 @@ const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
         const props = { ...b.data.repr.props, ...params.type.params };
         b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
         await b.data.repr.createOrUpdate(props, channel.data).runInContext(ctx);
+
+        // TODO: set the transform here as well in case the structure moves?
+        //       doing this here now breaks the code for some reason...
+        // const structure = spine.getAncestorOfType(SO.Molecule.Structure)?.data;
+        // const transform = structure?.models.length === 0 ? void 0 : GlobalModelTransformInfo.get(structure?.models[0]!);
+        // if (transform) b.data.repr.setState({ transform });
+
         return StateTransformer.UpdateResult.Updated;
     })
 });

src/mol-plugin/util/viewport-screenshot.ts

@@ -117,7 +117,7 @@ class ViewportScreenshotHelper extends PluginComponent {
             },
             postprocessing: {
                 ...c.props.postprocessing,
-                antialiasing: false
+                antialiasing: { name: 'off', params: {} }
             }
         });
     }
@@ -136,7 +136,7 @@ class ViewportScreenshotHelper extends PluginComponent {
                 // TODO: optimize because this creates a copy of a large object!
                 postprocessing: {
                     ...this.plugin.canvas3d!.props.postprocessing,
-                    antialiasing: false
+                    antialiasing: { name: 'off', params: {} }
                 }
             });
             return this._imagePass;

src/mol-repr/structure/visual/util/link.ts

@@ -131,7 +131,7 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
 
             addFixedCountDashedCylinder(builderState, va, vb, 0.5, 7, cylinderProps);
         } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple) {
-            const order = LinkStyle.Double ? 2 : 3;
+            const order = linkStyle === LinkStyle.Double ? 2 : 3;
             const multiRadius = linkRadius * (linkScale / (0.5 * order));
             const absOffset = (linkRadius - multiRadius) * linkSpacing;
 

src/mol-state/state.ts

@@ -328,6 +328,8 @@ class State {
         const oldTree = this._tree;
         this._tree = _tree;
 
+        const cells = this.cells;
+
         const ctx: UpdateContext = {
             parent: this,
             editInfo: StateBuilder.is(tree) ? tree.editInfo : void 0,
@@ -346,7 +348,9 @@ class State {
             changed: false,
             hadError: false,
             wasAborted: false,
-            newCurrent: void 0
+            newCurrent: void 0,
+
+            getCellData: ref => cells.get(ref)!.obj?.data
         };
 
         this.errorFree = true;
@@ -454,7 +458,9 @@ interface UpdateContext {
     changed: boolean,
     hadError: boolean,
     wasAborted: boolean,
-    newCurrent?: Ref
+    newCurrent?: Ref,
+
+    getCellData: (ref: string) => any
 }
 
 async function update(ctx: UpdateContext) {
@@ -841,7 +847,7 @@ function resolveParams(ctx: UpdateContext, transform: StateTransform, src: State
     (transform.params as any) = transform.params
         ? assignIfUndefined(transform.params, defaultValues)
         : defaultValues;
-    ParamDefinition.resolveValueRefs(definition, transform.params);
+    ParamDefinition.resolveRefs(definition, transform.params, ctx.getCellData);
     return { definition, values: transform.params };
 }
 

src/mol-util/param-definition.ts

@@ -296,6 +296,13 @@ export namespace ParamDefinition {
         return setInfo<ValueRef<T>>({ type: 'value-ref', defaultValue: { ref: info?.defaultRef ?? '', getValue: unsetGetValue as any }, getOptions, resolveRef }, info);
     }
 
+    export interface DataRef<T = any> extends Base<{ ref: string, getValue: () => T }> {
+        type: 'data-ref'
+    }
+    export function DataRef<T>(info?: Info & { defaultRef?: string }) {
+        return setInfo<DataRef<T>>({ type: 'data-ref', defaultValue: { ref: info?.defaultRef ?? '', getValue: unsetGetValue as any } }, info);
+    }
+
     export interface Converted<T, C> extends Base<T> {
         type: 'converted',
         converted: Any,
@@ -329,7 +336,7 @@ export namespace ParamDefinition {
 
     export type Any =
         | Value<any> | Select<any> | MultiSelect<any> | BooleanParam | Text | Color | Vec3 | Mat4 | Numeric | FileParam | UrlParam | FileListParam | Interval | LineGraph
-        | ColorList | Group<any> | Mapped<any> | Converted<any, any> | Conditioned<any, any, any> | Script | ObjectList | ValueRef
+        | ColorList | Group<any> | Mapped<any> | Converted<any, any> | Conditioned<any, any, any> | Script | ObjectList | ValueRef | DataRef
 
     export type Params = { [k: string]: Any }
     export type Values<T extends Params> = { [k in keyof T]: T[k]['defaultValue'] }
@@ -360,29 +367,33 @@ export namespace ParamDefinition {
         return () => resolve(ref);
     }
 
-    function resolveRefValue(p: Any, value: any) {
+    function resolveRefValue(p: Any, value: any, getData: (ref: string) => any) {
         if (!value) return;
 
         if (p.type === 'value-ref') {
             const v = value as ValueRef['defaultValue'];
             if (!v.ref) v.getValue = () => { throw new Error('Unset ref in ValueRef value.'); };
             else v.getValue = _resolveRef(p.resolveRef, v.ref);
+        } else if (p.type === 'data-ref') {
+            const v = value as ValueRef['defaultValue'];
+            if (!v.ref) v.getValue = () => { throw new Error('Unset ref in ValueRef value.'); };
+            else v.getValue = _resolveRef(getData, v.ref);
         } else if (p.type === 'group') {
-            resolveValueRefs(p.params, value);
+            resolveRefs(p.params, value, getData);
         } else if (p.type === 'mapped') {
             const v = value as NamedParams;
             const param = p.map(v.name);
-            resolveRefValue(param, v.params);
+            resolveRefValue(param, v.params, getData);
         } else if (p.type === 'object-list') {
             if (!hasValueRef(p.element)) return;
             for (const e of value) {
-                resolveValueRefs(p.element, e);
+                resolveRefs(p.element, e, getData);
             }
         }
     }
 
     function hasParamValueRef(p: Any) {
-        if (p.type === 'value-ref') {
+        if (p.type === 'value-ref' || p.type === 'data-ref') {
             return true;
         } else if (p.type === 'group') {
             if (hasValueRef(p.params)) return true;
@@ -403,9 +414,9 @@ export namespace ParamDefinition {
         return false;
     }
 
-    export function resolveValueRefs(params: Params, values: any) {
+    export function resolveRefs(params: Params, values: any, getData: (ref: string) => any) {
         for (const n of Object.keys(params)) {
-            resolveRefValue(params[n], values?.[n]);
+            resolveRefValue(params[n], values?.[n], getData);
         }
     }
 

src/servers/model/CHANGELOG.md

@@ -1,3 +1,6 @@
+# 0.9.5
+* Support molstar_global_model_transform_info category.
+
 # 0.9.4
 * bug fix for /ligand queries on metal ions
 

src/servers/model/server/query.ts

@@ -30,6 +30,7 @@ import { MolEncoder } from '../../../mol-io/writer/mol/encoder';
 import { Mol2Encoder } from '../../../mol-io/writer/mol2/encoder';
 import { ComponentAtom } from '../../../mol-model-formats/structure/property/atoms/chem_comp';
 import { Mat4 } from '../../../mol-math/linear-algebra';
+import { GlobalModelTransformInfo } from '../../../mol-model/structure/model/properties/global-transform';
 
 export interface Stats {
     structure: StructureWrapper,
@@ -247,6 +248,7 @@ async function resolveJobEntry(entry: JobEntry, structure: StructureWrapper, enc
 
         if (!entry.copyAllCategories && entry.queryDefinition.filter) encoder.setFilter(entry.queryDefinition.filter);
         if (result.length > 0) encode_mmCIF_categories(encoder, result, { copyAllCategories: entry.copyAllCategories });
+        if (entry.transform && !Mat4.isIdentity(entry.transform)) GlobalModelTransformInfo.writeMmCif(encoder, entry.transform);
         if (!entry.copyAllCategories && entry.queryDefinition.filter) encoder.setFilter();
         perf.end('encode');
 

src/servers/model/version.ts

@@ -4,4 +4,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export default '0.9.4';
+export default '0.9.5';