1.2.7

- remove unused/broken bilayer-spheres visual
- ensure anvil prop is calculated

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.2.0",
+  "version": "1.2.7",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -86,64 +86,64 @@
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^1.17.7",
-    "@graphql-codegen/cli": "^1.17.8",
-    "@graphql-codegen/time": "^1.17.10",
-    "@graphql-codegen/typescript": "^1.17.9",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.17.8",
-    "@graphql-codegen/typescript-graphql-request": "^1.17.7",
-    "@graphql-codegen/typescript-operations": "^1.17.8",
-    "@types/cors": "^2.8.7",
-    "@typescript-eslint/eslint-plugin": "^3.10.1",
-    "@typescript-eslint/parser": "^3.10.1",
+    "@graphql-codegen/add": "^2.0.2",
+    "@graphql-codegen/cli": "^1.19.4",
+    "@graphql-codegen/time": "^2.0.2",
+    "@graphql-codegen/typescript": "^1.19.0",
+    "@graphql-codegen/typescript-graphql-files-modules": "^1.18.1",
+    "@graphql-codegen/typescript-graphql-request": "^2.0.3",
+    "@graphql-codegen/typescript-operations": "^1.17.12",
+    "@types/cors": "^2.8.8",
+    "@typescript-eslint/eslint-plugin": "^4.9.1",
+    "@typescript-eslint/parser": "^4.9.1",
     "benchmark": "^2.1.4",
     "concurrently": "^5.3.0",
-    "cpx2": "^2.0.0",
-    "css-loader": "^3.6.0",
-    "eslint": "^7.8.1",
+    "cpx2": "^3.0.0",
+    "css-loader": "^5.0.1",
+    "eslint": "^7.15.0",
     "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^6.1.0",
+    "file-loader": "^6.2.0",
     "fs-extra": "^9.0.1",
-    "graphql": "^15.3.0",
+    "graphql": "^15.4.0",
     "http-server": "^0.12.3",
-    "jest": "^26.4.2",
-    "mini-css-extract-plugin": "^0.9.0",
-    "node-sass": "^4.14.1",
-    "raw-loader": "^4.0.1",
-    "sass-loader": "^8.0.2",
-    "simple-git": "^2.20.1",
-    "style-loader": "^1.2.1",
-    "ts-jest": "^26.3.0",
-    "typescript": "^4.0.2",
+    "jest": "^26.6.3",
+    "mini-css-extract-plugin": "^1.3.2",
+    "node-sass": "^5.0.0",
+    "raw-loader": "^4.0.2",
+    "sass-loader": "^10.1.0",
+    "simple-git": "^2.25.0",
+    "style-loader": "^2.0.0",
+    "ts-jest": "^26.4.4",
+    "typescript": "^4.1.2",
     "webpack": "^4.44.1",
     "webpack-cli": "^3.3.12",
     "webpack-version-file-plugin": "^0.4.0"
   },
   "dependencies": {
     "@types/argparse": "^1.0.38",
-    "@types/benchmark": "^1.0.33",
+    "@types/benchmark": "^2.1.0",
     "@types/compression": "1.7.0",
-    "@types/express": "^4.17.8",
-    "@types/jest": "^25.2.3",
-    "@types/node": "^14.10.1",
+    "@types/express": "^4.17.9",
+    "@types/jest": "^26.0.18",
+    "@types/node": "^14.14.11",
     "@types/node-fetch": "^2.5.7",
-    "@types/react": "^16.9.49",
-    "@types/react-dom": "^16.9.8",
-    "@types/swagger-ui-dist": "3.0.5",
+    "@types/react": "^17.0.0",
+    "@types/react-dom": "^17.0.0",
+    "@types/swagger-ui-dist": "3.30.0",
     "argparse": "^1.0.10",
     "body-parser": "^1.19.0",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
     "express": "^4.17.1",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^7.0.9",
+    "immer": "^8.0.0",
     "immutable": "^3.8.2",
-    "node-fetch": "^2.6.0",
-    "react": "^16.13.1",
-    "react-dom": "^16.13.1",
+    "node-fetch": "^2.6.1",
+    "react": "^17.0.1",
+    "react-dom": "^17.0.1",
     "rxjs": "^6.6.3",
-    "swagger-ui-dist": "^3.33.0",
-    "tslib": "^2.0.1",
+    "swagger-ui-dist": "^3.37.2",
+    "tslib": "^2.0.3",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

src/apps/viewer/embedded.html

@@ -37,6 +37,7 @@
             });
             viewer.loadPdb('7bv2');
             viewer.loadEmdb('EMD-30210', { detail: 6 });
+            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>
 </html>

src/apps/viewer/index.ts

@@ -68,7 +68,7 @@ const DefaultViewerOptions = {
     layoutShowLog: true,
     layoutShowLeftPanel: true,
     disableAntialiasing: false,
-    pixelScale: void 0 as number | undefined,
+    pixelScale: 1,
     enableWboit: false,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
@@ -115,16 +115,11 @@ export class Viewer {
             components: {
                 ...DefaultPluginSpec.components,
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
-                viewport: {
-                    canvas3d: {
-                        multiSample: { mode: 'on', sampleLevel: 2  }
-                    }
-                }
             },
             config: [
                 [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
                 [PluginConfig.General.PixelScale, o.pixelScale],
-                [PluginConfig.General.EnableWboit, true || o.enableWboit],
+                [PluginConfig.General.EnableWboit, o.enableWboit],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
@@ -170,13 +165,13 @@ export class Viewer {
         }));
     }
 
-    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false) {
+    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
         const plugin = this.plugin;
 
         const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
         const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
 
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true });
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
     }
 
     async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {

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

@@ -4,9 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Basis } from '../../extensions/alpha-orbitals/cubes';
-import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/orbitals';
-import { CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
+import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
+import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
 import { createPluginAsync, DefaultPluginSpec } from '../../mol-plugin';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { PluginConfig } from '../../mol-plugin/config';
@@ -20,23 +19,33 @@ import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
 import { BehaviorSubject } from 'rxjs';
 import { debounceTime, skip } from 'rxjs/operators';
 import './index.html';
+import { Basis, AlphaOrbital } from '../../extensions/alpha-orbitals/data-model';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 require('mol-plugin-ui/skin/light.scss');
 
 interface DemoInput {
     moleculeSdf: string,
     basis: Basis,
     order: SphericalBasisOrder,
-    orbitals: {
-        energy: number,
-        alpha: number[]
-    }[]
+    orbitals: AlphaOrbital[]
 }
 
 interface Params {
-    orbitalIndex: number,
+    show: { name: 'orbital', params: { index: number } } | { name: 'density', params: {} },
     isoValue: number,
-    gpuSurface: boolean,
-    cpuCompute: boolean
+    gpuSurface: boolean
+}
+
+type Selectors = {
+    type: 'orbital',
+    volume: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalVolume>,
+    positive: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
+    negative: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
+} | {
+    type: 'density',
+    volume: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalDensityVolume>,
+    positive: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
 }
 
 export class AlphaOrbitalsExample {
@@ -62,6 +71,14 @@ export class AlphaOrbitalsExample {
 
         this.plugin.managers.interactivity.setProps({ granularity: 'element' });
 
+        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).`
+            });
+            return;
+        }
+
         this.load({
             moleculeSdf: DemoMoleculeSDF,
             ...DemoOrbitals
@@ -71,40 +88,84 @@ export class AlphaOrbitalsExample {
     }
 
     readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
-    readonly state = new BehaviorSubject<Params>({ orbitalIndex: 32, isoValue: 1, gpuSurface: false, cpuCompute: false });
+    readonly state = new BehaviorSubject<Params>({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
+
+    private selectors?: Selectors = void 0;
+    private basis?: StateObjectSelector<BasisAndOrbitals> = void 0;
 
-    private volume?: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalVolume>;
-    private positive?: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>;
-    private negative?: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>;
     private currentParams: Params = { ...this.state.value };
 
-    private async setIndex() {
-        if (!this.volume?.isOk) return;
+    private clearVolume() {
+        if (!this.selectors) return;
+        const v = this.selectors.volume;
+        this.selectors = void 0;
+        return this.plugin.build().delete(v).commit();
+    }
+
+    private async syncVolume() {
+        if (!this.basis?.isOk) return;
+
         const state = this.state.value;
-        await this.plugin.build().to(this.volume).update(CreateOrbitalVolume, () => ({ index: state.orbitalIndex, cpuCompute: state.cpuCompute })).commit();
+
+        if (state.show.name !== this.selectors?.type) {
+            await this.clearVolume();
+        }
+
+        const update = this.plugin.build();
+        if (state.show.name === 'orbital') {
+            if (!this.selectors) {
+                const volume = update
+                    .to(this.basis)
+                    .apply(CreateOrbitalVolume, { index: state.show.params.index });
+
+                const positive = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
+                const negative = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('negative', ColorNames.red)).selector;
+
+                this.selectors = { type: 'orbital', volume: volume.selector, positive, negative };
+            } else {
+                const index = state.show.params.index;
+                update.to(this.selectors.volume).update(CreateOrbitalVolume, () => ({ index }));
+            }
+        } else {
+            if (!this.selectors) {
+                const volume = update
+                    .to(this.basis)
+                    .apply(CreateOrbitalDensityVolume);
+                const positive = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
+                this.selectors = { type: 'density', volume: volume.selector, positive };
+            }
+        }
+
+        await update.commit();
+
         if (this.currentParams.gpuSurface !== this.state.value.gpuSurface) {
             await this.setIsovalue();
         }
+
         this.currentParams = this.state.value;
     }
 
     private setIsovalue() {
+        if (!this.selectors) return;
+
         this.currentParams = this.state.value;
         const update = this.plugin.build();
-        update.to(this.positive!).update(this.volumeParams('positive', ColorNames.blue));
-        update.to(this.negative!).update(this.volumeParams('negative', ColorNames.red));
+        update.to(this.selectors.positive).update(this.volumeParams('positive', ColorNames.blue));
+        if (this.selectors?.type === 'orbital') {
+            update.to(this.selectors.negative).update(this.volumeParams('negative', ColorNames.red));
+        }
         return update.commit();
     }
 
     private volumeParams(kind: 'positive' | 'negative', color: Color): StateTransformer.Params<typeof CreateOrbitalRepresentation3D> {
         return {
-            alpha: 1.0,
+            alpha: 0.85,
             color,
             directVolume: this.state.value.gpuSurface,
             kind,
             relativeIsovalue: this.state.value.isoValue,
             pickable: false,
-            xrayShaded: false
+            xrayShaded: true
         };
     }
 
@@ -119,36 +180,28 @@ export class AlphaOrbitalsExample {
         const all = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'all');
         if (all) await this.plugin.builders.structure.representation.addRepresentation(all, { type: 'ball-and-stick', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
 
-        const state = this.state.value;
 
-        this.volume = await this.plugin.build().toRoot()
+        this.basis = await this.plugin.build().toRoot()
             .apply(StaticBasisAndOrbitals, { basis: input.basis, order: input.order, orbitals: input.orbitals })
-            .apply(CreateOrbitalVolume, { index: state.orbitalIndex, forceCpuCompute: this.currentParams.cpuCompute })
             .commit();
 
-        if (!this.volume.isOk) {
-            this.volume = void 0;
-            return;
-        }
-
-        const repr = this.plugin.build().to(this.volume);
-
-        this.positive = repr.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
-        this.negative = repr.apply(CreateOrbitalRepresentation3D, this.volumeParams('negative', ColorNames.red)).selector;
-
-        await repr.commit();
+        await this.syncVolume();
 
         this.params.next({
-            orbitalIndex: ParamDefinition.Numeric(this.currentParams.orbitalIndex, { min: 0, max: input.orbitals.length - 1 }, { immediateUpdate: true, isEssential: true }),
+            show: ParamDefinition.MappedStatic('orbital', {
+                'orbital': ParamDefinition.Group({
+                    index: ParamDefinition.Numeric(32, { min: 0, max: input.orbitals.length - 1 }, { immediateUpdate: true, isEssential: true }),
+                }),
+                'density': ParamDefinition.EmptyGroup()
+            }, { cycle: true }),
             isoValue: ParamDefinition.Numeric(this.currentParams.isoValue, { min: 0.5, max: 3, step: 0.1 }, { immediateUpdate: true, isEssential: false }),
-            gpuSurface: ParamDefinition.Boolean(this.currentParams.gpuSurface),
-            cpuCompute: ParamDefinition.Boolean(this.currentParams.cpuCompute, { label: 'CPU Compute' })
+            gpuSurface: ParamDefinition.Boolean(this.currentParams.gpuSurface, { isHidden: true })
         });
 
         this.state.pipe(skip(1), debounceTime(1000 / 24)).subscribe(async params => {
-            if (params.orbitalIndex !== this.currentParams.orbitalIndex
-                || params.cpuCompute !== this.currentParams.cpuCompute) {
-                this.setIndex();
+            if (params.show.name !== this.currentParams.show.name
+                || (params.show.name === 'orbital' && this.currentParams.show.name === 'orbital' && params.show.params.index !== this.currentParams.show.params.index)) {
+                this.syncVolume();
             } else if (params.isoValue !== this.currentParams.isoValue || params.gpuSurface !== this.currentParams.gpuSurface) {
                 this.setIsovalue();
             }

src/examples/alpha-orbitals/test-water.ts

@@ -1,190 +0,0 @@
-import { CollocationParams } from '../../extensions/alpha-orbitals/collocation';
-import { Basis } from '../../extensions/alpha-orbitals/cubes';
-import { Box3D } from '../../mol-math/geometry';
-import { Vec3 } from '../../mol-math/linear-algebra';
-
-const _testBasis: Basis = {
-    'atoms': [
-        {
-            'center': [
-                0.025886090588624934,
-                0.019164790004065606,
-                -0.013539970104105408
-            ] as Vec3,
-            'shells': [
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            -0.004151277818987536,
-                            -0.02067024147993795,
-                            -0.05150303336984537,
-                            0.33462711739899537,
-                            0.5621061300983125,
-                            0.17129946969948573
-                        ]
-                    ],
-                    'exponents': [
-                        152.28769660788095,
-                        27.928015215973073,
-                        7.848374792384515,
-                        1.1223350202705642,
-                        0.5093846587907856,
-                        0.24292266532510307
-                    ]
-                },
-                {
-                    'angularMomentum': [1],
-                    'coefficients': [
-                        [
-                            0.007924233646294425,
-                            0.051441048251911314,
-                            0.18984000600705359,
-                            0.4049863191150474,
-                            0.40123628611490797,
-                            0.1051855189039082
-                        ]
-                    ],
-                    'exponents': [
-                        27.203421487167727,
-                        7.09409912597673,
-                        2.5383362605345954,
-                        1.0610730767843852,
-                        0.4851948916410433,
-                        0.22938302550642545
-                    ]
-                }
-            ]
-        },
-        {
-            'center': [
-                0.5082729578468134,
-                1.6880351220025265,
-                0.4963443067810461
-            ] as Vec3,
-            'shells': [
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            0.009163596280542963,
-                            0.04936149294292479,
-                            0.16853830490998634,
-                            0.37056279972195677,
-                            0.4164915298246781,
-                            0.13033408410772263
-                        ]
-                    ],
-                    'exponents': [
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                },
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            -0.32279868167000036,
-                            3.209629817295221,
-                            2.4672629224617935,
-                            -0.048487066612842224,
-                            -0.2611850111200143,
-                            -0.8917817597810863,
-                            -1.9607480081275706,
-                            -2.203769342520311,
-                            -0.6896328935259993
-                        ]
-                    ],
-                    'exponents': [
-                        10.256286070314905,
-                        0.6227965325875392,
-                        0.2391007667853915,
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                }
-            ]
-        },
-        {
-            'center': [
-                1.1367367844436005,
-                -0.47018519422670163,
-                -1.356802622574504
-            ] as Vec3,
-            'shells': [
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            0.009163596280542963,
-                            0.04936149294292479,
-                            0.16853830490998634,
-                            0.37056279972195677,
-                            0.4164915298246781,
-                            0.13033408410772263
-                        ]
-                    ],
-                    'exponents': [
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                },
-                {
-                    'angularMomentum': [0],
-                    'coefficients': [
-                        [
-                            -0.32279868167000036,
-                            3.209629817295221,
-                            2.4672629224617935,
-                            -0.048487066612842224,
-                            -0.2611850111200143,
-                            -0.8917817597810863,
-                            -1.9607480081275706,
-                            -2.203769342520311,
-                            -0.6896328935259993
-                        ]
-                    ],
-                    'exponents': [
-                        10.256286070314905,
-                        0.6227965325875392,
-                        0.2391007667853915,
-                        33.710073211949485,
-                        6.180705022740464,
-                        1.7291385346152253,
-                        0.5940057549921978,
-                        0.2306698170449518,
-                        0.09500256906284119
-                    ]
-                }
-            ]
-        }
-    ]
-};
-
-const grid = {
-    box: Box3D.create(Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)),
-    delta: Vec3.create(2, 2, 2),
-    dimensions: Vec3.create(2, 2, 2),
-    npoints: 8,
-    size: Vec3.create(2, 2, 2)
-};
-
-export const TestWaterParams: CollocationParams = {
-    grid,
-    alphaOrbitals: [-2.2623991420609075e-16, 0.6360205395000592, 0.6672122399886391, -0.3876927909355508, -1.6780131293332933e-16, 2.844782862661151e-16, 4.977960694176068e-19, -2.3945919908996803e-16],
-    basis: _testBasis,
-    cutoffThreshold: 0,
-    sphericalOrder: 'cca-reverse'
-};

src/extensions/alpha-orbitals/_spec/collocation.spec.ts

@@ -8,11 +8,18 @@ import { Box3D } from '../../../mol-math/geometry';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { RuntimeContext } from '../../../mol-task';
 import { sphericalCollocation } from '../collocation';
-import { Basis } from '../cubes';
+import { Basis, CubeGridInfo } from '../data-model';
 
 describe('alpha-orbitals-cubes', () => {
     it('water', async () => {
-        const grid = {
+        const grid: CubeGridInfo = {
+            params: {
+                basis: _testBasis,
+                cutoffThreshold: 0,
+                sphericalOrder: 'cca-reverse',
+                boxExpand: 0,
+                gridSpacing: []
+            },
             box: Box3D.create(Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)),
             delta: Vec3.create(2, 2, 2),
             dimensions: Vec3.create(2, 2, 2),
@@ -20,12 +27,10 @@ describe('alpha-orbitals-cubes', () => {
             size: Vec3.create(2, 2, 2)
         };
 
-        const matrix = await sphericalCollocation({
-            grid,
-            alphaOrbitals: [-2.2623991420609075e-16, 0.6360205395000592, 0.6672122399886391, -0.3876927909355508, -1.6780131293332933e-16, 2.844782862661151e-16, 4.977960694176068e-19, -2.3945919908996803e-16],
-            basis: _testBasis,
-            cutoffThreshold: 0,
-            sphericalOrder: 'cca-reverse'
+        const matrix = await sphericalCollocation(grid, {
+            energy: 0,
+            occupancy: 0,
+            alpha: [-2.2623991420609075e-16, 0.6360205395000592, 0.6672122399886391, -0.3876927909355508, -1.6780131293332933e-16, 2.844782862661151e-16, 4.977960694176068e-19, -2.3945919908996803e-16]
         }, RuntimeContext.Synchronous);
 
         const expected = [-0.1451730622877498, 0.06479453956039086, -0.2777738736440713, -0.057116584776260436, 0.05929916178822645, 0.2742903371231049, -0.07221698722165386, 0.15389180241391376];

src/extensions/alpha-orbitals/collocation.ts

@@ -9,31 +9,15 @@
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { RuntimeContext } from '../../mol-task';
 import { arrayMin } from '../../mol-util/array';
-import { Basis, CubeGridInfo } from './cubes';
-import {
-    normalizeBasicOrder,
-
-    SphericalBasisOrder, SphericalFunctions
-} from './orbitals';
-
-export interface CollocationParams {
-    grid: CubeGridInfo;
-    basis: Basis;
-    sphericalOrder: SphericalBasisOrder;
-    cutoffThreshold: number;
-    alphaOrbitals: number[];
-}
+import { AlphaOrbital, CubeGridInfo } from './data-model';
+import { normalizeBasicOrder, SphericalFunctions } from './spherical-functions';
 
 export async function sphericalCollocation(
-    {
-        grid,
-        basis,
-        sphericalOrder,
-        cutoffThreshold,
-        alphaOrbitals,
-    }: CollocationParams,
+    grid: CubeGridInfo,
+    orbital: AlphaOrbital,
     taskCtx: RuntimeContext
 ) {
+    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
     let baseCount = 0;
 
     for (const atom of basis.atoms) {
@@ -58,7 +42,7 @@ export async function sphericalCollocation(
             for (const L of shell.angularMomentum) {
                 const alpha = normalizeBasicOrder(
                     L,
-                    alphaOrbitals.slice(baseIndex, baseIndex + 2 * L + 1),
+                    orbital.alpha.slice(baseIndex, baseIndex + 2 * L + 1),
                     sphericalOrder
                 );
                 baseIndex += 2 * L + 1;

src/extensions/alpha-orbitals/cubes.ts

@@ -1,260 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Inspired by https://github.com/dgasmith/gau2grid.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { sortArray } from '../../mol-data/util';
-import { WebGLContext } from '../../mol-gl/webgl/context';
-import { Box3D } from '../../mol-math/geometry';
-import { Mat4, Tensor, Vec3 } from '../../mol-math/linear-algebra';
-import { Grid } from '../../mol-model/volume';
-import { Task } from '../../mol-task';
-import { arrayMax, arrayMin, arrayRms } from '../../mol-util/array';
-import { CollocationParams, sphericalCollocation } from './collocation';
-import { canComputeAlphaOrbitalsOnGPU, gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
-import { SphericalBasisOrder } from './orbitals';
-
-export interface CubeGridInfo {
-    dimensions: Vec3;
-    box: Box3D;
-    size: Vec3;
-    npoints: number;
-    delta: Vec3;
-}
-
-export interface CubeGrid {
-    grid: Grid;
-    isovalues?: { negative?: number; positive?: number };
-}
-
-export interface Basis {
-    atoms: {
-        // in Bohr units!
-        center: Vec3;
-        shells: SphericalElectronShell[];
-    }[];
-}
-
-// Note: generally contracted gaussians are currently not supported.
-export interface SphericalElectronShell {
-    exponents: number[];
-    angularMomentum: number[];
-    // number[] for each angular momentum
-    coefficients: number[][];
-}
-
-export interface SphericalCollocationParams {
-    basis: Basis;
-    /**
-     * for each electron shell compute a cutoff radius as
-     *
-     *    const cutoffRadius = Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents));
-     *
-     */
-    cutoffThreshold: number;
-    sphericalOrder: SphericalBasisOrder;
-    boxExpand: number;
-    gridSpacing: number | [atomCountThreshold: number, spacing: number][];
-    alphaOrbitals: number[];
-    doNotComputeIsovalues?: boolean
-}
-
-export function createSphericalCollocationGrid(
-    params: SphericalCollocationParams, webgl?: WebGLContext
-): Task<CubeGrid> {
-    return Task.create('Spherical Collocation Grid', async (ctx) => {
-        const centers = params.basis.atoms.map(a => a.center);
-
-        const cParams: CollocationParams = {
-            grid: initBox(centers, params.gridSpacing, params.boxExpand),
-            basis: params.basis,
-            alphaOrbitals: params.alphaOrbitals,
-            cutoffThreshold: params.cutoffThreshold,
-            sphericalOrder: params.sphericalOrder
-        };
-
-        let matrix: Float32Array;
-        if (canComputeAlphaOrbitalsOnGPU(webgl)) {
-            // console.time('gpu');
-            matrix = gpuComputeAlphaOrbitalsGridValues(webgl!, cParams);
-            // console.timeEnd('gpu');
-        } else {
-            // console.time('cpu');
-            matrix = await sphericalCollocation(cParams, ctx);
-            // console.timeEnd('cpu');
-        }
-
-        return createCubeGrid(cParams.grid, matrix, [0, 1, 2], !params.doNotComputeIsovalues);
-    });
-}
-
-const BohrToAngstromFactor = 0.529177210859;
-
-function createCubeGrid(gridInfo: CubeGridInfo, values: Float32Array, axisOrder: number[], computeIsovalues: boolean) {
-    const boxSize = Box3D.size(Vec3(), gridInfo.box);
-    const boxOrigin = Vec3.clone(gridInfo.box.min);
-
-    Vec3.scale(boxSize, boxSize, BohrToAngstromFactor);
-    Vec3.scale(boxOrigin, boxOrigin, BohrToAngstromFactor);
-
-    const scale = Mat4.fromScaling(
-        Mat4(),
-        Vec3.div(
-            Vec3(),
-            boxSize,
-            Vec3.sub(Vec3(), gridInfo.dimensions, Vec3.create(1, 1, 1))
-        )
-    );
-    const translate = Mat4.fromTranslation(Mat4(), boxOrigin);
-    const matrix = Mat4.mul(Mat4(), translate, scale);
-
-    const grid: Grid = {
-        transform: { kind: 'matrix', matrix },
-        cells: Tensor.create(
-            Tensor.Space(gridInfo.dimensions, axisOrder, Float32Array),
-            (values as any) as Tensor.Data
-        ),
-        stats: {
-            min: arrayMin(values),
-            max: arrayMax(values),
-            mean: arrayMax(values),
-            sigma: arrayRms(values),
-        },
-    };
-
-    // TODO: when using GPU rendering, the cumulative sum can be computed
-    //       along the ray on the fly?
-    let isovalues: { negative?: number, positive?: number } | undefined;
-
-    if (computeIsovalues) {
-        isovalues = computeIsocontourValues(values, 0.85);
-    }
-
-    return { grid, isovalues };
-}
-
-function initBox(
-    geometry: Vec3[],
-    spacing: SphericalCollocationParams['gridSpacing'],
-    expand: number
-): CubeGridInfo {
-    const count = geometry.length;
-    const box = Box3D.expand(
-        Box3D(),
-        Box3D.fromVec3Array(Box3D(), geometry),
-        Vec3.create(expand, expand, expand)
-    );
-    const size = Box3D.size(Vec3(), box);
-
-    const spacingThresholds =
-        typeof spacing === 'number' ? [[0, spacing]] : [...spacing];
-    spacingThresholds.sort((a, b) => b[0] - a[0]);
-
-    let s = 0.4;
-    for (let i = 0; i <= spacingThresholds.length; i++) {
-        s = spacingThresholds[i][1];
-        if (spacingThresholds[i][0] <= count) break;
-    }
-
-    const dimensions = Vec3.ceil(Vec3(), Vec3.scale(Vec3(), size, 1 / s));
-
-    return {
-        box,
-        dimensions,
-        size,
-        npoints: dimensions[0] * dimensions[1] * dimensions[2],
-        delta: Vec3.div(Vec3(), size, Vec3.subScalar(Vec3(), dimensions, 1)),
-    };
-}
-
-export function computeIsocontourValues(
-    input: Float32Array,
-    cumulativeThreshold: number
-) {
-    let weightSum = 0;
-    for (let i = 0, _i = input.length; i < _i; i++) {
-        const v = input[i];
-        const w = v * v;
-        weightSum += w;
-    }
-    const avgWeight = weightSum / input.length;
-    let minWeight = 3 * avgWeight;
-
-    // do not try to identify isovalues for degenerate data
-    // e.g. all values are almost same
-    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
-        return { negative: void 0, positive: void 0 };
-    }
-
-    let size = 0;
-    while (true) {
-        let csum = 0;
-        size = 0;
-        for (let i = 0, _i = input.length; i < _i; i++) {
-            const v = input[i];
-            const w = v * v;
-            if (w >= minWeight) {
-                csum += w;
-                size++;
-            }
-        }
-
-        if (csum / weightSum > cumulativeThreshold) {
-            break;
-        }
-
-        minWeight -= avgWeight;
-    }
-
-    const values = new Float32Array(size);
-    const weights = new Float32Array(size);
-    const indices = new Int32Array(size);
-
-    let o = 0;
-    for (let i = 0, _i = input.length; i < _i; i++) {
-        const v = input[i];
-        const w = v * v;
-        if (w >= minWeight) {
-            values[o] = v;
-            weights[o] = w;
-            indices[o] = o;
-            o++;
-        }
-    }
-
-    sortArray(
-        indices,
-        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
-    );
-
-    let cweight = 0,
-        cutoffIndex = 0;
-    for (let i = 0; i < size; i++) {
-        cweight += weights[indices[i]];
-
-        if (cweight / weightSum >= cumulativeThreshold) {
-            cutoffIndex = i;
-            break;
-        }
-    }
-
-    let positive = Number.POSITIVE_INFINITY,
-        negative = Number.NEGATIVE_INFINITY;
-
-    for (let i = 0; i < cutoffIndex; i++) {
-        const v = values[indices[i]];
-        if (v > 0) {
-            if (v < positive) positive = v;
-        } else if (v < 0) {
-            if (v > negative) negative = v;
-        }
-    }
-
-    return {
-        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
-        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
-    };
-}

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

@@ -0,0 +1,131 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Mat4, Tensor, Vec3 } from '../../mol-math/linear-algebra';
+import { Grid } from '../../mol-model/volume';
+import { SphericalBasisOrder } from './spherical-functions';
+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 {
+    exponents: number[];
+    angularMomentum: number[];
+    // number[] for each angular momentum
+    coefficients: number[][];
+}
+
+export interface Basis {
+    atoms: {
+        // in Bohr units!
+        center: Vec3;
+        shells: SphericalElectronShell[];
+    }[];
+}
+
+export interface AlphaOrbital {
+    energy: number;
+    occupancy: number;
+    alpha: number[];
+}
+
+export interface CubeGridComputationParams {
+    basis: Basis;
+    /**
+     * for each electron shell compute a cutoff radius as
+     *    const cutoffRadius = Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents));
+     */
+    cutoffThreshold: number;
+    sphericalOrder: SphericalBasisOrder;
+    boxExpand: number;
+    gridSpacing: number | [atomCountThreshold: number, spacing: number][];
+    doNotComputeIsovalues?: boolean;
+}
+
+export interface CubeGridInfo {
+    params: CubeGridComputationParams;
+    dimensions: Vec3;
+    box: Box3D;
+    size: Vec3;
+    npoints: number;
+    delta: Vec3;
+}
+
+export interface CubeGrid {
+    grid: Grid;
+    isovalues?: { negative?: number; positive?: number };
+}
+
+export function initCubeGrid(params: CubeGridComputationParams): CubeGridInfo {
+    const geometry = params.basis.atoms.map(a => a.center);
+    const { gridSpacing: spacing, boxExpand: expand } = params;
+
+    const count = geometry.length;
+    const box = Box3D.expand(
+        Box3D(),
+        Box3D.fromVec3Array(Box3D(), geometry),
+        Vec3.create(expand, expand, expand)
+    );
+    const size = Box3D.size(Vec3(), box);
+
+    const spacingThresholds =
+        typeof spacing === 'number' ? [[0, spacing]] : [...spacing];
+    spacingThresholds.sort((a, b) => b[0] - a[0]);
+
+    let s = 0.4;
+    for (let i = 0; i <= spacingThresholds.length; i++) {
+        s = spacingThresholds[i][1];
+        if (spacingThresholds[i][0] <= count) break;
+    }
+
+    const dimensions = Vec3.ceil(Vec3(), Vec3.scale(Vec3(), size, 1 / s));
+
+    return {
+        params,
+        box,
+        dimensions,
+        size,
+        npoints: dimensions[0] * dimensions[1] * dimensions[2],
+        delta: Vec3.div(Vec3(), size, Vec3.subScalar(Vec3(), dimensions, 1)),
+    };
+}
+
+const BohrToAngstromFactor = 0.529177210859;
+
+export function createGrid(gridInfo: RegularGrid3d, values: Float32Array, axisOrder: number[]) {
+    const boxSize = Box3D.size(Vec3(), gridInfo.box);
+    const boxOrigin = Vec3.clone(gridInfo.box.min);
+
+    Vec3.scale(boxSize, boxSize, BohrToAngstromFactor);
+    Vec3.scale(boxOrigin, boxOrigin, BohrToAngstromFactor);
+
+    const scale = Mat4.fromScaling(
+        Mat4(),
+        Vec3.div(
+            Vec3(),
+            boxSize,
+            Vec3.sub(Vec3(), gridInfo.dimensions, Vec3.create(1, 1, 1))
+        )
+    );
+    const translate = Mat4.fromTranslation(Mat4(), boxOrigin);
+    const matrix = Mat4.mul(Mat4(), translate, scale);
+
+    const grid: Grid = {
+        transform: { kind: 'matrix', matrix },
+        cells: Tensor.create(
+            Tensor.Space(gridInfo.dimensions, axisOrder, Float32Array),
+            (values as any) as Tensor.Data
+        ),
+        stats: {
+            min: arrayMin(values),
+            max: arrayMax(values),
+            mean: arrayMean(values),
+            sigma: arrayRms(values),
+        },
+    };
+
+    return grid;
+}

src/extensions/alpha-orbitals/density.ts

@@ -0,0 +1,124 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+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 { gpuComputeAlphaOrbitalsDensityGridValues } from './gpu/compute';
+
+export function createSphericalCollocationDensityGrid(
+    params: CubeGridComputationParams, orbitals: AlphaOrbital[], webgl?: WebGLContext
+): Task<CubeGrid> {
+    return Task.create('Spherical Collocation Grid', async (ctx) => {
+        const cubeGrid = initCubeGrid(params);
+
+        let matrix: Float32Array;
+        if (canComputeGrid3dOnGPU(webgl)) {
+            // console.time('gpu');
+            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl!, cubeGrid, orbitals);
+            // console.timeEnd('gpu');
+        } else {
+            throw new Error('Missing OES_texture_float WebGL extension.');
+        }
+
+        const grid = createGrid(cubeGrid, matrix, [0, 1, 2]);
+        let isovalues: { negative?: number, positive?: number } | undefined;
+
+        if (!params.doNotComputeIsovalues) {
+            isovalues = computeDensityIsocontourValues(matrix, 0.85);
+        }
+
+        return { grid, isovalues };
+    });
+}
+
+export function computeDensityIsocontourValues(input: Float32Array, cumulativeThreshold: number) {
+    let weightSum = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = Math.abs(v);
+        weightSum += w;
+    }
+    const avgWeight = weightSum / input.length;
+    let minWeight = 3 * avgWeight;
+
+    // do not try to identify isovalues for degenerate data
+    // e.g. all values are almost same
+    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
+        return { negative: void 0, positive: void 0 };
+    }
+
+    let size = 0;
+    while (true) {
+        let csum = 0;
+        size = 0;
+        for (let i = 0, _i = input.length; i < _i; i++) {
+            const v = input[i];
+            const w = Math.abs(v);
+            if (w >= minWeight) {
+                csum += w;
+                size++;
+            }
+        }
+
+        if (csum / weightSum > cumulativeThreshold) {
+            break;
+        }
+
+        minWeight -= avgWeight;
+    }
+
+    const values = new Float32Array(size);
+    const weights = new Float32Array(size);
+    const indices = new Int32Array(size);
+
+    let o = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = Math.abs(v);
+        if (w >= minWeight) {
+            values[o] = v;
+            weights[o] = w;
+            indices[o] = o;
+            o++;
+        }
+    }
+
+    sortArray(
+        indices,
+        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
+    );
+
+    let cweight = 0,
+        cutoffIndex = 0;
+    for (let i = 0; i < size; i++) {
+        cweight += weights[indices[i]];
+
+        if (cweight / weightSum >= cumulativeThreshold) {
+            cutoffIndex = i;
+            break;
+        }
+    }
+
+    let positive = Number.POSITIVE_INFINITY,
+        negative = Number.NEGATIVE_INFINITY;
+
+    for (let i = 0; i < cutoffIndex; i++) {
+        const v = values[indices[i]];
+        if (v > 0) {
+            if (v < positive) positive = v;
+        } else if (v < 0) {
+            if (v > negative) negative = v;
+        }
+    }
+
+    return {
+        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
+        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
+    };
+}

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

@@ -4,46 +4,93 @@
  * @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 { CollocationParams } from '../collocation';
-import { normalizeBasicOrder } from '../orbitals';
-import shader_frag from './shader.frag';
+import { AlphaOrbital, Basis, CubeGridInfo } from '../data-model';
+import { normalizeBasicOrder, SphericalBasisOrder } from '../spherical-functions';
+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')
 };
-const AlphaOrbitalsName = 'alpha-orbitals';
-const AlphaOrbitalsShaderCode = ShaderCode(AlphaOrbitalsName, quad_vert, shader_frag);
-type AlphaOrbitalsRenderable = ComputeRenderable<Values<typeof AlphaOrbitalsSchema>>
 
-function createTextureData({
-    basis,
-    sphericalOrder,
-    alphaOrbitals,
-    cutoffThreshold
-}: CollocationParams) {
+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);
+
+    let aO = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            for (const L of shell.angularMomentum) {
+                const a0 = normalizeBasicOrder(L, alphaOrbitals.slice(aO, aO + 2 * L + 1), sphericalOrder);
+                for (let i = 0; i < a0.length; i++) alpha[aO + i] = a0[i];
+                aO += 2 * L + 1;
+            }
+        }
+    }
+
+    return alpha;
+}
+
+function createTextureData(grid: CubeGridInfo, orbital: AlphaOrbital): UnboxedValues<typeof Schema> {
+    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
+
     let centerCount = 0;
     let baseCount = 0;
     let coeffCount = 0;
@@ -75,7 +122,7 @@ function createTextureData({
 
             let amIndex = 0;
             for (const L of shell.angularMomentum) {
-                const a0 = normalizeBasicOrder(L, alphaOrbitals.slice(aO, aO + 2 * L + 1), sphericalOrder);
+                const a0 = normalizeBasicOrder(L, orbital.alpha.slice(aO, aO + 2 * L + 1), sphericalOrder);
 
                 const cutoffRadius = cutoffThreshold > 0
                     ? Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(shell.exponents))
@@ -110,105 +157,14 @@ function createTextureData({
         }
     }
 
-    return { nCenters: centerCount, nAlpha: baseCount, nCoeff: coeffCount, maxCoeffs, centers, info, alpha, coeff };
-}
-
-function createAlphaOrbitalsRenderable(ctx: WebGLContext, params: CollocationParams): AlphaOrbitalsRenderable {
-    const data = createTextureData(params);
-
-    const [nx, ny, nz] = params.grid.dimensions;
-    const width = Math.ceil(Math.sqrt(nx * ny * nz));
-
-    const values: Values<typeof AlphaOrbitalsSchema> = {
-        ...QuadValues,
-        uDimensions: ValueCell.create(params.grid.dimensions),
-        uMin: ValueCell.create(params.grid.box.min),
-        uDelta: ValueCell.create(params.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()),
+    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, params: CollocationParams): AlphaOrbitalsRenderable {
-    if (ctx.namedComputeRenderables[AlphaOrbitalsName]) {
-        const v = ctx.namedComputeRenderables[AlphaOrbitalsName].values;
-
-        const data = createTextureData(params);
-
-        const [nx, ny, nz] = params.grid.dimensions;
-        const width = Math.ceil(Math.sqrt(nx * ny * nz));
-
-        ValueCell.update(v.uDimensions, params.grid.dimensions);
-        ValueCell.update(v.uMin, params.grid.box.min);
-        ValueCell.update(v.uDelta, params.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());
-
-        ctx.namedComputeRenderables[AlphaOrbitalsName].update();
-    } else {
-        ctx.namedComputeRenderables[AlphaOrbitalsName] = createAlphaOrbitalsRenderable(ctx, params);
-    }
-    return ctx.namedComputeRenderables[AlphaOrbitalsName];
-}
-
-export function gpuComputeAlphaOrbitalsGridValues(webgl: WebGLContext, params: CollocationParams) {
-    const [nx, ny, nz] = params.grid.dimensions;
-    const renderable = getAlphaOrbitalsRenderable(webgl, params);
-    const width = renderable.values.uWidth.ref.value;
-
-    if (!webgl.namedFramebuffers[AlphaOrbitalsName]) {
-        webgl.namedFramebuffers[AlphaOrbitalsName] = webgl.resources.framebuffer();
-    }
-    const framebuffer = webgl.namedFramebuffers[AlphaOrbitalsName];
-
-    if (!webgl.namedTextures[AlphaOrbitalsName]) {
-        webgl.namedTextures[AlphaOrbitalsName] = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
-    }
-    webgl.namedTextures[AlphaOrbitalsName].define(width, width);
-    webgl.namedTextures[AlphaOrbitalsName].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;
 }

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

@@ -4,69 +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 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)
-    );
-}
-
+export const UTILS = `
 float L1(vec3 p, float a0, float a1, float a2) {
     return a0 * p.z + a1 * p.x + a2 * p.y;
 }
@@ -117,12 +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
 }
@@ -153,7 +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++) {
@@ -162,9 +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;
@@ -178,28 +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++) {
@@ -223,8 +142,4 @@ void main(void) {
 
         v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
     }
-
-    // TODO: render to single component float32 texture in WebGL2
-    gl_FragColor = floatToRgba(v);
-}
 `;

src/extensions/alpha-orbitals/orbitals.ts

@@ -6,88 +6,126 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-// gaussian:
-//     R_0, R^+_1, R^-_1, ..., R^+_l, R^-_l
-// cca:
-//     R^-_(l), R^-_(l-1), ..., R_0, ..., R^+_(l-1), R^+_l
-// cca-reverse:
-//     R^+_(l), R^+_(l-1), ..., R_0, ..., R^-_(l-1), R^-_l
-export type SphericalBasisOrder = 'gaussian' | 'cca' | 'cca-reverse';
+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 { gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
 
-export function normalizeBasicOrder(
-    L: number,
-    alpha: number[],
-    order: SphericalBasisOrder
-) {
-    if (order === 'gaussian' || L === 0) return alpha;
+// setDebugMode(true);
 
-    const ret: number[] = [alpha[L]];
-    for (let l = 0; l < L; l++) {
-        const a = alpha[L - l - 1],
-            b = alpha[L + l + 1];
-        if (order === 'cca') ret.push(b, a);
-        else ret.push(a, b);
+export function createSphericalCollocationGrid(
+    params: CubeGridComputationParams, orbital: AlphaOrbital, webgl?: WebGLContext
+): Task<CubeGrid> {
+    return Task.create('Spherical Collocation Grid', async (ctx) => {
+        const cubeGrid = initCubeGrid(params);
+
+        let matrix: Float32Array;
+        if (canComputeGrid3dOnGPU(webgl)) {
+            // console.time('gpu');
+            matrix = await gpuComputeAlphaOrbitalsGridValues(ctx, webgl!, cubeGrid, orbital);
+            // console.timeEnd('gpu');
+        } else {
+            // console.time('cpu');
+            matrix = await sphericalCollocation(cubeGrid, orbital, ctx);
+            // console.timeEnd('cpu');
+        }
+
+        const grid = createGrid(cubeGrid, matrix, [0, 1, 2]);
+        let isovalues: { negative?: number, positive?: number } | undefined;
+
+        if (!params.doNotComputeIsovalues) {
+            isovalues = computeOrbitalIsocontourValues(matrix, 0.85);
+        }
+
+        return { grid, isovalues };
+    });
+}
+
+export function computeOrbitalIsocontourValues(input: Float32Array, cumulativeThreshold: number) {
+    let weightSum = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = v * v;
+        weightSum += w;
     }
-    return ret;
-}
+    const avgWeight = weightSum / input.length;
+    let minWeight = 3 * avgWeight;
 
-export type SphericalFunc = (
-    alpha: number[],
-    x: number,
-    y: number,
-    z: number
-) => number;
+    // do not try to identify isovalues for degenerate data
+    // e.g. all values are almost same
+    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
+        return { negative: void 0, positive: void 0 };
+    }
 
-export const SphericalFunctions: SphericalFunc[] = [L0, L1, L2, L3, L4];
+    let size = 0;
+    while (true) {
+        let csum = 0;
+        size = 0;
+        for (let i = 0, _i = input.length; i < _i; i++) {
+            const v = input[i];
+            const w = v * v;
+            if (w >= minWeight) {
+                csum += w;
+                size++;
+            }
+        }
 
-// L_i functions were auto-generated.
+        if (csum / weightSum > cumulativeThreshold) {
+            break;
+        }
 
-function L0(alpha: number[], x: number, y: number, z: number) {
-    return alpha[0];
-}
+        minWeight -= avgWeight;
+    }
 
-function L1(alpha: number[], x: number, y: number, z: number) {
-    return alpha[0] * z + alpha[1] * x + alpha[2] * y;
-}
+    const values = new Float32Array(size);
+    const weights = new Float32Array(size);
+    const indices = new Int32Array(size);
 
-function L2(alpha: number[], x: number, y: number, z: number) {
-    const xx = x * x, yy = y * y, zz = z * z;
-    return (
-        alpha[0] * (-0.5 * xx - 0.5 * yy + zz) +
-        alpha[1] * (1.7320508075688772 * x * z) +
-        alpha[2] * (1.7320508075688772 * y * z) +
-        alpha[3] * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
-        alpha[4] * (1.7320508075688772 * x * y)
+    let o = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = v * v;
+        if (w >= minWeight) {
+            values[o] = v;
+            weights[o] = w;
+            indices[o] = o;
+            o++;
+        }
+    }
+
+    sortArray(
+        indices,
+        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
     );
-}
 
-function L3(alpha: number[], x: number, y: number, z: number) {
-    const xx = x * x, yy = y * y, zz = z * z;
-    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    return (
-        alpha[0] * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
-        alpha[1] * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
-        alpha[2] * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
-        alpha[3] * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
-        alpha[4] * (3.872983346207417 * x * y * z) +
-        alpha[5] * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
-        alpha[6] * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
-    );
-}
+    let cweight = 0,
+        cutoffIndex = 0;
+    for (let i = 0; i < size; i++) {
+        cweight += weights[indices[i]];
 
-function L4(alpha: number[], x: number, y: number, z: number) {
-    const xx = x * x, yy = y * y, zz = z * z;
-    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    const xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
-    return (
-        alpha[0] * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
-        alpha[1] * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
-        alpha[2] * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
-        alpha[3] * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
-        alpha[4] * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
-        alpha[5] * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
-        alpha[6] * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
-        alpha[7] * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
-        alpha[8] * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
-    );
-}
+        if (cweight / weightSum >= cumulativeThreshold) {
+            cutoffIndex = i;
+            break;
+        }
+    }
+
+    let positive = Number.POSITIVE_INFINITY,
+        negative = Number.NEGATIVE_INFINITY;
+
+    for (let i = 0; i < cutoffIndex; i++) {
+        const v = values[indices[i]];
+        if (v > 0) {
+            if (v < positive) positive = v;
+        } else if (v < 0) {
+            if (v > negative) negative = v;
+        }
+    }
+
+    return {
+        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
+        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
+    };
+}

src/extensions/alpha-orbitals/spherical-functions.ts

@@ -0,0 +1,93 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Inspired by https://github.com/dgasmith/gau2grid.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// gaussian:
+//     R_0, R^+_1, R^-_1, ..., R^+_l, R^-_l
+// cca:
+//     R^-_(l), R^-_(l-1), ..., R_0, ..., R^+_(l-1), R^+_l
+// cca-reverse:
+//     R^+_(l), R^+_(l-1), ..., R_0, ..., R^-_(l-1), R^-_l
+export type SphericalBasisOrder = 'gaussian' | 'cca' | 'cca-reverse';
+
+export function normalizeBasicOrder(
+    L: number,
+    alpha: number[],
+    order: SphericalBasisOrder
+) {
+    if (order === 'gaussian' || L === 0) return alpha;
+
+    const ret: number[] = [alpha[L]];
+    for (let l = 0; l < L; l++) {
+        const a = alpha[L - l - 1],
+            b = alpha[L + l + 1];
+        if (order === 'cca') ret.push(b, a);
+        else ret.push(a, b);
+    }
+    return ret;
+}
+
+export type SphericalFunc = (
+    alpha: number[],
+    x: number,
+    y: number,
+    z: number
+) => number;
+
+export const SphericalFunctions: SphericalFunc[] = [L0, L1, L2, L3, L4];
+
+// L_i functions were auto-generated.
+
+function L0(alpha: number[], x: number, y: number, z: number) {
+    return alpha[0];
+}
+
+function L1(alpha: number[], x: number, y: number, z: number) {
+    return alpha[0] * z + alpha[1] * x + alpha[2] * y;
+}
+
+function L2(alpha: number[], x: number, y: number, z: number) {
+    const xx = x * x, yy = y * y, zz = z * z;
+    return (
+        alpha[0] * (-0.5 * xx - 0.5 * yy + zz) +
+        alpha[1] * (1.7320508075688772 * x * z) +
+        alpha[2] * (1.7320508075688772 * y * z) +
+        alpha[3] * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
+        alpha[4] * (1.7320508075688772 * x * y)
+    );
+}
+
+function L3(alpha: number[], x: number, y: number, z: number) {
+    const xx = x * x, yy = y * y, zz = z * z;
+    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    return (
+        alpha[0] * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
+        alpha[1] * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
+        alpha[2] * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
+        alpha[3] * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
+        alpha[4] * (3.872983346207417 * x * y * z) +
+        alpha[5] * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
+        alpha[6] * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
+    );
+}
+
+function L4(alpha: number[], x: number, y: number, z: number) {
+    const xx = x * x, yy = y * y, zz = z * z;
+    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    const xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
+    return (
+        alpha[0] * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
+        alpha[1] * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
+        alpha[2] * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
+        alpha[3] * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
+        alpha[4] * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
+        alpha[5] * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
+        alpha[6] * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
+        alpha[7] * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
+        alpha[8] * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
+    );
+}

src/extensions/alpha-orbitals/transforms.ts

@@ -5,11 +5,11 @@
  */
 
 import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
-import { Basis, createSphericalCollocationGrid, CubeGrid } from './cubes';
+import { createSphericalCollocationGrid } from './orbitals';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Task } from '../../mol-task';
 import { CustomProperties } from '../../mol-model/custom-property';
-import { SphericalBasisOrder } from './orbitals';
+import { SphericalBasisOrder } from './spherical-functions';
 import { Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { ColorNames } from '../../mol-util/color/names';
@@ -17,8 +17,10 @@ import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers
 import { StateTransformer } from '../../mol-state';
 import { Theme } from '../../mol-theme/theme';
 import { VolumeRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
+import { AlphaOrbital, Basis, CubeGrid } from './data-model';
+import { createSphericalCollocationDensityGrid } from './density';
 
-export class BasisAndOrbitals extends PluginStateObject.Create<{ basis: Basis, order: SphericalBasisOrder, orbitals: { energy: number, alpha: number[] }[] }>({ name: 'Basis', typeClass: 'Object' }) { }
+export class BasisAndOrbitals extends PluginStateObject.Create<{ basis: Basis, order: SphericalBasisOrder, orbitals: AlphaOrbital[] }>({ name: 'Basis', typeClass: 'Object' }) { }
 
 export const StaticBasisAndOrbitals = PluginStateTransform.BuiltIn({
     name: 'static-basis-and-orbitals',
@@ -29,7 +31,7 @@ export const StaticBasisAndOrbitals = PluginStateTransform.BuiltIn({
         label: PD.Text('Orbital Data', { isHidden: true }),
         basis: PD.Value<Basis>(void 0 as any, { isHidden: true }),
         order: PD.Text<SphericalBasisOrder>('gaussian' as SphericalBasisOrder, { isHidden: true }),
-        orbitals: PD.Value<{ energy: number, alpha: number[] }[]>([], { isHidden: true })
+        orbitals: PD.Value<AlphaOrbital[]>([], { isHidden: true })
     },
 })({
     apply({ params }) {
@@ -38,7 +40,6 @@ export const StaticBasisAndOrbitals = PluginStateTransform.BuiltIn({
 });
 
 const CreateOrbitalVolumeParamBase = {
-    forceCpuCompute: PD.Boolean(false),
     cutoffThreshold: PD.Numeric(0.0015, { min: 0, max: 0.1, step: 0.0001 }),
     boxExpand: PD.Numeric(4.5, { min: 0, max: 7, step: 0.1 }),
     gridSpacing: PD.ObjectList({ atomCount: PD.Numeric(0), spacing: PD.Numeric(0.35, { min: 0.1, max: 2, step: 0.01 }) }, e => `Atoms ${e.atomCount}: ${e.spacing}`, {
@@ -72,11 +73,38 @@ export const CreateOrbitalVolume = PluginStateTransform.BuiltIn({
             const data = await createSphericalCollocationGrid({
                 basis: a.data.basis,
                 cutoffThreshold: params.cutoffThreshold,
-                alphaOrbitals: a.data.orbitals[params.index].alpha,
                 sphericalOrder: a.data.order,
                 boxExpand: params.boxExpand,
                 gridSpacing: params.gridSpacing.map(e => [e.atomCount, e.spacing] as [number, number])
-            }, params.forceCpuCompute ? void 0 : plugin.canvas3d?.webgl).runInContext(ctx);
+            }, a.data.orbitals[params.index], plugin.canvas3d?.webgl).runInContext(ctx);
+            const volume: Volume = {
+                grid: data.grid,
+                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
+                customProperties: new CustomProperties(),
+                _propertyData: Object.create(null),
+            };
+
+            return new PluginStateObject.Volume.Data(volume, { label: 'Orbital Volume' });
+        });
+    }
+});
+
+export const CreateOrbitalDensityVolume = PluginStateTransform.BuiltIn({
+    name: 'create-orbital-density-volume',
+    display: 'Orbital Density Volume',
+    from: BasisAndOrbitals,
+    to: PluginStateObject.Volume.Data,
+    params: CreateOrbitalVolumeParamBase
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Orbital Volume', async ctx => {
+            const data = await createSphericalCollocationDensityGrid({
+                basis: a.data.basis,
+                cutoffThreshold: params.cutoffThreshold,
+                sphericalOrder: a.data.order,
+                boxExpand: params.boxExpand,
+                gridSpacing: params.gridSpacing.map(e => [e.atomCount, e.spacing] as [number, number])
+            }, a.data.orbitals, plugin.canvas3d?.webgl).runInContext(ctx);
             const volume: Volume = {
                 grid: data.grid,
                 sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },

src/extensions/anvil/representation.ts

@@ -10,7 +10,6 @@ import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../mol-repr/representation';
 import { Structure } from '../../mol-model/structure';
 import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
-import { SpheresBuilder } from '../../mol-geo/geometry/spheres/spheres-builder';
 import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from '../../mol-repr/structure/representation';
 import { MembraneOrientation } from './prop';
 import { ThemeRegistryContext } from '../../mol-theme/theme';
@@ -27,6 +26,7 @@ import { MembraneOrientationProvider } from './prop';
 import { MarkerActions } from '../../mol-util/marker-action';
 import { lociLabel } from '../../mol-theme/label';
 import { ColorNames } from '../../mol-util/color/names';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
 
 const SharedParams = {
     color: PD.Color(ColorNames.lightgrey),
@@ -61,7 +61,6 @@ export type BilayerRimsParams = typeof BilayerRimsParams
 export type BilayerRimsProps = PD.Values<BilayerRimsParams>
 
 const MembraneOrientationVisuals = {
-    'bilayer-spheres': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerSpheresParams>) => ShapeRepresentation(getBilayerSpheres, Spheres.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }) }),
     'bilayer-planes': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerPlanesParams>) => ShapeRepresentation(getBilayerPlanes, Mesh.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }), modifyProps: p => ({ ...p, alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false }) }),
     'bilayer-rims': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerRimsParams>) => ShapeRepresentation(getBilayerRims, Lines.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }) })
 };
@@ -91,9 +90,13 @@ export const MembraneOrientationRepresentationProvider = StructureRepresentation
     factory: MembraneOrientationRepresentation,
     getParams: getMembraneOrientationParams,
     defaultValues: PD.getDefaultValues(MembraneOrientationParams),
-    defaultColorTheme: { name: 'uniform' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: (structure: Structure) => structure.elementCount > 0
+    defaultColorTheme: { name: 'shape-group' },
+    defaultSizeTheme: { name: 'shape-group' },
+    isApplicable: (structure: Structure) => structure.elementCount > 0,
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, structure: Structure) => MembraneOrientationProvider.attach(ctx, structure, void 0, true),
+        detach: (data) => MembraneOrientationProvider.ref(data, false)
+    }
 });
 
 function membraneLabel(data: Structure) {
@@ -151,28 +154,3 @@ function getLayerPlane(state: MeshBuilder.State, p: Vec3, centroid: Vec3, normal
     MeshBuilder.addPrimitive(state, Mat4.id, circle);
     MeshBuilder.addPrimitiveFlipped(state, Mat4.id, circle);
 }
-
-function getBilayerSpheres(ctx: RuntimeContext, data: Structure, props: BilayerSpheresProps, shape?: Shape<Spheres>): Shape<Spheres> {
-    const { density } = props;
-    const { radius, planePoint1, planePoint2, normalVector } = MembraneOrientationProvider.get(data).value!;
-    const scaledRadius = (props.radiusFactor * radius) * (props.radiusFactor * radius);
-
-    const spheresBuilder = SpheresBuilder.create(256, 128, shape?.geometry);
-    getLayerSpheres(spheresBuilder, planePoint1, normalVector, density, scaledRadius);
-    getLayerSpheres(spheresBuilder, planePoint2, normalVector, density, scaledRadius);
-    return Shape.create('Bilayer spheres', data, spheresBuilder.getSpheres(), () => props.color, () => props.sphereSize, () => membraneLabel(data));
-}
-
-function getLayerSpheres(spheresBuilder: SpheresBuilder, point: Vec3, normalVector: Vec3, density: number, sqRadius: number) {
-    Vec3.normalize(normalVector, normalVector);
-    const d = -Vec3.dot(normalVector, point);
-    const rep = Vec3();
-    for (let i = -1000, il = 1000; i < il; i += density) {
-        for (let j = -1000, jl = 1000; j < jl; j += density) {
-            Vec3.set(rep, i, j, normalVector[2] === 0 ? 0 : -(d + i * normalVector[0] + j * normalVector[1]) / normalVector[2]);
-            if (Vec3.squaredDistance(rep, point) < sqRadius) {
-                spheresBuilder.add(rep[0], rep[1], rep[2], 0);
-            }
-        }
-    }
-}

src/extensions/rcsb/validation-report/color/geometry-quality.ts

@@ -32,7 +32,7 @@ const ColorLegend = TableLegend([
 ]);
 
 export function getGeometricQualityColorThemeParams(ctx: ThemeDataContext) {
-    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]).value;
+    const validationReport = !!ctx.structure && ctx.structure.models.length > 0 && ValidationReportProvider.get(ctx.structure.models[0]).value;
     const options: [string, string][] = [];
     if (validationReport) {
         const kinds = new Set<string>();
@@ -48,7 +48,7 @@ export type GeometricQualityColorThemeParams = ReturnType<typeof getGeometricQua
 export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Values<GeometricQualityColorThemeParams>): ColorTheme<GeometricQualityColorThemeParams> {
     let color: LocationColor = () => DefaultColor;
 
-    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
+    const validationReport = !!ctx.structure && ctx.structure.models.length > 0 ? ValidationReportProvider.get(ctx.structure.models[0]) : void 0;
     const contextHash = validationReport?.version;
 
     const value = validationReport?.value;

src/mol-canvas3d/camera.ts

@@ -209,8 +209,8 @@ namespace Camera {
             up: Vec3.create(0, 1, 0),
             target: Vec3.create(0, 0, 0),
 
-            radius: 10,
-            radiusMax: 10,
+            radius: 0,
+            radiusMax: 0,
             fog: 50,
             clipFar: true
         };

src/mol-canvas3d/canvas3d.ts

@@ -149,10 +149,11 @@ namespace Canvas3D {
     export interface DragEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, pageStart: Vec2, pageEnd: Vec2 }
     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 }> = {}) {
+    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,
+            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 });
     }
 
@@ -420,7 +429,8 @@ namespace Canvas3D {
                 const b = r.values.boundingSphere.ref.value;
                 if (!b.radius) continue;
 
-                if (!Sphere3D.includes(oldBoundingSphereVisible, b)) return true;
+                const cameraDist = Vec3.distance(cameraSphere.center, b.center);
+                if ((cameraDist > cameraSphere.radius || cameraDist > b.radius || b.radius > camera.state.radiusMax) && !Sphere3D.includes(oldBoundingSphereVisible, b)) return true;
                 if (Sphere3D.overlaps(cameraSphere, b)) cameraSphereOverlapsNone = false;
             }
 

src/mol-canvas3d/helper/interaction-events.ts

@@ -93,7 +93,7 @@ export class Canvas3dInteractionHelper {
 
     private leave() {
         this.inside = false;
-        if (Representation.Loci.isEmpty(this.prevLoci)) {
+        if (!Representation.Loci.isEmpty(this.prevLoci)) {
             this.prevLoci = Representation.Loci.Empty;
             this.events.hover.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers });
         }

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);
@@ -195,7 +195,7 @@ export class DrawPass {
         if (!toDrawingBuffer) {
             if (!this.packedDepth) {
                 this.depthTextureVolumes.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-                renderer.clearDepth();
+                renderer.clearDepth(); // from previous frame
             }
             renderer.renderBlendedVolume(scene.volumes, camera, this.depthTexturePrimitives);
 
@@ -206,6 +206,10 @@ export class DrawPass {
                 renderer.renderDepth(scene.volumes, camera, this.depthTexturePrimitives);
                 this.colorTarget.bind();
             }
+
+            if (!this.packedDepth) {
+                this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+            }
         }
 
         renderer.renderBlendedTransparent(scene.primitives, camera, null);

src/mol-canvas3d/passes/postprocessing.ts

@@ -17,9 +17,9 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { DrawPass } from './draw';
 import { Camera, ICamera } from '../../mol-canvas3d/camera';
-
 import quad_vert from '../../mol-gl/shader/quad.vert';
 import postprocessing_frag from '../../mol-gl/shader/postprocessing.frag';
+import fxaa_frag from '../../mol-gl/shader/fxaa.frag';
 import { StereoCamera } from '../camera/stereo';
 
 const PostprocessingSchema = {
@@ -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),
@@ -92,30 +95,39 @@ export const PostprocessingParams = {
             threshold: PD.Numeric(0.8, { min: 0, max: 5, step: 0.01 }),
         }),
         off: PD.Group({})
-    }, { cycle: true, description: 'Draw outline around 3D objects' })
+    }, { cycle: true, description: 'Draw outline around 3D objects' }),
+    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';
     }
 
-    target: RenderTarget
-    renderable: PostprocessingRenderable
+    readonly target: RenderTarget
+
+    private readonly tmpTarget: RenderTarget
+    private readonly renderable: PostprocessingRenderable
+    private readonly fxaa: FxaaRenderable
 
     constructor(private webgl: WebGLContext, private drawPass: DrawPass) {
-        this.target = webgl.createRenderTarget(drawPass.colorTarget.getWidth(), drawPass.colorTarget.getHeight(), false);
         const { colorTarget, depthTexture } = drawPass;
-        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture);
-    }
+        const width = colorTarget.getWidth();
+        const height = colorTarget.getHeight();
 
-    private bindTarget(toDrawingBuffer: boolean) {
-        if (toDrawingBuffer) {
-            this.webgl.unbindFramebuffer();
-        } else {
-            this.target.bind();
-        }
+        this.target = 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);
     }
 
     syncSize() {
@@ -125,11 +137,29 @@ export class PostprocessingPass {
         const [w, h] = this.renderable.values.uTexSize.ref.value;
         if (width !== w || height !== h) {
             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.uTexSizeInv, Vec2.set(this.fxaa.values.uTexSizeInv.ref.value, 1 / width, 1 / height));
         }
     }
 
-    _render(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
+    private updateState(camera: ICamera) {
+        const { gl, state } = this.webgl;
+
+        state.enable(gl.SCISSOR_TEST);
+        state.disable(gl.BLEND);
+        state.disable(gl.DEPTH_TEST);
+        state.depthMask(false);
+
+        const { x, y, width, height } = camera.viewport;
+        gl.viewport(x, y, width, height);
+        gl.scissor(x, y, width, height);
+
+        state.clearColor(0, 0, 0, 1);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+    }
+
+    private _renderPostprocessing(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
         const { values } = this.renderable;
 
         ValueCell.updateIfChanged(values.uFar, camera.far);
@@ -166,21 +196,66 @@ export class PostprocessingPass {
             this.renderable.update();
         }
 
-        const { gl, state } = this.webgl;
-        this.bindTarget(toDrawingBuffer);
-
-        state.disable(gl.SCISSOR_TEST);
-        state.disable(gl.BLEND);
-        state.disable(gl.DEPTH_TEST);
-        state.depthMask(false);
-
-        const { x, y, width, height } = camera.viewport;
-        gl.viewport(x, y, width, height);
-        gl.scissor(x, y, width, height);
+        if (props.antialiasing.name === 'on') {
+            this.tmpTarget.bind();
+        } else if (toDrawingBuffer) {
+            this.webgl.unbindFramebuffer();
+        } else {
+            this.target.bind();
+        }
 
+        this.updateState(camera);
         this.renderable.render();
     }
 
+    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 (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();
+        }
+
+        if (toDrawingBuffer) {
+            this.webgl.unbindFramebuffer();
+        } else {
+            this.target.bind();
+        }
+
+        this.updateState(camera);
+        this.fxaa.render();
+    }
+
+    private _render(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
+        if (props.occlusion.name === 'on' || props.outline.name === 'on' || props.antialiasing.name === 'off') {
+            this._renderPostprocessing(camera, toDrawingBuffer, props);
+        }
+
+        if (props.antialiasing.name === 'on') {
+            this._renderFxaa(camera, toDrawingBuffer, props);
+        }
+    }
+
     render(camera: Camera | StereoCamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
         if (StereoCamera.is(camera)) {
             this._render(camera.left, toDrawingBuffer, props);
@@ -189,4 +264,40 @@ export class PostprocessingPass {
             this._render(camera, toDrawingBuffer, props);
         }
     }
-}
+}
+
+//
+
+const FxaaSchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    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),
+        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 };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', FxaaShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

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/renderer.ts

@@ -20,6 +20,7 @@ import { stringToWords } from '../mol-util/string';
 import { degToRad } from '../mol-math/misc';
 import { createNullTexture, Texture, Textures } from './webgl/texture';
 import { arrayMapUpsert } from '../mol-util/array';
+import { clamp } from '../mol-math/interpolate';
 
 export interface RendererStats {
     programCount: number
@@ -422,7 +423,6 @@ namespace Renderer {
 
         const renderBlendedTransparent = (group: Scene.Group, camera: ICamera, depthTexture: Texture | null) => {
             state.enable(gl.DEPTH_TEST);
-            state.depthMask(true);
 
             updateInternal(group, camera, depthTexture, false);
 
@@ -475,8 +475,11 @@ namespace Renderer {
             const { renderables } = group;
             for (let i = 0, il = renderables.length; i < il; ++i) {
                 const r = renderables[i];
+
                 // TODO: simplify, handle on renderable.state???
-                if (r.values.uAlpha.ref.value === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dRenderMode?.ref.value !== 'volume' && !r.values.dPointFilledCircle?.ref.value && !r.values.dXrayShaded?.ref.value) {
+                // uAlpha is updated in "render" so we need to recompute it here
+                const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
+                if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dRenderMode?.ref.value !== 'volume' && !r.values.dPointFilledCircle?.ref.value && !r.values.dXrayShaded?.ref.value) {
                     renderObject(r, 'colorWboit');
                 }
             }
@@ -488,8 +491,11 @@ namespace Renderer {
             const { renderables } = group;
             for (let i = 0, il = renderables.length; i < il; ++i) {
                 const r = renderables[i];
+
                 // TODO: simplify, handle on renderable.state???
-                if (r.values.uAlpha.ref.value < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dRenderMode?.ref.value === 'volume' || r.values.dPointFilledCircle?.ref.value || !!r.values.uBackgroundColor || r.values.dXrayShaded?.ref.value) {
+                // uAlpha is updated in "render" so we need to recompute it here
+                const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
+                if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dRenderMode?.ref.value === 'volume' || r.values.dPointFilledCircle?.ref.value || !!r.values.uBackgroundColor || r.values.dXrayShaded?.ref.value) {
                     renderObject(r, 'colorWboit');
                 }
             }

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/chunks/wboit-write.glsl.ts

@@ -5,7 +5,8 @@ export default `
             discard;
         }
     } else if (uRenderWboit) {
-        if (preFogAlpha != 1.0 && !interior && fragmentDepth < getDepth(gl_FragCoord.xy / uDrawingBufferSize)) {
+        // the 'fragmentDepth > 0.99' check is to handle precision issues with packed depth
+        if (preFogAlpha != 1.0 && !interior && (fragmentDepth < getDepth(gl_FragCoord.xy / uDrawingBufferSize) || fragmentDepth > 0.99)) {
             float alpha = gl_FragColor.a;
             float wboitWeight = alpha * clamp(pow(1.0 - fragmentDepth, 2.0), 0.01, 1.0);
             gl_FragColor = vec4(gl_FragColor.rgb * alpha * wboitWeight, alpha);

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

@@ -0,0 +1,229 @@
+export default `
+precision highp float;
+precision highp int;
+precision highp sampler2D;
+
+uniform sampler2D tColor;
+uniform vec2 uTexSizeInv;
+
+// adapted from https://github.com/kosua20/Rendu
+// MIT License Copyright (c) 2017 Simon Rodriguez
+
+#define QUALITY(q) ((q) < 5 ? 1.0 : ((q) > 5 ? ((q) < 10 ? 2.0 : ((q) < 11 ? 4.0 : 8.0)) : 1.5))
+
+float rgb2luma(vec3 rgb){
+    return sqrt(dot(rgb, vec3(0.299, 0.587, 0.114)));
+}
+
+float sampleLuma(vec2 uv) {
+    return rgb2luma(texture2D(tColor, uv).rgb);
+}
+
+float sampleLuma(vec2 uv, float uOffset, float vOffset) {
+    uv += uTexSizeInv * vec2(uOffset, vOffset);
+    return sampleLuma(uv);
+}
+
+void main(void) {
+    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-io/reader/3dg/parser.ts

@@ -1,57 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ReaderResult as Result } from '../result';
-import { Task } from '../../../mol-task';
-import { parseCsv } from '../csv/parser';
-import { Column, Table } from '../../../mol-data/db';
-import { toTable } from '../cif/schema';
-
-import Schema = Column.Schema
-import { CsvTable } from '../csv/data-model';
-
-
-export const Schema3DG = {
-    /** Chromosome name */
-    chromosome: Schema.str,
-    /** Base position */
-    position: Schema.int,
-    /** X coordinate */
-    x: Schema.float,
-    /** Y coordinate */
-    y: Schema.float,
-    /** Z coordinate */
-    z: Schema.float,
-};
-export type Schema3DG = typeof Schema3DG
-
-export interface File3DG {
-    table: Table<Schema3DG>
-}
-
-const FieldNames = [ 'chromosome', 'position', 'x', 'y', 'z' ];
-
-function categoryFromTable(name: string, table: CsvTable) {
-    return {
-        name,
-        rowCount: table.rowCount,
-        fieldNames: FieldNames,
-        getField: (name: string) => {
-            return table.getColumn(FieldNames.indexOf(name).toString());
-        }
-    };
-}
-
-export function parse3DG(data: string) {
-    return Task.create<Result<File3DG>>('Parse 3DG', async ctx => {
-        const opts = { quote: '', comment: '#', delimiter: '\t', noColumnNames: true };
-        const csvFile = await parseCsv(data, opts).runInContext(ctx);
-        if (csvFile.isError) return Result.error(csvFile.message, csvFile.line);
-        const category = categoryFromTable('3dg', csvFile.result.table);
-        const table = toTable(Schema3DG, category);
-        return Result.success({ table });
-    });
-}

src/mol-io/reader/_spec/3dg.spec.ts

@@ -1,33 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { parse3DG } from '../3dg/parser';
-
-const basic3dgString = `1(mat)	1420000	0.791377837067	10.9947291355	-13.1882897693
-1(mat)	1440000	-0.268241283699	10.5200875887	-13.0896257278
-1(mat)	1460000	-1.3853075236	10.5513787498	-13.1440142173
-1(mat)	1480000	-1.55984101733	11.4340829129	-13.6026301209
-1(mat)	1500000	-0.770991778399	11.4758488546	-14.5881137222
-1(mat)	1520000	-0.0848245107875	12.2624690808	-14.354289628
-1(mat)	1540000	-0.458643807046	12.5985791771	-13.4701149287
-1(mat)	1560000	-0.810322906201	12.2461643989	-12.3172933413
-1(mat)	1580000	-2.08211172035	12.8886838656	-12.8742007778
-1(mat)	1600000	-3.52093948201	13.1850935438	-12.4118684428`;
-
-describe('3dg reader', () => {
-    it('basic', async () => {
-        const parsed = await parse3DG(basic3dgString).run();
-        expect(parsed.isError).toBe(false);
-
-        if (parsed.isError) return;
-        const { chromosome, position, x, y, z } = parsed.result.table;
-        expect(chromosome.value(0)).toBe('1(mat)');
-        expect(position.value(1)).toBe(1440000);
-        expect(x.value(5)).toBe(-0.0848245107875);
-        expect(y.value(5)).toBe(12.2624690808);
-        expect(z.value(5)).toBe(-14.354289628);
-    });
-});

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/3dg.ts

@@ -1,83 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Task } from '../../mol-task';
-import { ModelFormat } from '../format';
-import { Column, Table } from '../../mol-data/db';
-import { EntityBuilder } from './common/entity';
-import { File3DG } from '../../mol-io/reader/3dg/parser';
-import { fillSerial } from '../../mol-util/array';
-import { MoleculeType } from '../../mol-model/structure/model/types';
-import { BasicSchema, createBasic } from './basic/schema';
-import { createModels } from './basic/parser';
-import { Trajectory } from '../../mol-model/structure';
-
-function getBasic(table: File3DG['table']) {
-    const entityIds = new Array<string>(table._rowCount);
-    const entityBuilder = new EntityBuilder();
-
-    const seqIdStarts = table.position.toArray({ array: Uint32Array });
-    const seqIdEnds = new Uint32Array(table._rowCount);
-    const stride = seqIdStarts[1] - seqIdStarts[0];
-
-    const objectRadius = stride / 3500;
-
-    for (let i = 0, il = table._rowCount; i < il; ++i) {
-        const chr = table.chromosome.value(i);
-        const entityId = entityBuilder.getEntityId(chr, MoleculeType.DNA, chr);
-        entityIds[i] = entityId;
-        seqIdEnds[i] = seqIdStarts[i] + stride - 1;
-    }
-
-    const ihm_sphere_obj_site = Table.ofPartialColumns(BasicSchema.ihm_sphere_obj_site, {
-        id: Column.ofIntArray(fillSerial(new Uint32Array(table._rowCount))),
-        entity_id: Column.ofStringArray(entityIds),
-        seq_id_begin: Column.ofIntArray(seqIdStarts),
-        seq_id_end: Column.ofIntArray(seqIdEnds),
-        asym_id: table.chromosome,
-
-        Cartn_x: Column.ofFloatArray(Column.mapToArray(table.x, x => x * 10, Float32Array)),
-        Cartn_y: Column.ofFloatArray(Column.mapToArray(table.y, y => y * 10, Float32Array)),
-        Cartn_z: Column.ofFloatArray(Column.mapToArray(table.z, z => z * 10, Float32Array)),
-
-        object_radius: Column.ofConst(objectRadius, table._rowCount, Column.Schema.float),
-        rmsf: Column.ofConst(0, table._rowCount, Column.Schema.float),
-        model_id: Column.ofConst(1, table._rowCount, Column.Schema.int),
-    }, table._rowCount);
-
-    return createBasic({
-        entity: entityBuilder.getEntityTable(),
-        ihm_model_list: Table.ofPartialColumns(BasicSchema.ihm_model_list, {
-            model_id: Column.ofIntArray([1]),
-            model_name: Column.ofStringArray(['3DG Model']),
-        }, 1),
-        ihm_sphere_obj_site
-    });
-}
-
-//
-
-export { Format3dg };
-
-type Format3dg = ModelFormat<File3DG>
-
-namespace Format3dg {
-    export function is(x: ModelFormat): x is Format3dg {
-        return x.kind === '3dg';
-    }
-
-    export function from3dg(file3dg: File3DG): Format3dg {
-        return { kind: '3dg', name: '3DG', data: file3dg };
-    }
-}
-
-export function trajectoryFrom3DG(file3dg: File3DG): Task<Trajectory> {
-    return Task.create('Parse 3DG', async ctx => {
-        const format = Format3dg.from3dg(file3dg);
-        const basic = getBasic(file3dg.table);
-        return createModels(basic, format, ctx);
-    });
-}

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/categories/atom_site.ts

@@ -83,13 +83,16 @@ export const _atom_site: CifCategory<CifExportContext> = {
     }
 };
 
-function prepostfixed(prefix: string | undefined, postfix: string | undefined, name: string) {
-    if (prefix && postfix) return `${prefix}_${name}_${postfix}`;
+function prepostfixed(prefix: string | undefined, name: string) {
     if (prefix) return `${prefix}_${name}`;
-    if (postfix) return `${name}_${postfix}`;
     return name;
 }
 
+function prefixedInsCode(prefix: string | undefined) {
+    if (!prefix) return 'pdbx_PDB_ins_code';
+    return `pdbx_${prefix}_PDB_ins_code`;
+}
+
 function mappedProp<K, D>(loc: (key: K, data: D) => StructureElement.Location, prop: (e: StructureElement.Location) => any) {
     return (k: K, d: D) => prop(loc(k, d));
 }
@@ -102,15 +105,14 @@ function addModelNum<K, D>(fields: CifWriter.Field.Builder<K, D>, getLocation: (
 
 export interface IdFieldsOptions {
     prefix?: string,
-    postfix?: string,
     includeModelNum?: boolean
 }
 
 export function residueIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement.Location, options?: IdFieldsOptions): CifField<K, D>[] {
-    const prefix = options && options.prefix, postfix = options && options.postfix;
+    const prefix = options && options.prefix;
     const ret = CifWriter.fields<K, D>()
-        .str(prepostfixed(prefix, postfix, `label_comp_id`), mappedProp(getLocation, P.atom.label_comp_id))
-        .int(prepostfixed(prefix, postfix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
+        .str(prepostfixed(prefix, `label_comp_id`), mappedProp(getLocation, P.atom.label_comp_id))
+        .int(prepostfixed(prefix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
             encoder: E.deltaRLE,
             valueKind: (k, d) => {
                 const e = getLocation(k, d);
@@ -118,45 +120,45 @@ export function residueIdFields<K, D>(getLocation: (key: K, data: D) => Structur
                 return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
             }
         })
-        .str(prepostfixed(prefix, postfix, `pdbx_PDB_ins_code`), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code))
+        .str(prefixedInsCode(prefix), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code))
 
-        .str(prepostfixed(prefix, postfix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
-        .str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
+        .str(prepostfixed(prefix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
+        .str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
 
-        .str(prepostfixed(prefix, postfix, `auth_comp_id`), mappedProp(getLocation, P.atom.auth_comp_id))
-        .int(prepostfixed(prefix, postfix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
-        .str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
+        .str(prepostfixed(prefix, `auth_comp_id`), mappedProp(getLocation, P.atom.auth_comp_id))
+        .int(prepostfixed(prefix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
+        .str(prepostfixed(prefix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
 
     addModelNum(ret, getLocation, options);
     return ret.getFields();
 }
 
 export function chainIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement.Location, options?: IdFieldsOptions): CifField<K, D>[] {
-    const prefix = options && options.prefix, postfix = options && options.postfix;
+    const prefix = options && options.prefix;
     const ret = CifField.build<K, D>()
-        .str(prepostfixed(prefix, postfix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
-        .str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
-        .str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
+        .str(prepostfixed(prefix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
+        .str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
+        .str(prepostfixed(prefix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
 
     addModelNum(ret, getLocation, options);
     return ret.getFields();
 }
 
 export function entityIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement.Location, options?: IdFieldsOptions): CifField<K, D>[] {
-    const prefix = options && options.prefix, postfix = options && options.postfix;
+    const prefix = options && options.prefix;
     const ret = CifField.build<K, D>()
-        .str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id));
+        .str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id));
 
     addModelNum(ret, getLocation, options);
     return ret.getFields();
 }
 
 export function atomIdFields<K, D>(getLocation: (key: K, data: D) => StructureElement.Location, options?: IdFieldsOptions): CifField<K, D>[] {
-    const prefix = options && options.prefix, postfix = options && options.postfix;
+    const prefix = options && options.prefix;
     const ret = CifWriter.fields<K, D>()
-        .str(prepostfixed(prefix, postfix, `label_atom_id`), mappedProp(getLocation, P.atom.label_atom_id))
-        .str(prepostfixed(prefix, postfix, `label_comp_id`), mappedProp(getLocation, P.atom.label_comp_id))
-        .int(prepostfixed(prefix, postfix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
+        .str(prepostfixed(prefix, `label_atom_id`), mappedProp(getLocation, P.atom.label_atom_id))
+        .str(prepostfixed(prefix, `label_comp_id`), mappedProp(getLocation, P.atom.label_comp_id))
+        .int(prepostfixed(prefix, `label_seq_id`), mappedProp(getLocation, P.residue.label_seq_id), {
             encoder: E.deltaRLE,
             valueKind: (k, d) => {
                 const e = getLocation(k, d);
@@ -164,16 +166,16 @@ export function atomIdFields<K, D>(getLocation: (key: K, data: D) => StructureEl
                 return m.atomicHierarchy.residues.label_seq_id.valueKind(m.atomicHierarchy.residueAtomSegments.index[e.element]);
             }
         })
-        .str(prepostfixed(prefix, postfix, `label_alt_id`), mappedProp(getLocation, P.atom.label_alt_id))
-        .str(prepostfixed(prefix, postfix, `pdbx_PDB_ins_code`), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code))
+        .str(prepostfixed(prefix, `label_alt_id`), mappedProp(getLocation, P.atom.label_alt_id))
+        .str(prefixedInsCode(prefix), mappedProp(getLocation, P.residue.pdbx_PDB_ins_code))
 
-        .str(prepostfixed(prefix, postfix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
-        .str(prepostfixed(prefix, postfix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
+        .str(prepostfixed(prefix, `label_asym_id`), mappedProp(getLocation, P.chain.label_asym_id))
+        .str(prepostfixed(prefix, `label_entity_id`), mappedProp(getLocation, P.chain.label_entity_id))
 
-        .str(prepostfixed(prefix, postfix, `auth_atom_id`), mappedProp(getLocation, P.atom.auth_atom_id))
-        .str(prepostfixed(prefix, postfix, `auth_comp_id`), mappedProp(getLocation, P.atom.auth_comp_id))
-        .int(prepostfixed(prefix, postfix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
-        .str(prepostfixed(prefix, postfix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
+        .str(prepostfixed(prefix, `auth_atom_id`), mappedProp(getLocation, P.atom.auth_atom_id))
+        .str(prepostfixed(prefix, `auth_comp_id`), mappedProp(getLocation, P.atom.auth_comp_id))
+        .int(prepostfixed(prefix, `auth_seq_id`), mappedProp(getLocation, P.residue.auth_seq_id), { encoder: E.deltaRLE })
+        .str(prepostfixed(prefix, `auth_asym_id`), mappedProp(getLocation, P.chain.auth_asym_id));
 
     addModelNum(ret, getLocation, options);
     return ret.getFields();

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/builder/structure/hierarchy-preset.ts

@@ -76,6 +76,7 @@ const defaultPreset = TrajectoryHierarchyPresetProvider({
 
 const AllModelsParams = (a: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext) => ({
     useDefaultIfSingleModel: PD.Optional(PD.Boolean(false)),
+    representationPresetParams: PD.Optional(PD.Group(StructureRepresentationPresetProvider.CommonParams)),
     ...CommonParams(a, plugin)
 });
 

src/mol-plugin-state/formats/trajectory.ts

@@ -113,15 +113,6 @@ export const GroProvider: TrajectoryFormatProvider = {
     visuals: defaultVisuals
 };
 
-export const Provider3dg: TrajectoryFormatProvider = {
-    label: '3DG',
-    description: '3DG',
-    category: TrajectoryFormatCategory,
-    stringExtensions: ['3dg'],
-    parse: directTrajectory(StateTransforms.Model.TrajectoryFrom3DG),
-    visuals: defaultVisuals
-};
-
 export const MolProvider: TrajectoryFormatProvider = {
     label: 'MOL/SDF',
     description: 'MOL/SDF',
@@ -146,7 +137,6 @@ export const BuiltInTrajectoryFormats = [
     ['pdb', PdbProvider] as const,
     ['pdbqt', PdbqtProvider] as const,
     ['gro', GroProvider] as const,
-    ['3dg', Provider3dg] as const,
     ['mol', MolProvider] as const,
     ['mol2', Mol2Provider] as const,
 ] as const;

src/mol-plugin-state/objects.ts

@@ -5,7 +5,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { File3DG } from '../mol-io/reader/3dg/parser';
 import { Ccp4File } from '../mol-io/reader/ccp4/schema';
 import { CifFile } from '../mol-io/reader/cif';
 import { DcdFile } from '../mol-io/reader/dcd/parser';
@@ -83,7 +82,6 @@ export namespace PluginStateObject {
             { kind: 'cif', data: CifFile } |
             { kind: 'pdb', data: CifFile } |
             { kind: 'gro', data: CifFile } |
-            { kind: '3dg', data: File3DG } |
             { kind: 'dcd', data: DcdFile } |
             { kind: 'ccp4', data: Ccp4File } |
             { kind: 'dsn6', data: Dsn6File } |

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

@@ -5,13 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { parse3DG } from '../../mol-io/reader/3dg/parser';
 import { parseDcd } from '../../mol-io/reader/dcd/parser';
 import { parseGRO } from '../../mol-io/reader/gro/parser';
 import { parsePDB } from '../../mol-io/reader/pdb/parser';
 import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { shapeFromPly } from '../../mol-model-formats/shape/ply';
-import { trajectoryFrom3DG } from '../../mol-model-formats/structure/3dg';
 import { coordinatesFromDcd } from '../../mol-model-formats/structure/dcd';
 import { trajectoryFromGRO } from '../../mol-model-formats/structure/gro';
 import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
@@ -52,7 +50,6 @@ export { TrajectoryFromMOL };
 export { TrajectoryFromMOL2 };
 export { TrajectoryFromCube };
 export { TrajectoryFromCifCore };
-export { TrajectoryFrom3DG };
 export { ModelFromTrajectory };
 export { StructureFromTrajectory };
 export { StructureFromModel };
@@ -339,24 +336,6 @@ const TrajectoryFromCifCore = PluginStateTransform.BuiltIn({
     }
 });
 
-type TrajectoryFrom3DG = typeof TrajectoryFrom3DG
-const TrajectoryFrom3DG = PluginStateTransform.BuiltIn({
-    name: 'trajectory-from-3dg',
-    display: { name: 'Parse 3DG', description: 'Parse 3DG string and create trajectory.' },
-    from: [SO.Data.String],
-    to: SO.Molecule.Trajectory
-})({
-    apply({ a }) {
-        return Task.create('Parse 3DG', async ctx => {
-            const parsed = await parse3DG(a.data).runInContext(ctx);
-            if (parsed.isError) throw new Error(parsed.message);
-            const models = await trajectoryFrom3DG(parsed.result).runInContext(ctx);
-            const props = trajectoryProps(models);
-            return new SO.Molecule.Trajectory(models, props);
-        });
-    }
-});
-
 const plus1 = (v: number) => v + 1, minus1 = (v: number) => v - 1;
 type ModelFromTrajectory = typeof ModelFromTrajectory
 const ModelFromTrajectory = PluginStateTransform.BuiltIn({

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/config.ts

@@ -24,7 +24,7 @@ export const PluginConfig = {
     General: {
         IsBusyTimeoutMs: item('plugin-config.is-busy-timeout', 750),
         DisableAntialiasing: item('plugin-config.disable-antialiasing', false),
-        PixelScale: item<number | undefined>('plugin-config.pixel-scale', void 0),
+        PixelScale: item('plugin-config.pixel-scale', 1),
         EnableWboit: item('plugin-config.enable-wboit', false)
     },
     State: {

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

@@ -115,7 +115,10 @@ class ViewportScreenshotHelper extends PluginComponent {
                 mode: mutlisample ? 'on' : 'off',
                 sampleLevel: colorBufferFloat && textureFloat ? 4 : 2
             },
-            postprocessing: c.props.postprocessing
+            postprocessing: {
+                ...c.props.postprocessing,
+                antialiasing: { name: 'off', params: {} }
+            }
         });
     }
 
@@ -131,7 +134,10 @@ class ViewportScreenshotHelper extends PluginComponent {
                 cameraHelper: { axes: this.values.axes },
                 transparentBackground: this.values.transparent,
                 // TODO: optimize because this creates a copy of a large object!
-                postprocessing: this.plugin.canvas3d!.props.postprocessing
+                postprocessing: {
+                    ...this.plugin.canvas3d!.props.postprocessing,
+                    antialiasing: { name: 'off', params: {} }
+                }
             });
             return this._imagePass;
         }

src/mol-repr/shape/representation.ts

@@ -23,6 +23,7 @@ import { PickingId } from '../../mol-geo/geometry/picking';
 import { Visual } from '../visual';
 import { RuntimeContext, Task } from '../../mol-task';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { isDebugMode } from '../../mol-util/debug';
 
 export interface ShapeRepresentation<D, G extends Geometry, P extends Geometry.Params<G>> extends Representation<D, P> { }
 
@@ -216,7 +217,9 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
             Representation.updateState(_state, state);
         },
         setTheme(theme: Theme) {
-            console.warn('The `ShapeRepresentation` theme is fixed to `ShapeGroupColorTheme` and `ShapeGroupSizeTheme`. Colors are taken from `Shape.getColor` and sizes from `Shape.getSize`');
+            if(isDebugMode) {
+                console.warn('The `ShapeRepresentation` theme is fixed to `ShapeGroupColorTheme` and `ShapeGroupSizeTheme`. Colors are taken from `Shape.getColor` and sizes from `Shape.getSize`');
+            }
         },
         destroy() {
             // TODO

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';