2.0.0-dev.6

- fixes #123

.eslintrc.json

@@ -3,60 +3,21 @@
         "browser": true,
         "node": true
     },
-    "parser": "@typescript-eslint/parser",
     "parserOptions": {
-        "project": ["tsconfig.json", "tsconfig.commonjs.json"],
-        "sourceType": "module"
+        "ecmaVersion": 2018,
+        "sourceType": "module",
+        "ecmaFeatures": {
+            "impliedStrict": true
+        }
     },
-    "plugins": [
-        "@typescript-eslint"
-    ],
     "rules": {
-        "@typescript-eslint/ban-types": "off",
-        "@typescript-eslint/class-name-casing": "off",
         "indent": "off",
-        "@typescript-eslint/indent": [
-            "error",
-            4
-        ],
-        "@typescript-eslint/member-delimiter-style": [
-            "off",
-            {
-                "multiline": {
-                    "delimiter": "none",
-                    "requireLast": true
-                },
-                "singleline": {
-                    "delimiter": "semi",
-                    "requireLast": false
-                }
-            }
-        ],
-        "@typescript-eslint/prefer-namespace-keyword": "warn",
-        "@typescript-eslint/quotes": [
-            "error",
-            "single",
-            {
-                "avoidEscape": true,
-                "allowTemplateLiterals": true
-            }
-        ],
-        "@typescript-eslint/semi": [
-            "off",
-            null
-        ],
-        "@typescript-eslint/type-annotation-spacing": "error",
         "arrow-parens": [
             "off",
             "as-needed"
         ],
         "brace-style": "off",
-        "@typescript-eslint/brace-style": [
-            "error",
-            "1tbs", { "allowSingleLine": true }
-        ],
         "comma-spacing": "off",
-        "@typescript-eslint/comma-spacing": "error",
         "space-infix-ops": "error",
         "comma-dangle": "off",
         "eqeqeq": [
@@ -70,6 +31,66 @@
         "no-unsafe-finally": "warn",
         "no-var": "error",
         "spaced-comment": "error",
-        "semi": "warn"
-    }
+        "semi": "warn",
+        "no-restricted-syntax": [
+            "error",
+            {
+                "selector": "ExportDefaultDeclaration",
+                "message": "Default exports are not allowed"
+            }
+        ]
+    },
+    "overrides": [
+        {
+            "files": ["**/*.ts", "**/*.tsx"],
+            "parser": "@typescript-eslint/parser",
+            "parserOptions": {
+                "project": ["tsconfig.json", "tsconfig.commonjs.json"],
+                "sourceType": "module"
+            },
+            "plugins": [
+                "@typescript-eslint"
+            ],
+            "rules": {
+                "@typescript-eslint/ban-types": "off",
+                "@typescript-eslint/class-name-casing": "off",
+                "@typescript-eslint/indent": [
+                    "error",
+                    4
+                ],
+                "@typescript-eslint/member-delimiter-style": [
+                    "off",
+                    {
+                        "multiline": {
+                            "delimiter": "none",
+                            "requireLast": true
+                        },
+                        "singleline": {
+                            "delimiter": "semi",
+                            "requireLast": false
+                        }
+                    }
+                ],
+                "@typescript-eslint/prefer-namespace-keyword": "warn",
+                "@typescript-eslint/quotes": [
+                    "error",
+                    "single",
+                    {
+                        "avoidEscape": true,
+                        "allowTemplateLiterals": true
+                    }
+                ],
+                "@typescript-eslint/semi": [
+                    "off",
+                    null
+                ],
+                "@typescript-eslint/type-annotation-spacing": "error",
+                "@typescript-eslint/brace-style": [
+                    "error",
+                    "1tbs", { "allowSingleLine": true }
+                ],
+                "@typescript-eslint/comma-spacing": "error"
+            }
+        }
+    ]
 }

README.md

@@ -99,6 +99,11 @@ and navigate to `build/viewer`
 
     node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
 
+**Ion names**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
+
+
 **GraphQL schemas**
 
     node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
@@ -172,3 +177,4 @@ Funding sources include but are not limited to:
 * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
 * [PDBe, EMBL-EBI](https://pdbe.org)
 * [CEITEC](https://www.ceitec.eu/)
+* [EntosAI](https://www.entos.ai)

docs/interesting-pdb-entries.md

@@ -24,4 +24,6 @@
 * Close backbone atoms but not linked (e.g. 4HIV)
 * Non-standard residues
     * Protein (1BRR, 5Z6Y)
-    * DNA (5D3G)
+    * DNA (5D3G)
+* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
+* Long linear sugar chain (4HG6)

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.1.16",
+  "version": "2.0.0-dev.6",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -11,8 +11,8 @@
     "url": "https://github.com/molstar/molstar/issues"
   },
   "scripts": {
-    "lint": "eslint ./**/*.{ts,tsx}",
-    "lint-fix": "eslint ./**/*.{ts,tsx} --fix",
+    "lint": "eslint .",
+    "lint-fix": "eslint . --fix",
     "test": "npm run lint && jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
@@ -29,11 +29,11 @@
     "watch-webpack": "webpack -w --mode development --display minimal",
     "watch-webpack-viewer": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.js",
     "watch-webpack-viewer-debug": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.debug.js",
-    "serve": "http-server -p 1338",
+    "serve": "http-server -p 1338 -g",
     "model-server": "node lib/commonjs/servers/model/server.js",
     "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
     "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
-    "plugin-state": "node lib/commonjs/servers/plugin-state/index.js",
+    "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
     "preversion": "npm run test",
     "version": "npm run build",
     "postversion": "git push && git push --tags"
@@ -80,69 +80,71 @@
     "Alexander Rose <alexander.rose@weirdbyte.de>",
     "David Sehnal <david.sehnal@gmail.com>",
     "Sebastian Bittrich <sebastian.bittrich@rcsb.org>",
+    "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
     "Ludovic Autin <autin@scripps.edu>",
     "Michal Malý <michal.maly@ibt.cas.cz>",
     "Jiří Černý <jiri.cerny@ibt.cas.cz>"
   ],
   "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": "^3.9.1",
-    "@typescript-eslint/parser": "^3.9.1",
+    "@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": "^7.7.0",
+    "cpx2": "^3.0.0",
+    "css-loader": "^5.0.1",
+    "eslint": "^7.15.0",
     "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^6.0.0",
+    "file-loader": "^6.2.0",
     "fs-extra": "^9.0.1",
-    "graphql": "^15.3.0",
+    "graphql": "^15.4.0",
     "http-server": "^0.12.3",
-    "jest": "^26.4.1",
-    "mini-css-extract-plugin": "^0.9.0",
-    "node-sass": "^4.14.1",
-    "raw-loader": "^4.0.1",
-    "sass-loader": "^8.0.2",
-    "simple-git": "^2.19.0",
-    "style-loader": "^1.2.1",
-    "ts-jest": "^26.2.0",
-    "typescript": "^3.9.7",
+    "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": "^4.2.3",
     "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": "^4.17.7",
-    "@types/jest": "^25.2.3",
-    "@types/node": "^14.6.0",
+    "@types/express": "^4.17.9",
+    "@types/jest": "^26.0.18",
+    "@types/node": "^14.14.11",
     "@types/node-fetch": "^2.5.7",
-    "@types/react": "^16.9.46",
-    "@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",
-    "immer": "^7.0.7",
+    "h264-mp4-encoder": "^1.0.12",
+    "immer": "^8.0.1",
     "immutable": "^3.8.2",
-    "node-fetch": "^2.6.0",
-    "react": "^16.13.1",
-    "react-dom": "^16.13.1",
-    "rxjs": "^6.6.2",
-    "swagger-ui-dist": "^3.32.4",
-    "tslib": "^2.0.1",
+    "node-fetch": "^2.6.1",
+    "react": "^17.0.1",
+    "react-dom": "^17.0.1",
+    "rxjs": "^6.6.6",
+    "swagger-ui-dist": "^3.37.2",
+    "tslib": "^2.1.0",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

scripts/deploy.js

@@ -4,40 +4,40 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-const git = require('simple-git')
-const path = require('path')
-const fs = require("fs")
-const fse = require("fs-extra")
+const git = require('simple-git');
+const path = require('path');
+const fs = require("fs");
+const fse = require("fs-extra");
 
-const remoteUrl = "https://github.com/molstar/molstar.github.io.git"
-const buildDir = path.resolve(__dirname, '../build/')
-const deployDir = path.resolve(buildDir, 'deploy/')
-const localPath = path.resolve(deployDir, 'molstar.github.io/')
+const remoteUrl = "https://github.com/molstar/molstar.github.io.git";
+const buildDir = path.resolve(__dirname, '../build/');
+const deployDir = path.resolve(buildDir, 'deploy/');
+const localPath = path.resolve(deployDir, 'molstar.github.io/');
 
 function log(command, stdout, stderr) {
     if (command) {
-        console.log('\n###', command)
-        stdout.pipe(process.stdout)
-        stderr.pipe(process.stderr)
+        console.log('\n###', command);
+        stdout.pipe(process.stdout);
+        stderr.pipe(process.stderr);
     }
 }
 
 function copyViewer() {
-    console.log('\n###', 'copy viewer files')
-    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/')
-    const viewerDeployPath = path.resolve(localPath, 'viewer/')
-    fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true })
+    console.log('\n###', 'copy viewer files');
+    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/');
+    const viewerDeployPath = path.resolve(localPath, 'viewer/');
+    fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true });
 }
 
 if (!fs.existsSync(localPath)) {
-    console.log('\n###', 'create localPath')
-    fs.mkdirSync(localPath, { recursive: true })
+    console.log('\n###', 'create localPath');
+    fs.mkdirSync(localPath, { recursive: true });
 }
 
 process.chdir(localPath);
 
 if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
-    console.log('\n###', 'clone repository')
+    console.log('\n###', 'clone repository');
     git()
         .outputHandler(log)
         .clone(remoteUrl, localPath)
@@ -45,9 +45,9 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .exec(copyViewer)
         .add(['-A'])
         .commit('updated viewer')
-        .push()
+        .push();
 } else {
-    console.log('\n###', 'update repository')
+    console.log('\n###', 'update repository');
     git()
         .outputHandler(log)
         .fetch(['--all'])
@@ -55,5 +55,5 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .exec(copyViewer)
         .add(['-A'])
         .commit('updated viewer')
-        .push()
+        .push();
 }

src/apps/docking-viewer/index.ts

@@ -6,7 +6,8 @@
  */
 
 import '../../mol-util/polyfill';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import './index.html';
 import { PluginContext } from '../../mol-plugin/context';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -69,9 +70,10 @@ class Viewer {
             viewportShowSelectionMode: false,
             viewportShowAnimation: false,
         } };
+        const defaultSpec = DefaultPluginSpec();
 
         const spec: PluginSpec = {
-            actions: [...DefaultPluginSpec.actions],
+            actions: [...defaultSpec.actions],
             behaviors: [
                 PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
                 PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
@@ -81,8 +83,8 @@ class Viewer {
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
             ],
-            animations: [...DefaultPluginSpec.animations || []],
-            customParamEditors: DefaultPluginSpec.customParamEditors,
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
             layout: {
                 initial: {
                     isExpanded: o.layoutIsExpanded,
@@ -90,14 +92,14 @@ class Viewer {
                     controlsDisplay: o.layoutControlsDisplay,
                 },
                 controls: {
-                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+                    ...defaultSpec.layout && defaultSpec.layout.controls,
                     top: o.layoutShowSequence ? undefined : 'none',
                     bottom: o.layoutShowLog ? undefined : 'none',
                     left: o.layoutShowLeftPanel ? undefined : 'none',
                 }
             },
             components: {
-                ...DefaultPluginSpec.components,
+                ...defaultSpec.components,
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
                 viewport: {
                     view: ViewportComponent

src/apps/docking-viewer/viewport.tsx

@@ -46,13 +46,14 @@ function occlusionStyle(plugin: PluginContext) {
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'on', params: {
-                kernelSize: 8,
-                bias: 0.8,
-                radius: 64
+                samples: 64,
+                radius: 8,
+                bias: 1.0,
+                blurKernelSize: 13
             } },
             outline: { name: 'on', params: {
                 scale: 1.0,
-                threshold: 0.8
+                threshold: 0.33
             } }
         }
     } });

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.html

@@ -46,12 +46,15 @@
             }
 
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode);
+            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
+                disableAntialiasing: disableAntialiasing,
+                pixelScale: pixelScale,
+                enableWboit: !disableWboit,
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
                 pdbProvider: pdbProvider || 'pdbe',

src/apps/viewer/index.ts

@@ -6,7 +6,8 @@
  */
 
 import '../../mol-util/polyfill';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import './index.html';
 import './embedded.html';
 import './favicon.ico';
@@ -28,6 +29,14 @@ import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { DnatcoConfalPyramids } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { Color } from '../../mol-util/color';
+import { StateObjectSelector } from '../../mol-state';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 
 require('mol-plugin-ui/skin/light.scss');
 
@@ -45,7 +54,8 @@ const Extensions = {
     'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
     'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
-    'g3d': PluginSpec.Behavior(G3DFormat)
+    'g3d': PluginSpec.Behavior(G3DFormat),
+    'mp4-export': PluginSpec.Behavior(Mp4Export)
 };
 
 const DefaultViewerOptions = {
@@ -58,6 +68,9 @@ const DefaultViewerOptions = {
     layoutShowSequence: true,
     layoutShowLog: true,
     layoutShowLeftPanel: true,
+    disableAntialiasing: false,
+    pixelScale: 1,
+    enableWboit: true,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -66,6 +79,7 @@ const DefaultViewerOptions = {
     viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
     pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
     volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
 };
@@ -76,15 +90,16 @@ export class Viewer {
 
     constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
         const o = { ...DefaultViewerOptions, ...options };
+        const defaultSpec = DefaultPluginSpec();
 
         const spec: PluginSpec = {
-            actions: [...DefaultPluginSpec.actions],
+            actions: [...defaultSpec.actions],
             behaviors: [
-                ...DefaultPluginSpec.behaviors,
+                ...defaultSpec.behaviors,
                 ...o.extensions.map(e => Extensions[e]),
             ],
-            animations: [...DefaultPluginSpec.animations || []],
-            customParamEditors: DefaultPluginSpec.customParamEditors,
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
             customFormats: o?.customFormats,
             layout: {
                 initial: {
@@ -93,17 +108,20 @@ export class Viewer {
                     controlsDisplay: o.layoutControlsDisplay,
                 },
                 controls: {
-                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+                    ...defaultSpec.layout && defaultSpec.layout.controls,
                     top: o.layoutShowSequence ? undefined : 'none',
                     bottom: o.layoutShowLog ? undefined : 'none',
                     left: o.layoutShowLeftPanel ? undefined : 'none',
                 }
             },
             components: {
-                ...DefaultPluginSpec.components,
-                remoteState: o.layoutShowRemoteState ? 'default' : 'none'
+                ...defaultSpec.components,
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
             },
             config: [
+                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.EnableWboit, o.enableWboit],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
@@ -112,6 +130,7 @@ export class Viewer {
                 [PluginConfig.State.DefaultServer, o.pluginStateServer],
                 [PluginConfig.State.CurrentServer, o.pluginStateServer],
                 [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
                 [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
             ]
@@ -133,7 +152,7 @@ export class Viewer {
         return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
     }
 
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false) {
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
@@ -142,19 +161,28 @@ export class Viewer {
                     url: Asset.Url(url),
                     format: format as any,
                     isBinary,
-                    options: params.source.params.options,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
                 }
             }
         }));
     }
 
+    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, representationPresetParams: options?.representationParams });
+    }
+
     async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
         const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
         const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
         await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
     }
 
-    loadPdb(pdb: string) {
+    loadPdb(pdb: string, options?: LoadStructureOptions) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
@@ -168,7 +196,7 @@ export class Viewer {
                             params: PdbDownloadProvider[provider].defaultValue as any
                         }
                     },
-                    options: params.source.params.options,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
                 }
             }
         }));
@@ -205,4 +233,47 @@ export class Viewer {
             }
         }));
     }
+
+    async loadVolumeFromUrl(url: string, format: BuildInVolumeFormat, isBinary: boolean, isovalues: VolumeIsovalueInfo[], entryId?: string) {
+        const plugin = this.plugin;
+
+        if (!plugin.dataFormats.get(format)) {
+            throw new Error(`Unknown density format: ${format}`);
+        }
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.builders.data.download({ url, isBinary, label: entryId }, { state: { isGhost: true } });
+
+            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId });
+            const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!volume?.isOk) throw new Error('Failed to parse any volume.');
+
+            const repr = plugin.build().to(volume);
+            for (const iso of isovalues) {
+                repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
+                    type: 'isosurface',
+                    typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ?  { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                    color: 'uniform',
+                    colorParams: { value: iso.color }
+                }));
+            }
+
+            await repr.commit();
+        });
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next();
+    }
+}
+
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams
+}
+
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative',
+    value: number,
+    color: Color,
+    alpha?: number
 }

src/cli/chem-comp-dict/create-ions.ts

@@ -0,0 +1,73 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ */
+
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+const writeFile = util.promisify(fs.writeFile);
+
+import { DatabaseCollection } from '../../mol-data/db';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { ensureDataAvailable, readCCD } from './util';
+
+function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
+    const ionNames: string[] = [];
+    for (const k in ccd) {
+        const {chem_comp} = ccd[k];
+        if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
+            ionNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra ions that don't have ION in their name
+    ionNames.push('NCO', 'OHX');
+    return ionNames;
+}
+
+function writeIonNamesFile(filePath: string, ionNames: string[]) {
+    const output = `/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/chem-comp-dict/create-table cli
+ */
+
+export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+    writeFile(filePath, output);
+}
+
+async function run(out: string, forceDownload = false) {
+    await ensureDataAvailable(forceDownload);
+    const ccd = await readCCD();
+    const ionNames = extractIonNames(ccd);
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeIonNamesFile(out, ionNames);
+}
+
+const parser = new argparse.ArgumentParser({
+    addHelp: true,
+    description: 'Extract and save IonNames from CCD.'
+});
+parser.addArgument('out', {
+    help: 'Generated file output path.'
+});
+parser.addArgument([ '--forceDownload', '-f' ], {
+    action: 'storeTrue',
+    help: 'Force download of CCD and PVCD.'
+});
+interface Args {
+    out: string,
+    forceDownload?: boolean,
+}
+const args: Args = parser.parseArgs();
+
+run(args.out, args.forceDownload);

src/cli/chem-comp-dict/create-table.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,70 +9,16 @@ import * as argparse from 'argparse';
 import * as util from 'util';
 import * as path from 'path';
 import * as fs from 'fs';
-import * as zlib from 'zlib';
-import fetch from 'node-fetch';
 require('util.promisify').shim();
-const readFile = util.promisify(fs.readFile);
 const writeFile = util.promisify(fs.writeFile);
 
-import { Progress } from '../../mol-task';
 import { Database, Table, DatabaseCollection } from '../../mol-data/db';
-import { CIF } from '../../mol-io/reader/cif';
-import { CifWriter } from '../../mol-io/writer/cif';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
 import { SetUtils } from '../../mol-util/set';
 import { DefaultMap } from '../../mol-util/map';
 import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
 import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
-
-export async function ensureAvailable(path: string, url: string) {
-    if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
-        console.log(`downloading ${url}...`);
-        const data = await fetch(url);
-        if (!fs.existsSync(DATA_DIR)) {
-            fs.mkdirSync(DATA_DIR);
-        }
-        if (url.endsWith('.gz')) {
-            await writeFile(path, zlib.gunzipSync(await data.buffer()));
-        } else {
-            await writeFile(path, await data.text());
-        }
-        console.log(`done downloading ${url}`);
-    }
-}
-
-export async function ensureDataAvailable() {
-    await ensureAvailable(CCD_PATH, CCD_URL);
-    await ensureAvailable(PVCD_PATH, PVCD_URL);
-}
-
-export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
-    const parsed = await parseCif(await readFile(path, 'utf8'));
-    return CIF.toDatabaseCollection(schema, parsed.result);
-}
-
-export async function readCCD() {
-    return readFileAsCollection(CCD_PATH, CCD_Schema);
-}
-
-export async function readPVCD() {
-    return readFileAsCollection(PVCD_PATH, CCD_Schema);
-}
-
-async function parseCif(data: string | Uint8Array) {
-    const comp = CIF.parse(data);
-    console.time('parse cif');
-    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
-    console.timeEnd('parse cif');
-    if (parsed.isError) throw parsed;
-    return parsed;
-}
-
-export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
-    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
-    CifWriter.Encoder.writeDatabase(encoder, name, database);
-    return encoder.getData();
-}
+import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
 
 type CCB = Table<CCD_Schema['chem_comp_bond']>
 type CCA = Table<CCD_Schema['chem_comp_atom']>
@@ -81,6 +27,10 @@ function ccbKey(compId: string, atomId1: string, atomId2: string) {
     return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`;
 }
 
+function ccaKey(compId: string, atomId: string) {
+    return `${compId}:${atomId}`;
+}
+
 function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
     for (let i = 0, il = ccb._rowCount; i < il; ++i) {
         set.add(ccbKey(ccb.comp_id.value(i), ccb.atom_id_1.value(i), ccb.atom_id_2.value(i)));
@@ -90,7 +40,7 @@ function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
 
 function addChemCompAtomToSet(set: Set<string>, cca: CCA) {
     for (let i = 0, il = cca._rowCount; i < il; ++i) {
-        set.add(cca.atom_id.value(i));
+        set.add(ccaKey(cca.comp_id.value(i), cca.atom_id.value(i)));
     }
     return set;
 }
@@ -136,11 +86,32 @@ function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
     }
 }
 
-async function createBonds(atomsRequested: boolean) {
-    await ensureDataAvailable();
-    const ccd = await readCCD();
-    const pvcd = await readPVCD();
+function checkAddingAtomsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
+    const ccaSetByParent = DefaultMap<string, Set<string>>(() => new Set());
 
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_atom } = pvcd[k];
+        if (chem_comp_atom._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
+            if (parentIds.length === 0) {
+                const set = ccaSetByParent.getDefault(chem_comp.id.value(0));
+                addChemCompAtomToSet(set, chem_comp_atom);
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    const parentId = parentIds[i];
+                    const set = ccaSetByParent.getDefault(parentId);
+                    addChemCompAtomToSet(set, chem_comp_atom);
+                }
+            }
+        }
+    }
+}
+
+async function createBonds(
+    ccd: DatabaseCollection<CCD_Schema>,
+    pvcd: DatabaseCollection<CCD_Schema>,
+    atomsRequested: boolean
+) {
     const ccbSet = new Set<string>();
 
     const comp_id: string[] = [];
@@ -206,10 +177,12 @@ async function createBonds(atomsRequested: boolean) {
         { chem_comp_bond: bondTable }
     );
 
-    return { bonds: bondDatabase, atoms: atomsRequested ? createAtoms(ccd) : void 0 };
+    return { bonds: bondDatabase, atoms: atomsRequested ? createAtoms(ccd, pvcd) : void 0 };
 }
 
-function createAtoms(ccd: DatabaseCollection<CCD_Schema>) {
+function createAtoms(ccd: DatabaseCollection<CCD_Schema>, pvcd: DatabaseCollection<CCD_Schema>) {
+    const ccaSet = new Set<string>();
+
     const comp_id: string[] = [];
     const atom_id: string[] = [];
     const charge: number[] = [];
@@ -217,10 +190,33 @@ function createAtoms(ccd: DatabaseCollection<CCD_Schema>) {
 
     function addAtoms(compId: string, cca: CCA) {
         for (let i = 0, il = cca._rowCount; i < il; ++i) {
-            atom_id.push(cca.atom_id.value(i));
-            comp_id.push(compId);
-            charge.push(cca.charge.value(i));
-            pdbx_stereo_config.push(cca.pdbx_stereo_config.value(i));
+            const atomId = cca.atom_id.value(i);
+            const k = ccaKey(compId, atomId);
+            if (!ccaSet.has(k)) {
+                atom_id.push(atomId);
+                comp_id.push(compId);
+                charge.push(cca.charge.value(i));
+                pdbx_stereo_config.push(cca.pdbx_stereo_config.value(i));
+                ccaSet.add(k);
+            }
+        }
+    }
+
+    // check adding atoms from PVCD
+    checkAddingAtomsFromPVCD(pvcd);
+
+    // add atoms from PVCD
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_atom } = pvcd[k];
+        if (chem_comp_atom._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
+            if (parentIds.length === 0) {
+                addAtoms(chem_comp.id.value(0), chem_comp_atom);
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    addAtoms(parentIds[i], chem_comp_atom);
+                }
+            }
         }
     }
 
@@ -243,8 +239,12 @@ function createAtoms(ccd: DatabaseCollection<CCD_Schema>) {
     );
 }
 
-async function run(out: string, binary = false, ccaOut?: string) {
-    const { bonds, atoms } = await createBonds(!!ccaOut);
+async function run(out: string, binary = false, forceDownload = false, ccaOut?: string) {
+    await ensureDataAvailable(forceDownload);
+    const ccd = await readCCD();
+    const pvcd = await readPVCD();
+
+    const { bonds, atoms } = await createBonds(ccd, pvcd, !!ccaOut);
 
     const ccbCif = getEncodedCif(CCB_TABLE_NAME, bonds, binary);
     if (!fs.existsSync(path.dirname(out))) {
@@ -264,12 +264,6 @@ async function run(out: string, binary = false, ccaOut?: string) {
 const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
 const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';
 
-const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
-const CCD_PATH = path.join(DATA_DIR, 'components.cif');
-const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
-const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
-const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
-
 const parser = new argparse.ArgumentParser({
     addHelp: true,
     description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
@@ -290,13 +284,11 @@ parser.addArgument(['--ccaOut', '-a'], {
     required: false
 });
 interface Args {
-    out: string
-    forceDownload?: boolean
+    out: string,
+    forceDownload?: boolean,
     binary?: boolean,
     ccaOut?: string
 }
 const args: Args = parser.parseArgs();
 
-const FORCE_DOWNLOAD = args.forceDownload;
-
-run(args.out, args.binary, args.ccaOut);
+run(args.out, args.binary, args.forceDownload, args.ccaOut);

src/cli/chem-comp-dict/util.ts

@@ -0,0 +1,75 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as util from 'util';
+import * as path from 'path';
+import * as fs from 'fs';
+import * as zlib from 'zlib';
+import fetch from 'node-fetch';
+require('util.promisify').shim();
+const readFile = util.promisify(fs.readFile);
+const writeFile = util.promisify(fs.writeFile);
+
+import { Progress } from '../../mol-task';
+import { Database } from '../../mol-data/db';
+import { CIF } from '../../mol-io/reader/cif';
+import { CifWriter } from '../../mol-io/writer/cif';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+
+export async function ensureAvailable(path: string, url: string, forceDownload = false) {
+    if (forceDownload || !fs.existsSync(path)) {
+        console.log(`downloading ${url}...`);
+        const data = await fetch(url);
+        if (!fs.existsSync(DATA_DIR)) {
+            fs.mkdirSync(DATA_DIR);
+        }
+        if (url.endsWith('.gz')) {
+            await writeFile(path, zlib.gunzipSync(await data.buffer()));
+        } else {
+            await writeFile(path, await data.text());
+        }
+        console.log(`done downloading ${url}`);
+    }
+}
+
+export async function ensureDataAvailable(forceDownload = false) {
+    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
+    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
+}
+
+export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
+    const parsed = await parseCif(await readFile(path, 'utf8'));
+    return CIF.toDatabaseCollection(schema, parsed.result);
+}
+
+export async function readCCD() {
+    return readFileAsCollection(CCD_PATH, CCD_Schema);
+}
+
+export async function readPVCD() {
+    return readFileAsCollection(PVCD_PATH, CCD_Schema);
+}
+
+async function parseCif(data: string | Uint8Array) {
+    const comp = CIF.parse(data);
+    console.time('parse cif');
+    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
+    console.timeEnd('parse cif');
+    if (parsed.isError) throw parsed;
+    return parsed;
+}
+
+export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
+    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
+    CifWriter.Encoder.writeDatabase(encoder, name, database);
+    return encoder.getData();
+}
+
+const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
+const CCD_PATH = path.join(DATA_DIR, 'components.cif');
+const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
+const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
+const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';

src/cli/cif2bcif/converter.ts

@@ -70,7 +70,7 @@ function classify(name: string, field: CifField): CifWriter.Field {
     }
 }
 
-export default function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
+export function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
     return Task.create<Uint8Array>('BinaryCIF', async ctx => {
         const encodingProvider: BinaryEncodingProvider = hints
             ? CifWriter.createEncodingProviderFromJsonConfig(hints)

src/cli/cif2bcif/index.ts

@@ -10,7 +10,7 @@ import * as argparse from 'argparse';
 import * as util from 'util';
 import * as fs from 'fs';
 import * as zlib from 'zlib';
-import convert from './converter';
+import { convert } from './converter';
 
 require('util.promisify').shim();
 

src/cli/cifschema/index.ts

@@ -12,7 +12,7 @@ import fetch from 'node-fetch';
 
 import { parseCsv } from '../../mol-io/reader/csv/parser';
 import { CifFrame, CifBlock } from '../../mol-io/reader/cif';
-import parseText from '../../mol-io/reader/cif/text/parser';
+import { parseCifText } from '../../mol-io/reader/cif/text/parser';
 import { generateSchema } from './util/cif-dic';
 import { generate } from './util/generate';
 import { Filter, Database } from './util/schema';
@@ -28,19 +28,19 @@ function getDicNamespace(block: CifBlock) {
 
 async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
     await ensureMmcifDicAvailable();
-    const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
+    const mmcifDic = await parseCifText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
     if (mmcifDic.isError) throw mmcifDic;
 
     await ensureIhmDicAvailable();
-    const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
+    const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
     if (ihmDic.isError) throw ihmDic;
 
     await ensureCarbBranchDicAvailable();
-    const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
+    const carbBranchDic = await parseCifText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
     if (carbBranchDic.isError) throw carbBranchDic;
 
     await ensureCarbCompDicAvailable();
-    const carbCompDic = await parseText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
+    const carbCompDic = await parseCifText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
     if (carbCompDic.isError) throw carbCompDic;
 
     const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
@@ -56,7 +56,7 @@ async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, type
 
 async function runGenerateSchemaCifCore(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
     await ensureCifCoreDicAvailable();
-    const cifCoreDic = await parseText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
+    const cifCoreDic = await parseCifText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
     if (cifCoreDic.isError) throw cifCoreDic;
 
     const cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
@@ -80,7 +80,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
                 if (!file) continue;
                 if (imports.has(file)) continue;
 
-                const dic = await parseText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
+                const dic = await parseCifText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
                 if (dic.isError) throw dic;
 
                 imports.set(file, [...dic.result.blocks[0].saveFrames]);
@@ -92,7 +92,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
 }
 
 async function runGenerateSchemaDic(name: string, dicPath: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
-    const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
+    const dic = await parseCifText(fs.readFileSync(dicPath, 'utf8')).run();
     if (dic.isError) throw dic;
 
     const dicVersion = getDicVersion(dic.result.blocks[0]);

src/cli/lipid-params/index.ts

@@ -31,6 +31,8 @@ async function ensureAvailable(path: string, url: string) {
 
 async function ensureLipidsAvailable() { await ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL); }
 
+const extraLipids = ['DMPC'];
+
 async function run(out: string) {
     await ensureLipidsAvailable();
     const lipidsItpStr = fs.readFileSync(MARTINI_LIPIDS_PATH, 'utf8');
@@ -44,17 +46,20 @@ async function run(out: string) {
         UniqueArray.add(lipids, v, v);
     }
 
+    for (const v of extraLipids) {
+        UniqueArray.add(lipids, v, v);
+    }
 
     const lipidNames = JSON.stringify(lipids.array);
 
     if (out) {
         const output = `/**
-* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
-*
-* Code-generated lipid params file. Names extracted from Martini FF lipids itp.
-*
-* @author molstar/lipid-params cli
-*/
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+ *
+ * @author molstar/lipid-params cli
+ */
 
 export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
 `;

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

@@ -26,6 +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 ${oToS(param.options)}`;
+        case 'value-ref': return `Reference to a runtime defined value.`;
+        case 'data-ref': return `Reference to a computed data value.`;
         case 'text': return 'String';
         case 'interval': return `Interval [min, max]`;
         case 'group': return `Object with:\n${getParams(param.params, offset + 2)}`;

src/examples/alpha-orbitals/controls.tsx

@@ -0,0 +1,25 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as React from 'react';
+import * as ReactDOM from 'react-dom';
+import { AlphaOrbitalsExample } from '.';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { PluginContextContainer } from '../../mol-plugin-ui/plugin';
+
+export function mountControls(orbitals: AlphaOrbitalsExample, parent: Element) {
+    ReactDOM.render(<PluginContextContainer plugin={orbitals.plugin}>
+        <Controls orbitals={orbitals} />
+    </PluginContextContainer>, parent);
+}
+
+function Controls({ orbitals }: { orbitals: AlphaOrbitalsExample }) {
+    const params = useBehavior(orbitals.params);
+    const values = useBehavior(orbitals.state);
+
+    return <ParameterControls params={params as any} values={values} onChangeValues={(vs: any) => orbitals.state.next(vs)} />;
+}

src/examples/alpha-orbitals/index.html

@@ -0,0 +1,61 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Alpha Orbitals Example</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            #app {
+                position: absolute;
+                left: 0;
+                top: 0;
+                bottom: 0;
+                right: 0;
+            }
+            #controls {
+                position: absolute;
+                left: 8px;
+                top: 8px;
+                width: 300px;
+            }
+            #sponsor {
+                position: absolute;
+                left: 8px;
+                bottom: 8px;
+                font-family: "Helvetica Neue", "Segoe UI", Helvetica, "Source Sans Pro", Arial, sans-serif;
+                font-size: 12px;
+                text-align: center;
+            }
+            #sponsor svg {
+                fill: #128EA4;
+                width: 100px;
+            }
+            #sponsor a {
+                text-decoration: none;
+                color: #128EA4;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <script type="text/javascript" src="./index.js"></script>
+    </head>
+    <body>
+        <div id="app"></div>
+        <div id='controls'></div>
+        <div id='sponsor'>
+            <a href='https://www.entos.ai/envision' target="_blank" rel="noopener">
+                <svg class="makeStyles-root-46" viewBox="0 0 190 36" xmlns="http://www.w3.org/2000/svg"><path d="M32.2591 28.6707C32.2591 32.3914 29.2421 35.407 25.5214 35.407C22.0752 35.407 19.2338 32.8206 18.8325 29.4831V29.4775C18.8143 29.3312 18.8018 29.1835 18.7934 29.0344C18.7934 29.0316 18.7921 29.0274 18.7921 29.0246V29.0177C18.7865 28.902 18.7837 28.7864 18.7837 28.6707C18.7837 26.2557 20.0532 24.1389 21.9609 22.9503C21.9623 22.9489 21.9651 22.9489 21.9665 22.9475C22.0933 22.8666 22.2243 22.7914 22.3581 22.7203C22.3581 22.7203 22.3595 22.7203 22.3595 22.7189C23.3029 22.2173 24.3787 21.933 25.5214 21.933C29.2421 21.933 32.2591 24.9486 32.2591 28.6707Z"></path><path d="M25.5214 14.0692C29.2421 14.0692 32.2591 11.0522 32.2591 7.33146C32.2591 3.61074 29.2421 0.59375 25.5214 0.59375C22.0529 0.59375 19.1962 3.21637 18.8255 6.58592C18.8185 6.67092 18.8116 6.75454 18.8018 6.83815C18.7893 7.00119 18.7837 7.16563 18.7837 7.33146C18.7837 9.73669 20.0434 11.8465 21.94 13.038C22.0891 13.116 22.2355 13.201 22.3776 13.2916C22.3783 13.2923 22.379 13.2926 22.3797 13.293C22.3804 13.2933 22.3811 13.2937 22.3818 13.2944C23.3196 13.7891 24.3871 14.0692 25.5214 14.0692Z"></path><path d="M19.3645 12.4113C20.2926 12.4113 21.1694 12.638 21.94 13.038C20.0434 11.8465 18.7837 9.73669 18.7837 7.33146C18.7837 7.16563 18.7893 7.00119 18.8018 6.83815C18.4688 9.76455 16.1385 12.0866 13.2065 12.4044C13.8545 13.1193 14.3785 13.9484 14.745 14.857C15.7497 13.3798 17.4443 12.4113 19.3645 12.4113Z"></path><path d="M14.7312 21.1249V21.1236C14.1279 20.2331 13.7767 19.1587 13.7767 18.0007V17.9728C13.7767 15.3084 12.2285 13.0035 9.9835 11.911C9.98141 11.9103 9.97967 11.9096 9.97793 11.9089C9.97619 11.9082 9.97444 11.9075 9.97235 11.9068C9.96817 11.904 9.96538 11.9026 9.9612 11.9012C9.95981 11.9012 9.95981 11.8998 9.95981 11.8998C9.9417 11.8915 9.92394 11.8831 9.90618 11.8747C9.8884 11.8664 9.87063 11.858 9.85251 11.8497C9.82046 11.8343 9.78701 11.819 9.75357 11.8051L9.74521 11.8009C8.91745 11.4372 8.0019 11.2351 7.03898 11.2351C3.31826 11.2351 0.30127 14.2521 0.30127 17.9728C0.30127 21.6935 3.31826 24.7105 7.03898 24.7105C7.98797 24.7105 8.89098 24.514 9.71037 24.1601C9.71246 24.1594 9.7142 24.1583 9.71594 24.1573C9.71768 24.1562 9.71943 24.1552 9.72152 24.1545C9.8107 24.1169 9.8985 24.0765 9.9849 24.0333L9.98629 24.0319C10.7625 23.6919 11.6181 23.5037 12.5197 23.5037C12.7524 23.5037 12.9824 23.5163 13.2081 23.54C13.2082 23.5399 13.2081 23.54 13.2081 23.54C15.0168 23.7365 16.5971 24.695 17.6185 26.0885C17.9195 25.1688 18.3752 24.3201 18.9563 23.5732C17.1964 23.4464 15.6635 22.5058 14.7312 21.1249Z"></path><g clip-path="url(#clip0)"><path d="M106.391 18.0021C106.391 11.3724 101.039 6 94.4389 6H88.4585C81.8581 6 76.5061 11.3724 76.5061 18.0021V30.0042H81.2845V18.0021C81.2845 14.0268 84.4941 10.8008 88.4585 10.8008H94.4347C98.395 10.8008 101.609 14.0226 101.609 18.0021V30.0042H106.391V18.0021Z"></path><path d="M149.432 6H142.258C135.653 6 130.301 11.3724 130.301 18.0021C130.301 24.6319 135.653 30.0042 142.258 30.0042H149.432C156.036 30.0042 161.388 24.6319 161.388 18.0021C161.388 11.3724 156.032 6 149.432 6ZM149.432 25.1992H142.258C138.297 25.1992 135.084 21.9774 135.084 17.9979C135.084 14.0183 138.293 10.7966 142.258 10.7966H149.432C153.392 10.7966 156.606 14.0183 156.606 17.9979C156.606 21.9774 153.392 25.1992 149.432 25.1992Z"></path><path d="M74.1151 25.1992H58.5736C55.4526 25.1992 52.804 23.1924 51.8171 20.3983H74.1151V17.9979C74.1151 17.1808 74.1868 16.3807 74.3175 15.5975H51.8171C52.804 12.8033 55.4526 10.7966 58.5736 10.7966H76.0383C77.1475 8.87458 78.6911 7.22773 80.5299 6H58.5736C51.969 6 46.6169 11.3724 46.6169 18.0021C46.6169 24.6276 51.969 30 58.5736 30H74.1151V25.1992Z"></path><path d="M120.74 6H115.958H102.369C104.212 7.22773 105.751 8.87458 106.861 10.8008H115.958V30H120.74V10.8008H129.838C130.947 8.87458 132.486 7.22773 134.329 6H120.74Z"></path><path d="M182.906 15.6017H169.756C168.436 15.6017 167.365 14.5264 167.365 13.2013C167.365 11.8762 168.436 10.8008 169.756 10.8008H188.882V6H169.756C165.796 6 162.582 9.22173 162.582 13.2013C162.582 17.1808 165.791 20.4025 169.756 20.4025H182.906C184.226 20.4025 185.297 21.4779 185.297 22.803C185.297 24.1281 184.226 25.2034 182.906 25.2034H161.852C160.743 27.1297 159.199 28.7765 157.361 30.0042H182.906C186.866 30.0042 190.08 26.7825 190.08 22.803C190.08 18.8234 186.866 15.6017 182.906 15.6017Z"></path></g><defs><clipPath id="clip0"><rect width="190" height="24" fill="white" transform="translate(0 6)"></rect></clipPath></defs></svg>
+                <div>
+                    Entos Envision
+                </div>
+            </a>
+        </div>
+        <script>
+            AlphaOrbitalsExample.init('app')
+        </script>
+    </body>
+</html>

src/examples/alpha-orbitals/index.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 { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
+import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
+import { createPluginAsync } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectSelector, StateTransformer } from '../../mol-state';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { mountControls } from './controls';
+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: AlphaOrbital[]
+}
+
+interface Params {
+    show: { name: 'orbital', params: { index: number } } | { name: 'density', params: {} },
+    isoValue: number,
+    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 {
+    plugin: PluginContext;
+
+    async init(target: string | HTMLElement) {
+        const defaultSpec = DefaultPluginSpec();
+        this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
+            ...defaultSpec,
+            layout: {
+                initial: {
+                    isExpanded: false,
+                    showControls: false
+                },
+                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
+            },
+            components: {
+                viewport: {
+                    canvas3d: {
+                        camera: {
+                            helper: { axes: { name: 'off', params: { } } }
+                        }
+                    }
+                }
+            },
+            config: [
+                [PluginConfig.Viewport.ShowExpand, false],
+                [PluginConfig.Viewport.ShowControls, false],
+                [PluginConfig.Viewport.ShowSelectionMode, false],
+                [PluginConfig.Viewport.ShowAnimation, false],
+            ]
+        });
+
+        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
+        });
+
+        mountControls(this, document.getElementById('controls')!);
+    }
+
+    readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
+    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 currentParams: Params = { ...this.state.value };
+
+    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;
+
+        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.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: 0.85,
+            color,
+            directVolume: this.state.value.gpuSurface,
+            kind,
+            relativeIsovalue: this.state.value.isoValue,
+            pickable: false,
+            xrayShaded: true
+        };
+    }
+
+    async load(input: DemoInput) {
+        await this.plugin.clear();
+
+        const data = await this.plugin.builders.data.rawData({ data: input.moleculeSdf }, { state: { isGhost: true } });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(data, 'mol');
+        const model = await this.plugin.builders.structure.createModel(trajectory);
+        const structure = await this.plugin.builders.structure.createStructure(model);
+
+        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: {} } } });
+
+
+        this.basis = await this.plugin.build().toRoot()
+            .apply(StaticBasisAndOrbitals, { basis: input.basis, order: input.order, orbitals: input.orbitals })
+            .commit();
+
+        await this.syncVolume();
+
+        this.params.next({
+            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, { isHidden: true })
+        });
+
+        this.state.pipe(skip(1), debounceTime(1000 / 24)).subscribe(async params => {
+            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();
+            }
+        });
+    }
+}
+
+(window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();

src/examples/basic-wrapper/index.html

@@ -86,7 +86,7 @@
 
             // adjust this number to make the animation faster or slower
             // requires to "restart" the animation if changed
-            BasicMolStarWrapper.animate.modelIndex.maxFPS = 30;
+            BasicMolStarWrapper.animate.modelIndex.targetFps = 30;
 
             addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());

src/examples/basic-wrapper/index.ts

@@ -6,10 +6,10 @@
 
 import { EmptyLoci } from '../../mol-model/loci';
 import { StructureSelection } from '../../mol-model/structure';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
 import { Script } from '../../mol-script/script';
@@ -29,7 +29,7 @@ class BasicWrapper {
 
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
+            ...DefaultPluginSpec(),
             layout: {
                 initial: {
                     isExpanded: false,
@@ -83,13 +83,17 @@ class BasicWrapper {
         if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
     }
 
+    private animateModelIndexTargetFps() {
+        return Math.max(1, this.animate.modelIndex.targetFps | 0);
+    }
+
     animate = {
         modelIndex: {
-            maxFPS: 8,
-            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
-            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
-            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
-            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
+            targetFps: 8,
+            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
+            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
+            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
+            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: { direction: 'forward' } } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
     }
@@ -113,8 +117,10 @@ class BasicWrapper {
 
     interactivity = {
         highlightOn: () => {
+            const data = this.plugin.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data;
+            if (!data) return;
+
             const seq_id = 7;
-            const data = (this.plugin.state.data.select('asm')[0].obj as PluginStateObject.Molecule.Structure).data;
             const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
                 'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), seq_id]),
                 'group-by': Q.struct.atomProperty.macromolecular.residueKey()

src/examples/basic-wrapper/superposition.ts

@@ -10,7 +10,7 @@ import { superpose } from '../../mol-model/structure/structure/util/superpositio
 import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import Expression from '../../mol-script/language/expression';
+import { Expression } from '../../mol-script/language/expression';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { StateObjectRef } from '../../mol-state';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';

src/examples/domain-annotation-server/mapping.ts

@@ -9,7 +9,7 @@ import { CifWriter } from '../../mol-io/writer/cif';
 import * as S from './schemas';
 // import { getCategoryInstanceProvider } from './utils'
 
-export default function create(allData: any) {
+export function createMapping(allData: any) {
     const mols = Object.keys(allData);
     const enc = CifWriter.createEncoder();
     enc.startDataBlock(mols[0]);

src/examples/domain-annotation-server/server.ts

@@ -6,7 +6,7 @@
 
 import express from 'express';
 import fetch from 'node-fetch';
-import createMapping from './mapping';
+import { createMapping } from './mapping';
 
 async function getMappings(id: string) {
     const data = await fetch(`https://www.ebi.ac.uk/pdbe/api/mappings/${id}`);

src/examples/domain-annotation-server/test.ts

@@ -5,7 +5,7 @@
  */
 
 import fetch from 'node-fetch';
-import createMapping from './mapping';
+import { createMapping } from './mapping';
 
 (async function () {
     const data = await fetch('https://www.ebi.ac.uk/pdbe/api/mappings/1tqn?pretty=true');

src/examples/lighting/index.html

@@ -12,18 +12,18 @@
             }
             #app {
                 position: absolute;
-                left: 160px;
-                top: 100px;
-                width: 600px;
-                height: 600px;
-                border: 1px solid #ccc;
+                width: 100%;
+                height: 100%;
             }
 
             #controls {
                 position: absolute;
                 width: 150px;
-                top: 100px;
-                left: 780px;
+                bottom: 100px;
+                right: 50px;
+                z-index: 10;
+                font-family: sans-serif;
+                font-size: smaller;
             }
 
             #controls > button {
@@ -46,13 +46,13 @@
         <div id="app"></div>
         <script>
             LightingDemo.init('app')
-            LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' })
+            LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3)
 
             addHeader('Example PDB IDs');
-            addControl('1M07', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' }));
-            addControl('6HY0', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6HY0.cif', assemblyId: '1' }));
-            addControl('6QVK', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6QVK.cif', assemblyId: '1' }));
-            addControl('1RB8', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1RB8.cif', assemblyId: '1' }));
+            addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
+            addControl('5FJ5', () => LightingDemo.load({ url: 'https://models.rcsb.org/5FJ5.bcif', assemblyId: '1' }, 8, 1.8));
+            addControl('1UPN', () => LightingDemo.load({ url: 'https://models.rcsb.org/1UPN.bcif', assemblyId: '1' }, 7, 1.6));
+            addControl('1RB8', () => LightingDemo.load({ url: 'https://models.rcsb.org/1RB8.bcif', assemblyId: '1' }, 6, 1.3));
 
             addSeparator()
 

src/examples/lighting/index.ts

@@ -5,7 +5,8 @@
  */
 
 import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
@@ -24,12 +25,11 @@ const Canvas3DPresets = {
             mode: 'temporal' as Canvas3DProps['multiSample']['mode']
         },
         postprocessing: {
-            occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
-            outline: { name: 'on', params: { scale: 1, threshold: 0.8 } }
+            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+            outline: { name: 'on', params: { scale: 1, threshold: 0.1 } }
         },
         renderer: {
-            ambientIntensity: 1,
-            lightIntensity: 0,
+            style: { name: 'flat', params: {} }
         }
     },
     occlusion: <Preset> {
@@ -37,12 +37,11 @@ const Canvas3DPresets = {
             mode: 'temporal' as Canvas3DProps['multiSample']['mode']
         },
         postprocessing: {
-            occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
+            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
             outline: { name: 'off', params: { } }
         },
         renderer: {
-            ambientIntensity: 0.4,
-            lightIntensity: 0.6,
+            style: { name: 'matte', params: {} }
         }
     },
     standard: <Preset> {
@@ -54,20 +53,24 @@ const Canvas3DPresets = {
             outline: { name: 'off', params: { } }
         },
         renderer: {
-            ambientIntensity: 0.4,
-            lightIntensity: 0.6,
+            style: { name: 'matte', params: {} }
         }
     }
 };
 
+
 type Canvas3DPreset = keyof typeof Canvas3DPresets
 
 class LightingDemo {
     plugin: PluginContext;
 
+    private radius = 5;
+    private bias = 1.1;
+    private preset: Canvas3DPreset = 'illustrative';
+
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
+            ...DefaultPluginSpec(),
             layout: {
                 initial: {
                     isExpanded: false,
@@ -82,6 +85,10 @@ class LightingDemo {
 
     setPreset(preset: Canvas3DPreset) {
         const props = Canvas3DPresets[preset];
+        if (props.postprocessing.occlusion?.name === 'on') {
+            props.postprocessing.occlusion.params.radius = this.radius;
+            props.postprocessing.occlusion.params.bias = this.bias;
+        }
         PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
             ...props,
             multiSample: {
@@ -99,7 +106,7 @@ class LightingDemo {
         }});
     }
 
-    async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
+    async load({ url, format = 'mmcif', isBinary = true, assemblyId = '' }: LoadParams, radius: number, bias: number) {
         await this.plugin.clear();
 
         const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
@@ -111,7 +118,11 @@ class LightingDemo {
         if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });
 
         const ligand = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand');
-        if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick' });
+        if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
+
+        this.radius = radius;
+        this.bias = bias;
+        this.setPreset(this.preset);
     }
 }
 

src/examples/proteopedia-wrapper/index.html

@@ -147,7 +147,7 @@
 
             // adjust this number to make the animation faster or slower
             // requires to "restart" the animation if changed
-            PluginWrapper.animate.modelIndex.maxFPS = 30;
+            PluginWrapper.animate.modelIndex.targetFps = 30;
 
             addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());

src/examples/proteopedia-wrapper/index.ts

@@ -6,8 +6,9 @@
 
 import * as ReactDOM from 'react-dom';
 import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
@@ -46,7 +47,7 @@ class MolStarProteopediaWrapper {
         customColorList?: number[]
     }) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
+            ...DefaultPluginSpec(),
             animations: [
                 AnimateModelIndex
             ],
@@ -271,13 +272,17 @@ class MolStarProteopediaWrapper {
         resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
     }
 
+    private animateModelIndexTargetFps() {
+        return Math.max(1, this.animate.modelIndex.targetFps | 0);
+    }
+
     animate = {
         modelIndex: {
-            maxFPS: 8,
-            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
-            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
-            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
-            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
+            targetFps: 8,
+            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
+            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
+            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
+            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: { direction: 'forward' } } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
     }
@@ -403,7 +408,7 @@ class MolStarProteopediaWrapper {
         },
         download: async (type: 'molj' | 'molx' = 'molj', params?: PluginState.SnapshotParams) => {
             const data = await this.plugin.managers.snapshot.serialize({ type, params });
-            download(data, `mol-star_state_${(name || getFormattedTime())}.${type}`);
+            download(data, `mol-star_state_${getFormattedTime()}.${type}`);
         },
         fetch: async (url: string, type: 'molj' | 'molx' = 'molj') => {
             try {

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

@@ -0,0 +1,214 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Box3D } from '../../../mol-math/geometry';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../../mol-task';
+import { sphericalCollocation } from '../collocation';
+import { Basis, CubeGridInfo } from '../data-model';
+
+describe('alpha-orbitals-cubes', () => {
+    it('water', async () => {
+        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),
+            npoints: 8,
+            size: Vec3.create(2, 2, 2)
+        };
+
+        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];
+
+        expect(matrix.length).toBe(expected.length);
+
+        for (let i = 0; i < matrix.length; i++) {
+            expect(Math.abs(matrix[i] - expected[i]) < 1e-6).toBe(true);
+        }
+    });
+});
+
+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
+                    ]
+                }
+            ]
+        }
+    ]
+};

src/extensions/alpha-orbitals/collocation.ts

@@ -0,0 +1,162 @@
+/**
+ * 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 { Vec3 } from '../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../mol-task';
+import { arrayMin } from '../../mol-util/array';
+import { AlphaOrbital, CubeGridInfo } from './data-model';
+import { normalizeBasicOrder, SphericalFunctions } from './spherical-functions';
+
+export async function sphericalCollocation(
+    grid: CubeGridInfo,
+    orbital: AlphaOrbital,
+    taskCtx: RuntimeContext
+) {
+    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
+    let baseCount = 0;
+
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            for (const L of shell.angularMomentum) {
+                if (L > 4) {
+                    // TODO: will L > 4 be required? Would need to precompute more functions in that case.
+                    throw new Error('Angular momentum L > 4 not supported.');
+                }
+
+                baseCount += 2 * L + 1;
+            }
+        }
+    }
+
+    const matrix = new Float32Array(grid.npoints);
+
+    let baseIndex = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            let amIndex = 0;
+            for (const L of shell.angularMomentum) {
+                const alpha = normalizeBasicOrder(
+                    L,
+                    orbital.alpha.slice(baseIndex, baseIndex + 2 * L + 1),
+                    sphericalOrder
+                );
+                baseIndex += 2 * L + 1;
+
+                collocationBasis(
+                    matrix,
+                    grid,
+                    L,
+                    shell.coefficients[amIndex++],
+                    shell.exponents,
+                    atom.center,
+                    cutoffThreshold,
+                    alpha
+                );
+
+                if (taskCtx.shouldUpdate) {
+                    await taskCtx.update({
+                        message: 'Computing...',
+                        current: baseIndex,
+                        max: baseCount,
+                        isIndeterminate: false,
+                    });
+                }
+            }
+        }
+    }
+
+    return matrix;
+}
+
+function collocationBasis(
+    matrix: Float32Array,
+    grid: CubeGridInfo,
+    L: number,
+    coefficients: number[],
+    exponents: number[],
+    center: Vec3,
+    cutoffThreshold: number,
+    alpha: number[]
+) {
+    const ncoeff = exponents.length;
+    const sphericalFunc = SphericalFunctions[L];
+
+    const cx = center[0],
+        cy = center[1],
+        cz = center[2];
+    const ny = grid.dimensions[1],
+        nz = grid.dimensions[2];
+    const gdx = grid.delta[0],
+        gdy = grid.delta[1],
+        gdz = grid.delta[2];
+    const sx = grid.box.min[0],
+        sy = grid.box.min[1],
+        sz = grid.box.min[2];
+
+    const cutoffRadius =
+        cutoffThreshold > 0
+            ? Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents))
+            : 10000;
+    const cutoffSquared = cutoffRadius * cutoffRadius;
+
+    const radiusBox = getRadiusBox(grid, center, cutoffRadius);
+    const iMin = radiusBox[0][0],
+        jMin = radiusBox[0][1],
+        kMin = radiusBox[0][2];
+    const iMax = radiusBox[1][0],
+        jMax = radiusBox[1][1],
+        kMax = radiusBox[1][2];
+
+    for (let i = iMin; i <= iMax; i++) {
+        const x = sx + gdx * i - cx;
+        const oX = i * ny * nz;
+
+        for (let j = jMin; j <= jMax; j++) {
+            const y = sy + gdy * j - cy;
+            const oY = oX + j * nz;
+            for (let k = kMin; k <= kMax; k++) {
+                const z = sz + gdz * k - cz;
+                const R2 = x * x + y * y + z * z;
+
+                if (R2 > cutoffSquared) {
+                    continue;
+                }
+
+                let gaussianSum = 0;
+                for (let c = 0; c < ncoeff; c++) {
+                    gaussianSum +=
+                        coefficients[c] * Math.exp(-exponents[c] * R2);
+                }
+
+                const sphericalSum = L === 0 ? alpha[0] : sphericalFunc(alpha, x, y, z);
+
+
+                matrix[k + oY] += gaussianSum * sphericalSum;
+            }
+        }
+    }
+}
+
+function getRadiusBox(grid: CubeGridInfo, center: Vec3, radius: number) {
+    const r = Vec3.create(radius, radius, radius);
+    const min = Vec3.scaleAndAdd(Vec3(), center, r, -1);
+    const max = Vec3.add(Vec3(), center, r);
+
+    Vec3.sub(min, min, grid.box.min);
+    Vec3.sub(max, max, grid.box.min);
+
+    Vec3.div(min, min, grid.delta);
+    Vec3.floor(min, min);
+    Vec3.max(min, min, Vec3());
+
+    Vec3.div(max, max, grid.delta);
+    Vec3.ceil(max, max);
+    Vec3.min(max, max, Vec3.subScalar(Vec3(), grid.dimensions, 1));
+
+    return [min, max];
+}

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

@@ -0,0 +1,170 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { createGrid3dComputeRenderable } from '../../../mol-gl/compute/grid3d';
+import { TextureSpec, UnboxedValues, UniformSpec } from '../../../mol-gl/renderable/schema';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { RuntimeContext } from '../../../mol-task';
+import { ValueCell } from '../../../mol-util';
+import { arrayMin } from '../../../mol-util/array';
+import { AlphaOrbital, Basis, CubeGridInfo } from '../data-model';
+import { normalizeBasicOrder, SphericalBasisOrder } from '../spherical-functions';
+import { MAIN, UTILS } from './shader.frag';
+
+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'),
+    uNCenters: UniformSpec('i'),
+    uNAlpha: UniformSpec('i'),
+    uNCoeff: UniformSpec('i'),
+    uMaxCoeffs: UniformSpec('i'),
+};
+
+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;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            for (const L of shell.angularMomentum) {
+                if (L > 4) {
+                    // TODO: will L > 4 be required? Would need to precompute more functions in that case.
+                    throw new Error('Angular momentum L > 4 not supported.');
+                }
+
+                centerCount++;
+                baseCount += 2 * L + 1;
+                coeffCount += shell.exponents.length;
+            }
+        }
+    }
+
+    const centers = new Float32Array(4 * centerCount);
+    // L, alpha_offset, coeff_offset_start, coeff_offset_end
+    const info = new Float32Array(4 * centerCount);
+    const alpha = new Float32Array(baseCount);
+    const coeff = new Float32Array(3 * coeffCount);
+
+    let maxCoeffs = 0;
+    let cO = 0, aO = 0, coeffO = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+
+            let amIndex = 0;
+            for (const L of shell.angularMomentum) {
+                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))
+                    : 10000;
+
+                centers[4 * cO + 0] = atom.center[0];
+                centers[4 * cO + 1] = atom.center[1];
+                centers[4 * cO + 2] = atom.center[2];
+                centers[4 * cO + 3] = cutoffRadius * cutoffRadius;
+
+                info[4 * cO + 0] = L;
+                info[4 * cO + 1] = aO;
+                info[4 * cO + 2] = coeffO;
+                info[4 * cO + 3] = coeffO + shell.exponents.length;
+
+                for (let i = 0; i < a0.length; i++) alpha[aO + i] = a0[i];
+
+                const c0 = shell.coefficients[amIndex++];
+                for (let i = 0; i < shell.exponents.length; i++) {
+                    coeff[3 * (coeffO + i) + 0] = c0[i];
+                    coeff[3 * (coeffO + i) + 1] = shell.exponents[i];
+                }
+
+                if (c0.length > maxCoeffs) {
+                    maxCoeffs = c0.length;
+                }
+
+                cO++;
+                aO += 2 * L + 1;
+                coeffO += shell.exponents.length;
+            }
+        }
+    }
+
+    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 },
+    };
+}

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

@@ -0,0 +1,145 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export const UTILS = `
+float L1(vec3 p, float a0, float a1, float a2) {
+    return a0 * p.z + a1 * p.x + a2 * p.y;
+}
+
+float L2(vec3 p, float a0, float a1, float a2, float a3, float a4) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    return (
+        a0 * (-0.5 * xx - 0.5 * yy + zz) +
+        a1 * (1.7320508075688772 * x * z) +
+        a2 * (1.7320508075688772 * y * z) +
+        a3 * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
+        a4 * (1.7320508075688772 * x * y)
+    );
+}
+
+float L3(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    return (
+        a0 * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
+        a1 * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
+        a2 * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
+        a3 * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
+        a4 * (3.872983346207417 * x * y * z) +
+        a5 * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
+        a6 * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
+    );
+}
+
+float L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6, float a7, float a8) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    float xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
+    return (
+        a0 * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
+        a1 * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
+        a2 * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
+        a3 * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
+        a4 * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
+        a5 * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
+        a6 * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
+        a7 * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
+        a8 * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
+    );
+}
+
+float alpha(float offset, float f) {
+    #ifdef WEBGL1
+        // in webgl1, the value is in the alpha channel!
+        return texture2D(tAlpha, vec2(offset * f, 0.5)).a;
+    #else
+        return texture2D(tAlpha, vec2(offset * f, 0.5)).x;
+    #endif
+}
+
+float Y(int L, vec3 X, float aO, float fA) {
+    if (L == 0) {
+        return alpha(aO, fA);
+    } else if (L == 1) {
+        return L1(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA)
+        );
+    } else if (L == 2) {
+        return L2(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA)
+        );
+    } else if (L == 3) {
+        return L3(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
+            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA)
+        );
+    } else if (L == 4) {
+        return L4(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
+            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA), alpha(aO + 7.0, fA), alpha(aO + 8.0, fA)
+        );
+    }
+    // TODO: do we need L > 4?
+    return 0.0;
+}
+
+#ifndef WEBGL1
+    float R(float R2, int start, int end, float fCoeff) {
+        float gauss = 0.0;
+        for (int i = start; i < end; i++) {
+            vec2 c = texture2D(tCoeff, vec2(float(i) * fCoeff, 0.5)).xy;
+            gauss += c.x * exp(-c.y * R2);
+        }
+        return gauss;
+    }
+#else
+    float R(float R2, int start, int end, float fCoeff) {
+        float gauss = 0.0;
+        int o = start;
+        for (int i = 0; i < uMaxCoeffs; i++) {
+            if (o >= end) break;
+
+            vec2 c = texture2D(tCoeff, vec2(float(o) * fCoeff, 0.5)).xy;
+            gauss += c.x * exp(-c.y * R2);
+            o++;
+        }
+        return gauss;
+    }
+#endif
+`;
+
+export const MAIN = `
+    float fCenter = 1.0 / float(uNCenters - 1);
+    float fCoeff = 1.0 / float(uNCoeff - 1);
+    float fA = 1.0 / float(uNAlpha - 1);
+
+    float v = 0.0;
+
+    for (int i = 0; i < uNCenters; i++) {
+        vec2 cCoord = vec2(float(i) * fCenter, 0.5);
+
+        vec4 center = texture2D(tCenters, cCoord);
+        vec3 X = xyz - center.xyz;
+        float R2 = dot(X, X);
+
+        // center.w is squared cutoff radius
+        if (R2 > center.w) {
+            continue;
+        }
+
+        vec4 info = texture2D(tInfo, cCoord);
+
+        int L = int(info.x);
+        float aO = info.y;
+        int coeffStart = int(info.z);
+        int coeffEnd = int(info.w);
+
+        v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
+    }
+`;

src/extensions/alpha-orbitals/orbitals.ts

@@ -0,0 +1,131 @@
+/**
+ * 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 { 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';
+
+// setDebugMode(true);
+
+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;
+    }
+    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/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

@@ -0,0 +1,236 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
+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 './spherical-functions';
+import { Volume } from '../../mol-model/volume';
+import { PluginContext } from '../../mol-plugin/context';
+import { ColorNames } from '../../mol-util/color/names';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+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';
+import { Tensor } from '../../mol-math/linear-algebra';
+
+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',
+    display: 'Basis and Orbitals',
+    from: PluginStateObject.Root,
+    to: BasisAndOrbitals,
+    params: {
+        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<AlphaOrbital[]>([], { isHidden: true })
+    },
+})({
+    apply({ params }) {
+        return new BasisAndOrbitals({ basis: params.basis, order: params.order, orbitals: params.orbitals }, { label: params.label });
+    }
+});
+
+const CreateOrbitalVolumeParamBase = {
+    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}: ${e.spacing}`, {
+        defaultValue: [
+            { atomCount: 55, spacing: 0.5 },
+            { atomCount: 40, spacing: 0.45 },
+            { atomCount: 25, spacing: 0.4 },
+            { atomCount: 0, spacing: 0.35 },
+        ]
+    }),
+    clampValues: PD.MappedStatic('off', {
+        off: PD.EmptyGroup(),
+        on: PD.Group({
+            sigma: PD.Numeric(8, { min: 1, max: 20 }, { description: 'Clamp values to range [sigma * negIsoValue, sigma * posIsoValue].' })
+        })
+    })
+};
+
+function clampData(matrix: Tensor.Data, min: number, max: number) {
+    for (let i = 0, _i = matrix.length; i < _i; i++) {
+        const v = matrix[i];
+        if (v < min) matrix[i] = min;
+        else if (v > max) matrix[i] = max;
+    }
+}
+
+function clampGrid(data: CubeGrid, v: number) {
+    const grid = data.grid;
+    const min = (data.isovalues?.negative ?? data.grid.stats.min) * v;
+    const max = (data.isovalues?.positive ?? data.grid.stats.max) * v;
+
+    // clamp values for better direct volume resolution
+    // current implementation uses Byte array for values
+    // if this is not enough, update mol* to use float
+    // textures instead
+    if (grid.stats.min < min || grid.stats.max > max) {
+        clampData(data.grid.cells.data, min, max);
+        if (grid.stats.min < min) {
+            (grid.stats.min as number) = min;
+        }
+        if (grid.stats.max > max) {
+            (grid.stats.max as number) = max;
+        }
+    }
+}
+
+export const CreateOrbitalVolume = PluginStateTransform.BuiltIn({
+    name: 'create-orbital-volume',
+    display: 'Orbital Volume',
+    from: BasisAndOrbitals,
+    to: PluginStateObject.Volume.Data,
+    params: (a) => {
+        if (!a) {
+            return { index: PD.Numeric(0), ...CreateOrbitalVolumeParamBase };
+        }
+
+        return {
+            index: PD.Select(0, a.data.orbitals.map((o, i) => [i, `[${i + 1}] ${o.energy.toFixed(4)}`])),
+            ...CreateOrbitalVolumeParamBase
+        };
+    }
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Orbital Volume', async ctx => {
+            const data = await createSphericalCollocationGrid({
+                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[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),
+            };
+
+            if (params.clampValues?.name === 'on') {
+                clampGrid(data, params.clampValues?.params?.sigma ?? 8);
+            }
+
+            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 },
+                customProperties: new CustomProperties(),
+                _propertyData: Object.create(null),
+            };
+
+            if (params.clampValues?.name === 'on') {
+                clampGrid(data, params.clampValues?.params?.sigma ?? 8);
+            }
+
+            return new PluginStateObject.Volume.Data(volume, { label: 'Orbital Volume' });
+        });
+    }
+});
+
+export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
+    name: 'create-orbital-representation-3d',
+    display: 'Orbital Representation 3D',
+    from: PluginStateObject.Volume.Data,
+    to: PluginStateObject.Volume.Representation3D,
+    params: {
+        directVolume: PD.Boolean(false),
+        relativeIsovalue: PD.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
+        kind: PD.Select<'positive' | 'negative'>('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
+        color: PD.Color(ColorNames.blue),
+        alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+        xrayShaded: PD.Boolean(false),
+        pickable: PD.Boolean(true)
+    }
+})({
+    canAutoUpdate() {
+        return true;
+    },
+    apply({ a, params: srcParams }, plugin: PluginContext) {
+        return Task.create('Orbitals Representation 3D', async ctx => {
+            const params = volumeParams(plugin, a, srcParams);
+
+            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));
+            await repr.createOrUpdate(props, a.data).runInContext(ctx);
+            repr.setState({ pickable: srcParams.pickable });
+            return new PluginStateObject.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
+        });
+    },
+    update({ a, b, newParams: srcParams }, plugin: PluginContext) {
+        return Task.create('Orbitals Representation 3D', async ctx => {
+            const newParams = volumeParams(plugin, a, srcParams);
+
+            const props = { ...b.data.repr.props, ...newParams.type.params };
+            b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
+            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            b.data.repr.setState({ pickable: srcParams.pickable });
+            b.description = VolumeRepresentation3DHelpers.getDescription(props);
+            return StateTransformer.UpdateResult.Updated;
+        });
+    }
+});
+
+function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Data, params: StateTransformer.Params<typeof CreateOrbitalRepresentation3D>) {
+    if (volume.data.sourceData.kind !== 'alpha-orbitals') throw new Error('Invalid data source kind.');
+
+    const { isovalues } = volume.data.sourceData.data as CubeGrid;
+    if (!isovalues) throw new Error('Isovalues are not computed.');
+
+    const value = isovalues[params.kind];
+
+    return createVolumeRepresentationParams(plugin, volume.data, params.directVolume ? {
+        type: 'direct-volume',
+        typeParams: {
+            alpha: params.alpha,
+            renderMode: {
+                name: 'isosurface',
+                params: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, singleLayer: false }
+            },
+            xrayShaded: params.xrayShaded
+        },
+        color: 'uniform',
+        colorParams: { value: params.color }
+    } : {
+        type: 'isosurface',
+        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded },
+        color: 'uniform',
+        colorParams: { value: params.color }
+    });
+}

src/extensions/anvil/algorithm.ts

@@ -54,13 +54,13 @@ export function computeANVIL(structure: Structure, props: ANVILProps) {
     });
 }
 
-const l = StructureElement.Location.create(void 0);
+
 const centroidHelper = new CentroidHelper();
 function initialize(structure: Structure, props: ANVILProps): ANVILContext {
+    const l = StructureElement.Location.create(structure);
     const { label_atom_id, x, y, z } = StructureProperties.atom;
     const elementCount = structure.polymerResidueCount;
     centroidHelper.reset();
-    l.structure = structure;
 
     let offsets = new Int32Array(elementCount);
     let exposed = new Array<boolean>(elementCount);
@@ -328,6 +328,7 @@ namespace HphobHphil {
     const testPoint = Vec3();
     export function filtered(ctx: ANVILContext, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil {
         const { offsets, exposed, structure } = ctx;
+        const l = StructureElement.Location.create(structure);
         const { x, y, z } = StructureProperties.atom;
         let hphob = 0;
         let hphil = 0;

src/extensions/anvil/prop.ts

@@ -15,7 +15,7 @@ import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/ac
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
 import { CustomPropSymbol } from '../../mol-script/language/symbol';
-import Type from '../../mol-script/language/type';
+import { Type } from '../../mol-script/language/type';
 
 export const MembraneOrientationParams = {
     ...ANVILParams

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) {
@@ -106,7 +109,7 @@ function getBilayerRims(ctx: RuntimeContext, data: Structure, props: BilayerRims
     const builder = LinesBuilder.create(128, 64, shape?.geometry);
     getLayerCircle(builder, p1, centroid, normal, scaledRadius, props);
     getLayerCircle(builder, p2, centroid, normal, scaledRadius, props);
-    return Shape.create(name, data, builder.getLines(), () => props.color, () => props.linesSize, () => membraneLabel(data));
+    return Shape.create('Bilayer rims', data, builder.getLines(), () => props.color, () => props.linesSize, () => membraneLabel(data));
 }
 
 function getLayerCircle(builder: LinesBuilder, p: Vec3, centroid: Vec3, normal: Vec3, radius: number, props: BilayerRimsProps, shape?: Shape<Lines>) {
@@ -142,7 +145,7 @@ function getBilayerPlanes(ctx: RuntimeContext, data: Structure, props: BilayerPl
     const scaledRadius = props.radiusFactor * radius;
     getLayerPlane(state, p1, centroid, normal, scaledRadius);
     getLayerPlane(state, p2, centroid, normal, scaledRadius);
-    return Shape.create(name, data, MeshBuilder.getMesh(state), () => props.color, () => 1, () => membraneLabel(data));
+    return Shape.create('Bilayer planes', data, MeshBuilder.getMesh(state), () => props.color, () => 1, () => membraneLabel(data));
 }
 
 function getLayerPlane(state: MeshBuilder.State, p: Vec3, centroid: Vec3, normal: Vec3, radius: number) {
@@ -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(name, 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/cellpack/color/generate.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -46,10 +46,9 @@ export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Valu
             name: 'generate',
             params: {
                 hue, chroma: [30, 80], luminance: [15, 85],
-                clusteringStepCount: 50, minSampleCount: 800, maxCount: 75,
-                minLabel: 'Min', maxLabel: 'Max', valueLabel: (i: number) => `${i + 1}`,
+                clusteringStepCount: 50, minSampleCount: 800, maxCount: 75
             }
-        }});
+        }}, { minLabel: 'Min', maxLabel: 'Max' });
         legend = palette.legend;
         const modelColor = new Map<number, Color>();
         for (let i = 0, il = models.length; i < il; ++i) {
@@ -89,7 +88,6 @@ export const CellPackGenerateColorThemeProvider: ColorTheme.Provider<CellPackGen
     isApplicable: (ctx: ThemeDataContext) => {
         return (
             !!ctx.structure && ctx.structure.elementCount > 0 &&
-            Model.TrajectoryInfo.get(ctx.structure.models[0]).size > 1 &&
             !!CellPackInfoProvider.get(ctx.structure).value
         );
     }

src/extensions/cellpack/color/provided.ts

@@ -9,7 +9,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Color } from '../../../mol-util/color';
 import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
-import { StructureElement, Model } from '../../../mol-model/structure';
+import { StructureElement, Model, Bond } from '../../../mol-model/structure';
 import { Location } from '../../../mol-model/location';
 import { CellPackInfoProvider } from '../property';
 
@@ -37,9 +37,12 @@ export function CellPackProvidedColorTheme(ctx: ThemeDataContext, props: PD.Valu
         }
 
         color = (location: Location): Color => {
-            return StructureElement.Location.is(location)
-                ? modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!
-                : DefaultColor;
+            if (StructureElement.Location.is(location)) {
+                return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
+            } else if (Bond.isLocation(location)) {
+                return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).index)!;
+            }
+            return DefaultColor;
         };
     } else {
         color = () => DefaultColor;

src/extensions/cellpack/model.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -396,21 +396,25 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
         }
 
         if (ctx.shouldUpdate) await ctx.update(`${name} - units`);
-        const builder = Structure.Builder({ label: name });
+        const units: Unit[] = [];
         let offsetInvariantId = 0;
+        let offsetChainGroupId = 0;
         for (const s of structures) {
             if (ctx.shouldUpdate) await ctx.update(`${s.label}`);
             let maxInvariantId = 0;
+            let maxChainGroupId = 0;
             for (const u of s.units) {
                 const invariantId = u.invariantId + offsetInvariantId;
+                const chainGroupId = u.chainGroupId + offsetChainGroupId;
                 if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
-                builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+                units.push(Unit.create(units.length, invariantId, chainGroupId, u.traits, u.kind, u.model, u.conformation.operator, u.elements, u.props));
             }
             offsetInvariantId += maxInvariantId + 1;
+            offsetChainGroupId += maxChainGroupId + 1;
         }
 
         if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
-        const structure = builder.getStructure();
+        const structure = new Structure(units);
         for( let i = 0, il = structure.models.length; i < il; ++i) {
             Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
         }
@@ -442,9 +446,9 @@ async function handleHivRna(plugin: PluginContext, packings: CellPacking[], base
 
 async function loadMembrane(plugin: PluginContext, name: string, state: State, params: LoadCellPackModelParams) {
     let file: Asset.File | undefined = undefined;
-    if (params.ingredients.files !== null) {
+    if (params.ingredients !== null) {
         const fileName = `${name}.bcif`;
-        for (const f of params.ingredients.files) {
+        for (const f of params.ingredients) {
             if (fileName === f.name) {
                 file = f;
                 break;
@@ -453,7 +457,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
         if (!file){
             // check for cif directly
             const cifileName = `${name}.cif`;
-            for (const f of params.ingredients.files) {
+            for (const f of params.ingredients) {
                 if (cifileName === f.name) {
                     file = f;
                     break;
@@ -488,7 +492,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
 }
 
 async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
-    const ingredientFiles = params.ingredients.files || [];
+    const ingredientFiles = params.ingredients || [];
 
     let cellPackJson: StateBuilder.To<PSO.Format.Json, StateTransformer<PSO.Data.String, PSO.Format.Json>>;
     if (params.source.name === 'id') {
@@ -563,9 +567,7 @@ const LoadCellPackModelParams = {
     }, { options: [['id', 'Id'], ['file', 'File']] }),
     baseUrl: PD.Text(DefaultCellPackBaseUrl),
     membrane: PD.Boolean(true),
-    ingredients : PD.Group({
-        files: PD.FileList({ accept: '.cif,.bcif,.pdb' })
-    }, { isExpanded: true }),
+    ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredients' }),
     preset: PD.Group({
         traceOnly: PD.Boolean(false),
         representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))

src/extensions/cellpack/state.ts

@@ -125,7 +125,7 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
                     const s = await StructureSymmetry.buildAssembly(initial_structure, a.id).runInContext(ctx);
                     structures.push(s);
                 }
-                const builder = Structure.Builder({ label: name });
+                const builder = Structure.Builder();
                 let offsetInvariantId = 0;
                 for (const s of structures) {
                     let maxInvariantId = 0;

src/extensions/dnatco/confal-pyramids/representation.ts

@@ -55,7 +55,7 @@ function createConfalPyramidsIterator(structureGroup: StructureGroup): LocationI
 
     const prop = ConfalPyramidsProvider.get(structure.model).value;
     if (prop === undefined || prop.data === undefined) {
-        return LocationIterator(0, 1, () => NullLocation);
+        return LocationIterator(0, 1, 1, () => NullLocation);
     }
 
     const { locations } = prop.data;
@@ -64,7 +64,7 @@ function createConfalPyramidsIterator(structureGroup: StructureGroup): LocationI
         if (locations.length <= groupIndex) return NullLocation;
         return locations[groupIndex];
     };
-    return LocationIterator(locations.length, instanceCount, getLocation);
+    return LocationIterator(locations.length, instanceCount, 1, getLocation);
 }
 
 function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ConfalPyramidsMeshParams>, mesh?: Mesh) {

src/extensions/g3d/data.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import msgpackDecode from '../../mol-io/common/msgpack/decode';
+import { decodeMsgPack } from '../../mol-io/common/msgpack/decode';
 import { PluginContext } from '../../mol-plugin/context';
 import { Task } from '../../mol-task';
 import { inflate } from '../../mol-util/zip/zip';
@@ -41,7 +41,7 @@ export async function getG3dHeader(ctx: PluginContext, urlOrData: string | Uint8
     for (; last >= 0; last--) {
         if (data[last] !== 0) break;
     }
-    const header = msgpackDecode(data.slice(0, last + 1));
+    const header = decodeMsgPack(data.slice(0, last + 1));
     return header;
 }
 
@@ -53,7 +53,7 @@ export async function getG3dDataBlock(ctx: PluginContext, header: G3dHeader, url
     return {
         header,
         resolution,
-        data: msgpackDecode(unzipped)
+        data: decodeMsgPack(unzipped)
     };
 }
 

src/extensions/g3d/model.ts

@@ -16,7 +16,7 @@ import { MoleculeType } from '../../mol-model/structure/model/types';
 import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { CustomPropSymbol } from '../../mol-script/language/symbol';
-import Type from '../../mol-script/language/type';
+import { Type } from '../../mol-script/language/type';
 import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
 import { RuntimeContext, Task } from '../../mol-task';
 import { objectForEach } from '../../mol-util/object';
@@ -142,7 +142,7 @@ async function getTraj(ctx: RuntimeContext, data: G3dDataBlock) {
         entity: entityBuilder.getEntityTable(),
         ihm_model_list: Table.ofPartialColumns(BasicSchema.ihm_model_list, {
             model_id: Column.ofIntArray([1]),
-            model_name: Column.ofStringArray(['3DG Model']),
+            model_name: Column.ofStringArray(['G3D Model']),
         }, 1),
         ihm_sphere_obj_site
     });
@@ -153,7 +153,8 @@ async function getTraj(ctx: RuntimeContext, data: G3dDataBlock) {
         haplotypes: Object.keys(data.data),
         haplotype: normalized.haplotype,
         resolution: data.resolution,
-        start: normalized.start
+        start: normalized.start,
+        chroms: normalized.chromosome,
     });
 
     return models;
@@ -174,6 +175,22 @@ export const G3dSymbols = {
             const seqId = ctx.element.unit.model.coarseHierarchy.spheres.seq_id_begin.value(ctx.element.element);
             return info.haplotype[seqId] || '';
         }
+    ),
+    chromosome: QuerySymbolRuntime.Dynamic(CustomPropSymbol('g3d', 'chromosome', Type.Str),
+        ctx => {
+            if (Unit.isAtomic(ctx.element.unit)) return '';
+            const { asym_id } = ctx.element.unit.model.coarseHierarchy.spheres;
+            return asym_id.value(ctx.element.element) || '';
+        }
+    ),
+    region: QuerySymbolRuntime.Dynamic(CustomPropSymbol('g3d', 'region', Type.Num),
+        ctx => {
+            if (Unit.isAtomic(ctx.element.unit)) return '';
+            const info = (G3dInfoDataProperty as any).get(ctx.element.unit.model);
+            if (!info) return 0;
+            const seqId = ctx.element.unit.model.coarseHierarchy.spheres.seq_id_begin.value(ctx.element.element);
+            return info.start[seqId] || 0;
+        }
     )
 };
 
@@ -185,11 +202,31 @@ export function g3dHaplotypeQuery(haplotype: string) {
     });
 }
 
+export function g3dChromosomeQuery(chr: string) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.logic.and([
+            MS.core.rel.eq([MS.ammp('objectPrimitive'), 'sphere']),
+            MS.core.rel.eq([G3dSymbols.chromosome.symbol(), chr])
+        ])
+    });
+}
+
+export function g3dRegionQuery(chr: string, start: number, end: number) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.logic.and([
+            MS.core.rel.eq([MS.ammp('objectPrimitive'), 'sphere']),
+            MS.core.rel.eq([G3dSymbols.chromosome.symbol(), chr])
+        ]),
+        'residue-test': MS.core.rel.inRange([G3dSymbols.region.symbol(), start, end])
+    });
+}
+
 export interface G3dInfoData {
     haplotypes: string[],
     haplotype: string[],
     start: Int32Array,
-    resolution: number
+    resolution: number,
+    chroms: string[]
 };
 
 export const G3dLabelProvider: LociLabelProvider = {

src/extensions/mp4-export/controls.ts

@@ -0,0 +1,144 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { debounceTime } from 'rxjs/operators';
+import { PluginStateAnimation } from '../../mol-plugin-state/animation/model';
+import { PluginComponent } from '../../mol-plugin-state/component';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { encodeMp4Animation } from './encoder';
+
+export interface Mp4AnimationInfo {
+    width: number,
+    height: number
+}
+
+export const Mp4AnimationParams = {
+    quantization: PD.Numeric(18, { min: 10, max: 51 }, { description: 'Lower is better, but slower.' })
+};
+
+export class Mp4Controls extends PluginComponent {
+    private currentNames = new Set<string>();
+    private animations: PluginStateAnimation[] = [];
+
+    readonly behaviors = {
+        animations: this.ev.behavior<PD.Params>({ }),
+        current: this.ev.behavior<{ anim: PluginStateAnimation, params: PD.Params, values: any } | undefined>(void 0),
+        canApply: this.ev.behavior<PluginStateAnimation.CanApply>({ canApply: false }),
+        info: this.ev.behavior<Mp4AnimationInfo>({ width: 0, height: 0 }),
+        params: this.ev.behavior<PD.Values<typeof Mp4AnimationParams>>(PD.getDefaultValues(Mp4AnimationParams))
+    }
+
+    setCurrent(name?: string) {
+        const anim = this.animations.find(a => a.name === name);
+        if (!anim) {
+            this.behaviors.current.next(anim);
+            return;
+        }
+
+        const params = anim.params(this.plugin) as PD.Params;
+        const values = PD.getDefaultValues(params);
+
+        this.behaviors.current.next({ anim, params, values });
+        this.behaviors.canApply.next(anim.canApply?.(this.plugin) ?? { canApply: true });
+    }
+
+    setCurrentParams(values: any) {
+        this.behaviors.current.next({ ...this.behaviors.current.value!, values });
+    }
+
+    get current() {
+        return this.behaviors.current.value;
+    }
+
+    render() {
+        const task = Task.create('Export Animation', async ctx => {
+            try {
+                const resolution = this.plugin.helpers.viewportScreenshot?.getSizeAndViewport()!;
+                const anim = this.current!;
+                const movie = await encodeMp4Animation(this.plugin, ctx, {
+                    animation: {
+                        definition: anim.anim,
+                        params: anim.values,
+                    },
+                    ...resolution,
+                    quantizationParameter: this.behaviors.params.value.quantization,
+                    pass: this.plugin.helpers.viewportScreenshot?.imagePass!,
+                });
+
+                const filename = anim.anim.display.name.toLowerCase().replace(/\s/g, '-').replace(/[^a-z0-9_\-]/g, '');
+                return { movie, filename: `${this.plugin.helpers.viewportScreenshot?.getFilename('')}_${filename}.mp4` };
+            } catch (e) {
+                this.plugin.log.error('' + e);
+                throw e;
+            }
+        });
+
+        return this.plugin.runTask(task, { useOverlay: true });
+    }
+
+    private get manager() {
+        return this.plugin.managers.animation;
+    }
+
+    private syncInfo() {
+        const helper = this.plugin.helpers.viewportScreenshot;
+        const size = helper?.getSizeAndViewport();
+        if (!size) return;
+
+        this.behaviors.info.next({ width: size.viewport.width, height: size.viewport.height });
+    }
+
+    private sync() {
+        const animations = this.manager.animations.filter(a => a.isExportable);
+
+        const hasAll = animations.every(a => this.currentNames.has(a.name));
+        if (hasAll && this.currentNames.size === animations.length) {
+            return;
+        }
+
+        const params = {
+            current: PD.Select(animations[0]?.name,
+                animations.map(a => [a.name, a.display.name] as [string, string]),
+                { label: 'Animation' })
+        };
+
+        const current = this.behaviors.current.value;
+        const hasCurrent = !!animations.find(a => a.name === current?.anim.name);
+
+        this.animations = animations;
+        if (!hasCurrent) {
+            this.setCurrent(animations[0]?.name);
+        }
+        this.behaviors.animations.next(params);
+    }
+
+    private init() {
+        this.subscribe(this.plugin.managers.animation.events.updated.pipe(debounceTime(16)), () => {
+            this.sync();
+        });
+
+        this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
+        this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
+
+        this.subscribe(this.plugin.behaviors.state.isBusy, b => {
+            const anim = this.current;
+            if (!b && anim) {
+                this.behaviors.canApply.next(anim.anim.canApply?.(this.plugin) ?? { canApply: true });
+            }
+        });
+
+        this.sync();
+        this.syncInfo();
+    }
+
+    constructor(private plugin: PluginContext) {
+        super();
+
+        this.init();
+    }
+}

src/extensions/mp4-export/encoder.ts

@@ -0,0 +1,105 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as HME from 'h264-mp4-encoder';
+import { Viewport } from '../../mol-canvas3d/camera/util';
+import { ImagePass } from '../../mol-canvas3d/passes/image';
+import { PluginStateAnimation } from '../../mol-plugin-state/animation/model';
+import { PluginContext } from '../../mol-plugin/context';
+import { RuntimeContext } from '../../mol-task';
+import { Color } from '../../mol-util/color';
+
+export interface Mp4EncoderParams<A extends PluginStateAnimation = PluginStateAnimation> {
+    pass: ImagePass,
+    customBackground?: Color,
+    animation: PluginStateAnimation.Instance<A>,
+    width: number,
+    height: number,
+    viewport: Viewport,
+    /** default is 30 */
+    fps?: number,
+    /** Number from 10 (best quality, slowest) to 51 (worst, fastest) */
+    quantizationParameter?: number
+}
+
+export async function encodeMp4Animation<A extends PluginStateAnimation>(plugin: PluginContext, ctx: RuntimeContext, params: Mp4EncoderParams<A>) {
+    await ctx.update({ message: 'Initializing...', isIndeterminate: true });
+
+    validateViewport(params);
+    const durationMs = PluginStateAnimation.getDuration(plugin, params.animation);
+    if (durationMs === void 0) {
+        throw new Error('The animation does not have the duration specified.');
+    }
+
+    const encoder = await HME.createH264MP4Encoder();
+
+    const { width, height } = params;
+    let vw = params.viewport.width, vh = params.viewport.height;
+
+    // dimensions must be a multiple of 2
+    if (vw % 2 !== 0) vw -= 1;
+    if (vh % 2 !== 0) vh -= 1;
+
+    const normalizedViewport: Viewport = { ...params.viewport, width: vw, height: vh };
+
+    encoder.width = vw;
+    encoder.height = vh;
+    if (params.quantizationParameter) encoder.quantizationParameter = params.quantizationParameter;
+    if (params.fps) encoder.frameRate = params.fps;
+    encoder.initialize();
+
+    const loop = plugin.animationLoop;
+    const canvasProps = plugin.canvas3d?.props;
+    const wasAnimating = loop.isAnimating;
+    let stoppedAnimation = true, finalized = false;
+
+    try {
+        loop.stop();
+        loop.resetTime(0);
+
+        if (params.customBackground !== void 0) {
+            plugin.canvas3d?.setProps({ renderer: { backgroundColor: params.customBackground }, transparentBackground: false }, true);
+        }
+
+        const fps = encoder.frameRate;
+        const N = Math.ceil(durationMs / 1000 * fps);
+        const dt = durationMs / N;
+
+        await ctx.update({ message: 'Rendering...', isIndeterminate: false, current: 0, max: N + 1 });
+
+        await plugin.managers.animation.play(params.animation.definition, params.animation.params);
+        stoppedAnimation = false;
+        for (let i = 0; i <= N; i++) {
+            await loop.tick(i * dt, { isSynchronous: true, manualDraw: true });
+
+            const image = params.pass.getImageData(width, height, normalizedViewport);
+            encoder.addFrameRgba(image.data);
+
+            if (ctx.shouldUpdate) {
+                await ctx.update({ current: i + 1 });
+            }
+        }
+        await ctx.update({ message: 'Applying finishing touches...', isIndeterminate: true });
+        await plugin.managers.animation.stop();
+        stoppedAnimation = true;
+        encoder.finalize();
+        finalized = true;
+        return encoder.FS.readFile(encoder.outputFilename);
+    } finally {
+        if (finalized) encoder.delete();
+        if (params.customBackground !== void 0) {
+            plugin.canvas3d?.setProps({ renderer: { backgroundColor: canvasProps?.renderer!.backgroundColor }, transparentBackground: canvasProps?.transparentBackground });
+        }
+        if (!stoppedAnimation) await plugin.managers.animation.stop();
+        if (wasAnimating) loop.start();
+    }
+}
+
+function validateViewport(params: Mp4EncoderParams) {
+    if (params.viewport.x + params.viewport.width > params.width || params.viewport.y + params.viewport.height > params.height) {
+        throw new Error('Viewport exceeds the canvas dimensions.');
+    }
+}

src/extensions/mp4-export/index.ts

@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { Mp4EncoderUI } from './ui';
+
+export const Mp4Export = PluginBehavior.create<{ }>({
+    name: 'extension-mp4-export',
+    category: 'misc',
+    display: {
+        name: 'MP4 Animation Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.customStructureControls.set('mp4-export', Mp4EncoderUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customStructureControls.delete('mp4-export');
+        }
+    },
+    params: () => ({ })
+});

src/extensions/mp4-export/ui.tsx

@@ -0,0 +1,123 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import React from 'react';
+import { merge } from 'rxjs';
+import { debounceTime } from 'rxjs/operators';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { CameraOutlinedSvg, GetAppSvg, Icon, SubscriptionsOutlinedSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { download } from '../../mol-util/download';
+import { Mp4AnimationParams, Mp4Controls } from './controls';
+
+interface State {
+    busy?: boolean,
+    data?: { movie: Uint8Array, filename: string };
+}
+
+export class Mp4EncoderUI extends CollapsableControls<{}, State> {
+    private _controls: Mp4Controls | undefined;
+
+    get controls() {
+        return this._controls || (this._controls = new Mp4Controls(this.plugin));
+    }
+
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Export Animation',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: SubscriptionsOutlinedSvg }
+        };
+    }
+
+    private downloadControls() {
+        return <>
+            <div className='msp-control-offset msp-help-text'>
+                <div className='msp-help-description' style={{ textAlign: 'center' }}>
+                    Rendering successful!
+                </div>
+            </div>
+            <Button icon={GetAppSvg} onClick={this.save} style={{ marginTop: 1 }}>Save Animation</Button>
+            <Button onClick={() => this.setState({ data: void 0 })} style={{ marginTop: 6 }}>Clear</Button>
+        </>;
+    }
+
+    protected renderControls(): JSX.Element | null {
+        if (this.state.data) {
+            return this.downloadControls();
+        }
+
+        const ctrl = this.controls;
+        const current = ctrl.behaviors.current.value;
+        const info = ctrl.behaviors.info.value;
+        const canApply = ctrl.behaviors.canApply.value;
+        return <>
+            <ParameterControls
+                params={ctrl.behaviors.animations.value}
+                values={{ current: current?.anim.name }}
+                onChangeValues={xs => ctrl.setCurrent(xs.current)}
+                isDisabled={this.state.busy}
+            />
+            {current && <ParameterControls
+                params={current.params}
+                values={current.values}
+                onChangeValues={xs => ctrl.setCurrentParams(xs)}
+                isDisabled={this.state.busy}
+            />}
+            <div className='msp-control-offset msp-help-text'>
+                <div className='msp-help-description' style={{ textAlign: 'center' }}>
+                    Resolution: {info.width}x{info.height}<br />
+                    Adjust in viewport using <Icon svg={CameraOutlinedSvg} inline />
+                </div>
+            </div>
+            <ParameterControls
+                params={Mp4AnimationParams}
+                values={ctrl.behaviors.params.value}
+                onChangeValues={xs => ctrl.behaviors.params.next(xs)}
+                isDisabled={this.state.busy}
+            />
+            <Button onClick={this.generate} style={{ marginTop: 1 }}
+                disabled={this.state.busy || !canApply.canApply}
+                commit={canApply.canApply ? 'on' : 'off'}>
+                {canApply.canApply ? 'Render' : canApply.reason ?? 'Invalid params/state'}
+            </Button>
+        </>;
+    }
+
+    componentDidMount() {
+        const merged = merge(
+            this.controls.behaviors.animations,
+            this.controls.behaviors.current,
+            this.controls.behaviors.canApply,
+            this.controls.behaviors.info,
+            this.controls.behaviors.params
+        );
+
+        this.subscribe(merged.pipe(debounceTime(10)), () => {
+            if (!this.state.isCollapsed) this.forceUpdate();
+        });
+    }
+
+    componentWillUnmount() {
+        this._controls?.dispose();
+        this._controls = void 0;
+    }
+
+    save = () => {
+        download(new Blob([this.state.data!.movie]), this.state.data!.filename);
+    }
+
+    generate = async () => {
+        try {
+            this.setState({ busy: true });
+            const data = await this.controls.render();
+            this.setState({ busy: false, data });
+        } catch {
+            this.setState({ busy: false });
+        }
+    }
+}

src/extensions/pdbe/structure-quality-report/color.ts

@@ -6,7 +6,7 @@
 
 import { StructureQualityReport, StructureQualityReportProvider } from './prop';
 import { Location } from '../../../mol-model/location';
-import { StructureElement } from '../../../mol-model/structure';
+import { Bond, StructureElement } from '../../../mol-model/structure';
 import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ThemeDataContext } from '../../../mol-theme/theme';
 import { Color } from '../../../mol-util/color';
@@ -46,11 +46,16 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
 
     if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(StructureQualityReportProvider.descriptor)) {
         const getIssues = StructureQualityReport.getIssues;
+        const l = StructureElement.Location.create(ctx.structure);
 
         if (props.type.name === 'issue-count') {
             color = (location: Location) => {
                 if (StructureElement.Location.is(location)) {
                     return ValidationColors[Math.min(3, getIssues(location).length) + 1];
+                } else if (Bond.isLocation(location)) {
+                    l.unit = location.aUnit;
+                    l.element = location.aUnit.elements[location.aIndex];
+                    return ValidationColors[Math.min(3, getIssues(l).length) + 1];
                 }
                 return ValidationColors[0];
             };
@@ -59,6 +64,10 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
             color = (location: Location) => {
                 if (StructureElement.Location.is(location) && getIssues(location).indexOf(issue) >= 0) {
                     return ValidationColors[4];
+                } else if (Bond.isLocation(location)) {
+                    l.unit = location.aUnit;
+                    l.element = location.aUnit.elements[location.aIndex];
+                    return ValidationColors[Math.min(3, getIssues(l).length) + 1];
                 }
                 return ValidationColors[0];
             };

src/extensions/pdbe/structure-quality-report/prop.ts

@@ -13,7 +13,7 @@ import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-m
 import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
 import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
-import Type from '../../../mol-script/language/type';
+import { Type } from '../../../mol-script/language/type';
 import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { arraySetAdd } from '../../../mol-util/array';

src/extensions/rcsb/assembly-symmetry/color.ts

@@ -9,7 +9,7 @@ import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { AssemblySymmetryProvider, AssemblySymmetry } from './prop';
 import { Color } from '../../../mol-util/color';
-import { Unit, StructureElement, StructureProperties } from '../../../mol-model/structure';
+import { Unit, StructureElement, StructureProperties, Bond } from '../../../mol-model/structure';
 import { Location } from '../../../mol-model/location';
 import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
 import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
@@ -50,6 +50,8 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
     const clusters = assemblySymmetry?.value?.clusters;
 
     if (clusters?.length && ctx.structure) {
+        const l = StructureElement.Location.create(ctx.structure);
+
         const clusterByMember = new Map<string, number>();
         for (let i = 0, il = clusters.length; i < il; ++i) {
             const { members } = clusters[i]!;
@@ -67,12 +69,20 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
         legend = palette.legend;
 
         const _emptyList: any[] = [];
+        const getColor = (location: StructureElement.Location) => {
+            const { assembly } = location.unit.conformation.operator;
+            const asymId = getAsymId(location.unit)(location);
+            const cluster = clusterByMember.get(clusterMemberKey(asymId, assembly?.operList || _emptyList));
+            return cluster !== undefined ? palette.color(cluster) : DefaultColor;
+        };
+
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location)) {
-                const { assembly } = location.unit.conformation.operator;
-                const asymId = getAsymId(location.unit)(location);
-                const cluster = clusterByMember.get(clusterMemberKey(asymId, assembly?.operList || _emptyList));
-                return cluster !== undefined ? palette.color(cluster) : DefaultColor;
+                return getColor(location);
+            } else if (Bond.isLocation(location)) {
+                l.unit = location.aUnit;
+                l.element = location.aUnit.elements[location.aIndex];
+                return getColor(l);
             }
             return DefaultColor;
         };

src/extensions/rcsb/assembly-symmetry/prop.ts

@@ -5,7 +5,7 @@
  */
 
 import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphql/types';
-import query from '../graphql/symmetry.gql';
+import { symmetry_gql } from '../graphql/symmetry.gql';
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
@@ -66,7 +66,7 @@ export namespace AssemblySymmetry {
             assembly_id: structure.units[0].conformation.operator.assembly?.id || '',
             entry_id: structure.units[0].model.entryId
         };
-        const result = await client.request(ctx.runtime, query, variables);
+        const result = await client.request(ctx.runtime, symmetry_gql, variables);
         let value: AssemblySymmetryDataValue = [];
 
         if (!result.data.assembly?.rcsb_struct_symmetry) {

src/extensions/rcsb/graphql/symmetry.gql.ts

@@ -1,4 +1,4 @@
-export default /* GraphQL */ `
+export const symmetry_gql = /* GraphQL */ `
 query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
     assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
         rcsb_struct_symmetry {

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -8,7 +8,7 @@ import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Color, ColorScale } from '../../../../mol-util/color';
-import { StructureElement, Model } from '../../../../mol-model/structure';
+import { StructureElement, Model, ElementIndex, Bond } from '../../../../mol-model/structure';
 import { Location } from '../../../../mol-model/location';
 import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
 import { ValidationReportProvider, ValidationReport } from '../prop';
@@ -37,13 +37,19 @@ export function DensityFitColorTheme(ctx: ThemeDataContext, props: {}): ColorThe
     if (validationReport?.value && model) {
         const { rsrz, rscc } = validationReport.value;
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        const getColor = (element: ElementIndex) => {
+            const rsrzValue = rsrz.get(residueIndex[element]);
+            if (rsrzValue !== undefined) return scaleRsrz.color(rsrzValue);
+            const rsccValue = rscc.get(residueIndex[element]);
+            if (rsccValue !== undefined) return scaleRscc.color(rsccValue);
+            return DefaultColor;
+        };
+
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location) && location.unit.model === model) {
-                const rsrzValue = rsrz.get(residueIndex[location.element]);
-                if (rsrzValue !== undefined) return scaleRsrz.color(rsrzValue);
-                const rsccValue = rscc.get(residueIndex[location.element]);
-                if (rsccValue !== undefined) return scaleRscc.color(rsccValue);
-                return DefaultColor;
+                return getColor(location.element);
+            } else if (Bond.isLocation(location) && location.aUnit.model === model) {
+                return getColor(location.aUnit.elements[location.aIndex]);
             }
             return DefaultColor;
         };

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

@@ -8,7 +8,7 @@ import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Color } from '../../../../mol-util/color';
-import { StructureElement } from '../../../../mol-model/structure';
+import { Bond, ElementIndex, StructureElement } from '../../../../mol-model/structure';
 import { Location } from '../../../../mol-model/location';
 import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
 import { ValidationReportProvider, ValidationReport } from '../prop';
@@ -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;
@@ -59,31 +59,35 @@ export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Value
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
         const { polymerType } = model.atomicHierarchy.derived.residue;
         const ignore = new Set(props.ignore);
+        const getColor = (element: ElementIndex) => {
+            const rI = residueIndex[element];
+
+            const value = geometryIssues.get(rI);
+            if (value === undefined) return DefaultColor;
+
+            let count = SetUtils.differenceSize(value, ignore);
+
+            if (count > 0 && polymerType[rI] === PolymerType.NA) {
+                count = 0;
+                if (!ignore.has('clash') && clashes.getVertexEdgeCount(element) > 0) count += 1;
+                if (!ignore.has('mog-bond-outlier') && bondOutliers.index.has(element)) count += 1;
+                if (!ignore.has('mog-angle-outlier') && angleOutliers.index.has(element)) count += 1;
+            }
+
+            switch (count) {
+                case undefined: return DefaultColor;
+                case 0: return NoIssuesColor;
+                case 1: return OneIssueColor;
+                case 2: return TwoIssuesColor;
+                default: return ThreeOrMoreIssuesColor;
+            }
+        };
 
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location) && location.unit.model === model) {
-                const { element } = location;
-                const rI = residueIndex[element];
-
-                const value = geometryIssues.get(rI);
-                if (value === undefined) return DefaultColor;
-
-                let count = SetUtils.differenceSize(value, ignore);
-
-                if (count > 0 && polymerType[rI] === PolymerType.NA) {
-                    count = 0;
-                    if (!ignore.has('clash') && clashes.getVertexEdgeCount(element) > 0) count += 1;
-                    if (!ignore.has('mog-bond-outlier') && bondOutliers.index.has(element)) count += 1;
-                    if (!ignore.has('mog-angle-outlier') && angleOutliers.index.has(element)) count += 1;
-                }
-
-                switch (count) {
-                    case undefined: return DefaultColor;
-                    case 0: return NoIssuesColor;
-                    case 1: return OneIssueColor;
-                    case 2: return TwoIssuesColor;
-                    default: return ThreeOrMoreIssuesColor;
-                }
+                return getColor(location.element);
+            } else if (Bond.isLocation(location) && location.aUnit.model === model) {
+                return getColor(location.aUnit.elements[location.aIndex]);
             }
             return DefaultColor;
         };

src/extensions/rcsb/validation-report/color/random-coil-index.ts

@@ -8,7 +8,7 @@ import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Color, ColorScale } from '../../../../mol-util/color';
-import { StructureElement, Model } from '../../../../mol-model/structure';
+import { StructureElement, Model, ElementIndex, Bond } from '../../../../mol-model/structure';
 import { Location } from '../../../../mol-model/location';
 import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
 import { ValidationReportProvider, ValidationReport } from '../prop';
@@ -31,10 +31,16 @@ export function RandomCoilIndexColorTheme(ctx: ThemeDataContext, props: {}): Col
 
     if (rci && model) {
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        const getColor = (element: ElementIndex) => {
+            const value = rci.get(residueIndex[element]);
+            return value === undefined ? DefaultColor : scale.color(value);
+        };
+
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location) && location.unit.model === model) {
-                const value = rci.get(residueIndex[location.element]);
-                return value === undefined ? DefaultColor : scale.color(value);
+                return getColor(location.element);
+            } else if (Bond.isLocation(location) && location.aUnit.model === model) {
+                return getColor(location.aUnit.elements[location.aIndex]);
             }
             return DefaultColor;
         };

src/extensions/rcsb/validation-report/prop.ts

@@ -19,7 +19,7 @@ import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
-import Type from '../../../mol-script/language/type';
+import { Type } from '../../../mol-script/language/type';
 import { Asset } from '../../../mol-util/assets';
 import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 

src/extensions/rcsb/validation-report/representation.ts

@@ -143,7 +143,7 @@ function createIntraClashIterator(structureGroup: StructureGroup): LocationItera
         location.element = unit.elements[a[groupIndex]];
         return location;
     };
-    return LocationIterator(groupCount, instanceCount, getLocation);
+    return LocationIterator(groupCount, instanceCount, 1, getLocation);
 }
 
 //
@@ -255,7 +255,7 @@ function createInterClashIterator(structure: Structure): LocationIterator {
         location.element = location.unit.elements[clash.indexA];
         return location;
     };
-    return LocationIterator(groupCount, instanceCount, getLocation, true);
+    return LocationIterator(groupCount, instanceCount, 1, getLocation, true);
 }
 
 //

src/mol-canvas3d/camera.ts

@@ -10,22 +10,37 @@ import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 
-export { Camera };
+export { ICamera, Camera };
 
-class Camera {
+interface ICamera {
+    readonly viewport: Viewport,
+    readonly view: Mat4,
+    readonly projection: Mat4,
+    readonly projectionView: Mat4,
+    readonly inverseProjectionView: Mat4,
+    readonly state: Readonly<Camera.Snapshot>,
+    readonly viewOffset: Camera.ViewOffset,
+    readonly far: number,
+    readonly near: number,
+    readonly fogFar: number,
+    readonly fogNear: number,
+}
+
+class Camera implements ICamera {
     readonly view: Mat4 = Mat4.identity();
     readonly projection: Mat4 = Mat4.identity();
     readonly projectionView: Mat4 = Mat4.identity();
     readonly inverseProjectionView: Mat4 = Mat4.identity();
 
+    private pixelScale: number
+    get pixelRatio () {
+        const dpr = (typeof window !== 'undefined') ? window.devicePixelRatio : 1;
+        return dpr * this.pixelScale;
+    }
+
     readonly viewport: Viewport;
     readonly state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
-    readonly viewOffset: Camera.ViewOffset = {
-        enabled: false,
-        fullWidth: 1, fullHeight: 1,
-        offsetX: 0, offsetY: 0,
-        width: 1, height: 1
-    }
+    readonly viewOffset = Camera.ViewOffset();
 
     near = 1
     far = 10000
@@ -52,6 +67,10 @@ class Camera {
 
     update() {
         const snapshot = this.state as Camera.Snapshot;
+        if (snapshot.radiusMax === 0) {
+            return false;
+        }
+
         const height = 2 * Math.tan(snapshot.fov / 2) * Vec3.distance(snapshot.position, snapshot.target);
         this.zoom = this.viewport.height / height;
 
@@ -86,12 +105,7 @@ class Camera {
     }
 
     getTargetDistance(radius: number) {
-        const r = Math.max(radius, 0.01);
-        const { fov } = this.state;
-        const { width, height } = this.viewport;
-        const aspect = width / height;
-        const aspectFactor = (height < width ? 1 : aspect);
-        return Math.abs((r / aspectFactor) / Math.sin(fov / 2));
+        return Camera.targetDistance(radius, this.state.fov, this.viewport.width, this.viewport.height);
     }
 
     getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot> {
@@ -126,8 +140,9 @@ class Camera {
         return cameraUnproject(out, point, this.viewport, this.inverseProjectionView);
     }
 
-    constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(-1, -1, 1, 1)) {
+    constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(0, 0, 128, 128), props: Partial<{ pixelScale: number }> = {}) {
         this.viewport = viewport;
+        this.pixelScale = props.pixelScale || 1;
         Camera.copySnapshot(this.state, state);
     }
 }
@@ -150,6 +165,15 @@ namespace Camera {
         height: number
     }
 
+    export function ViewOffset(): ViewOffset {
+        return {
+            enabled: false,
+            fullWidth: 1, fullHeight: 1,
+            offsetX: 0, offsetY: 0,
+            width: 1, height: 1
+        };
+    }
+
     export function setViewOffset(out: ViewOffset, fullWidth: number, fullHeight: number, offsetX: number, offsetY: number, width: number, height: number) {
         out.fullWidth = fullWidth;
         out.fullHeight = fullHeight;
@@ -159,6 +183,23 @@ namespace Camera {
         out.height = height;
     }
 
+    export function copyViewOffset(out: ViewOffset, view: ViewOffset) {
+        out.enabled = view.enabled;
+        out.fullWidth = view.fullWidth;
+        out.fullHeight = view.fullHeight;
+        out.offsetX = view.offsetX;
+        out.offsetY = view.offsetY;
+        out.width = view.width;
+        out.height = view.height;
+    }
+
+    export function targetDistance(radius: number, fov: number, width: number, height: number) {
+        const r = Math.max(radius, 0.01);
+        const aspect = width / height;
+        const aspectFactor = (height < width ? 1 : aspect);
+        return Math.abs((r / aspectFactor) / Math.sin(fov / 2));
+    }
+
     export function createDefaultSnapshot(): Snapshot {
         return {
             mode: 'perspective',
@@ -168,8 +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
         };
@@ -211,10 +252,10 @@ namespace Camera {
 function updateOrtho(camera: Camera) {
     const { viewport, zoom, near, far, viewOffset } = camera;
 
-    const fullLeft = -(viewport.width - viewport.x) / 2;
-    const fullRight = (viewport.width - viewport.x) / 2;
-    const fullTop = (viewport.height - viewport.y) / 2;
-    const fullBottom = -(viewport.height - viewport.y) / 2;
+    const fullLeft = -viewport.width / 2;
+    const fullRight = viewport.width / 2;
+    const fullTop = viewport.height / 2;
+    const fullBottom = -viewport.height / 2;
 
     const dx = (fullRight - fullLeft) / (2 * zoom);
     const dy = (fullTop - fullBottom) / (2 * zoom);
@@ -278,12 +319,12 @@ function updateClip(camera: Camera) {
     let far = cameraDistance + normalizedFar;
 
     const fogNearFactor = -(50 - fog) / 50;
-    let fogNear = cameraDistance - (normalizedFar * fogNearFactor);
-    let fogFar = far;
+    const fogNear = cameraDistance - (normalizedFar * fogNearFactor);
+    const fogFar = far;
 
     if (mode === 'perspective') {
         // set at least to 5 to avoid slow sphere impostor rendering
-        near = Math.max(5, near);
+        near = Math.max(Math.min(radiusMax, 5), near);
         far = Math.max(5, far);
     } else {
         near = Math.max(0, near);
@@ -296,7 +337,7 @@ function updateClip(camera: Camera) {
     }
 
     camera.near = near;
-    camera.far = far;
+    camera.far = 2 * far; // avoid precision issues distingushing far objects from background
     camera.fogNear = fogNear;
     camera.fogFar = fogFar;
 }

src/mol-canvas3d/camera/stereo.ts

@@ -0,0 +1,141 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
+ * Adapted from three.js, The MIT License, Copyright © 2010-2020 three.js authors
+ */
+
+import { Mat4 } from '../../mol-math/linear-algebra';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Camera, ICamera } from '../camera';
+import { Viewport } from './util';
+
+export const StereoCameraParams = {
+    eyeSeparation: PD.Numeric(0.064, { min: 0.01, max: 0.5, step: 0.001 }),
+    focus: PD.Numeric(10, { min: 1, max: 100, step: 0.01 }),
+};
+export const DefaultStereoCameraProps = PD.getDefaultValues(StereoCameraParams);
+export type StereoCameraProps = PD.Values<typeof StereoCameraParams>
+
+export { StereoCamera };
+
+class StereoCamera {
+    readonly left: ICamera = new EyeCamera();
+    readonly right: ICamera = new EyeCamera();
+
+    get viewport() {
+        return this.parent.viewport;
+    }
+
+    get viewOffset() {
+        return this.parent.viewOffset;
+    }
+
+    private props: StereoCameraProps
+
+    constructor(private parent: Camera, props: Partial<StereoCameraProps> = {}) {
+        this.props = { ...DefaultStereoCameraProps, ...props };
+    }
+
+    setProps(props: Partial<StereoCameraProps>) {
+        Object.assign(this.props, props);
+    }
+
+    update() {
+        this.parent.update();
+        update(this.parent, this.props, this.left as EyeCamera, this.right as EyeCamera);
+    }
+}
+
+namespace StereoCamera {
+    export function is(camera: Camera | StereoCamera): camera is StereoCamera {
+        return 'left' in camera && 'right' in camera;
+    }
+}
+
+class EyeCamera implements ICamera {
+    viewport = Viewport.create(0, 0, 0, 0);
+    view = Mat4();
+    projection = Mat4();
+    projectionView = Mat4();
+    inverseProjectionView = Mat4();
+    state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
+    viewOffset: Readonly<Camera.ViewOffset> = Camera.ViewOffset();
+    far: number = 0;
+    near: number = 0;
+    fogFar: number = 0;
+    fogNear: number = 0;
+}
+
+const eyeLeft = Mat4.identity(), eyeRight = Mat4.identity();
+
+function update(camera: Camera, props: StereoCameraProps, left: EyeCamera, right: EyeCamera) {
+    // Copy the states
+
+    Viewport.copy(left.viewport, camera.viewport);
+    Mat4.copy(left.view, camera.view);
+    Mat4.copy(left.projection, camera.projection);
+    Camera.copySnapshot(left.state, camera.state);
+    Camera.copyViewOffset(left.viewOffset, camera.viewOffset);
+    left.far = camera.far;
+    left.near = camera.near;
+    left.fogFar = camera.fogFar;
+    left.fogNear = camera.fogNear;
+
+    Viewport.copy(right.viewport, camera.viewport);
+    Mat4.copy(right.view, camera.view);
+    Mat4.copy(right.projection, camera.projection);
+    Camera.copySnapshot(right.state, camera.state);
+    Camera.copyViewOffset(right.viewOffset, camera.viewOffset);
+    right.far = camera.far;
+    right.near = camera.near;
+    right.fogFar = camera.fogFar;
+    right.fogNear = camera.fogNear;
+
+    // update the view offsets
+
+    const w = Math.floor(camera.viewport.width / 2);
+    const aspect = w / camera.viewport.height;
+
+    left.viewport.width = w;
+    right.viewport.x += w;
+    right.viewport.width -= w;
+
+    // update the projection and view matrices
+
+    const eyeSepHalf = props.eyeSeparation / 2;
+    const eyeSepOnProjection = eyeSepHalf * camera.near / props.focus;
+    const ymax = camera.near * Math.tan(camera.state.fov * 0.5);
+    let xmin, xmax;
+
+    // translate xOffset
+
+    eyeLeft[12] = -eyeSepHalf;
+    eyeRight[12] = eyeSepHalf;
+
+    // for left eye
+
+    xmin = -ymax * aspect + eyeSepOnProjection;
+    xmax = ymax * aspect + eyeSepOnProjection;
+
+    left.projection[0] = 2 * camera.near / (xmax - xmin);
+    left.projection[8] = (xmax + xmin) / (xmax - xmin);
+
+    Mat4.mul(left.view, left.view, eyeLeft);
+    Mat4.mul(left.projectionView, left.projection, left.view);
+    Mat4.invert(left.inverseProjectionView, left.projectionView);
+
+    // for right eye
+
+    xmin = -ymax * aspect - eyeSepOnProjection;
+    xmax = ymax * aspect - eyeSepOnProjection;
+
+    right.projection[0] = 2 * camera.near / (xmax - xmin);
+    right.projection[8] = (xmax + xmin) / (xmax - xmin);
+
+    Mat4.mul(right.view, right.view, eyeRight);
+    Mat4.mul(right.projectionView, right.projection, right.view);
+    Mat4.invert(right.inverseProjectionView, right.projectionView);
+}

src/mol-canvas3d/canvas3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -8,44 +8,50 @@
 import { BehaviorSubject, Subscription } from 'rxjs';
 import { now } from '../mol-util/now';
 import { Vec3, Vec2 } from '../mol-math/linear-algebra';
-import InputObserver, { ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
-import Renderer, { RendererStats, RendererParams } from '../mol-gl/renderer';
+import { InputObserver, ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
+import { Renderer, RendererStats, RendererParams } from '../mol-gl/renderer';
 import { GraphicsRenderObject } from '../mol-gl/render-object';
 import { TrackballControls, TrackballControlsParams } from './controls/trackball';
 import { Viewport } from './camera/util';
 import { createContext, WebGLContext, getGLContext } from '../mol-gl/webgl/context';
 import { Representation } from '../mol-repr/representation';
-import Scene from '../mol-gl/scene';
-import { GraphicsRenderVariant } from '../mol-gl/webgl/render-item';
+import { Scene } from '../mol-gl/scene';
 import { PickingId } from '../mol-geo/geometry/picking';
 import { MarkerAction } from '../mol-util/marker-action';
 import { Loci, EmptyLoci, isEmptyLoci } from '../mol-model/loci';
 import { Camera } from './camera';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
-import { BoundingSphereHelper, DebugHelperParams } from './helper/bounding-sphere-helper';
+import { DebugHelperParams } from './helper/bounding-sphere-helper';
 import { SetUtils } from '../mol-util/set';
 import { Canvas3dInteractionHelper } from './helper/interaction-events';
-import { PostprocessingParams, PostprocessingPass } from './passes/postprocessing';
-import { MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
-import { PixelData } from '../mol-util/image';
-import { readTexture } from '../mol-gl/compute/util';
-import { DrawPass } from './passes/draw';
-import { PickPass } from './passes/pick';
+import { PostprocessingParams } from './passes/postprocessing';
+import { MultiSampleHelper, MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
+import { PickData } from './passes/pick';
+import { PickHelper } from './passes/pick';
 import { ImagePass, ImageProps } from './passes/image';
 import { Sphere3D } from '../mol-math/geometry';
 import { isDebugMode } from '../mol-util/debug';
 import { CameraHelperParams } from './helper/camera-helper';
 import { produce } from 'immer';
-import { HandleHelper, HandleHelperParams } from './helper/handle-helper';
+import { HandleHelperParams } from './helper/handle-helper';
+import { StereoCamera, StereoCameraParams } from './camera/stereo';
+import { Helper } from './helper/helper';
+import { Passes } from './passes/passes';
+import { shallowEqual } from '../mol-util';
 
 export const Canvas3DParams = {
     camera: PD.Group({
-        mode: PD.Select('perspective', [['perspective', 'Perspective'], ['orthographic', 'Orthographic']] as const, { label: 'Camera' }),
-        helper: PD.Group(CameraHelperParams, { isFlat: true })
+        mode: PD.Select('perspective', PD.arrayToOptions(['perspective', 'orthographic'] as const), { label: 'Camera' }),
+        helper: PD.Group(CameraHelperParams, { isFlat: true }),
+        stereo: PD.MappedStatic('off', {
+            on: PD.Group(StereoCameraParams),
+            off: PD.Group({})
+        }, { cycle: true, hideIf: p => p?.mode !== 'perspective' }),
+        manualReset: PD.Boolean(false, { isHidden: true }),
     }, { pivot: 'mode' }),
     cameraFog: PD.MappedStatic('on', {
         on: PD.Group({
-            intensity: PD.Numeric(50, { min: 1, max: 100, step: 1 }),
+            intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Show fog in the distance' }),
@@ -53,6 +59,15 @@ export const Canvas3DParams = {
         radius: PD.Numeric(100, { min: 0, max: 99, step: 1 }, { label: 'Clipping', description: 'How much of the scene to show.' }),
         far: PD.Boolean(true, { description: 'Hide scene in the distance' }),
     }, { pivot: 'radius' }),
+    viewport: PD.MappedStatic('canvas', {
+        canvas: PD.Group({}),
+        custom: PD.Group({
+            x: PD.Numeric(0),
+            y: PD.Numeric(0),
+            width: PD.Numeric(128),
+            height: PD.Numeric(128)
+        })
+    }),
 
     cameraResetDurationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time it takes to reset the camera.' }),
     transparentBackground: PD.Boolean(false),
@@ -66,72 +81,57 @@ export const Canvas3DParams = {
 };
 export const DefaultCanvas3DParams = PD.getDefaultValues(Canvas3DParams);
 export type Canvas3DProps = PD.Values<typeof Canvas3DParams>
-export type PartialCanvas3DProps = { [K in keyof Canvas3DProps]?: Partial<Canvas3DProps[K]> }
-
-export { Canvas3D };
-
-interface Canvas3D {
-    readonly webgl: WebGLContext,
-
-    add(repr: Representation.Any): void
-    remove(repr: Representation.Any): void
-    /**
-     * This function must be called if animate() is not set up so that add/remove actions take place.
-     */
-    commit(isSynchronous?: boolean): void
-    update(repr?: Representation.Any, keepBoundingSphere?: boolean): void
-    clear(): void
-    syncVisibility(): void
-
-    requestDraw(force?: boolean): void
-    animate(): void
-    identify(x: number, y: number): PickingId | undefined
-    mark(loci: Representation.Loci, action: MarkerAction): void
-    getLoci(pickingId: PickingId): Representation.Loci
-
-    readonly didDraw: BehaviorSubject<now.Timestamp>
-    readonly reprCount: BehaviorSubject<number>
-
-    handleResize(): void
-    /** Focuses camera on scene's bounding sphere, centered and zoomed. */
-    requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
-    readonly camera: Camera
-    readonly boundingSphere: Readonly<Sphere3D>
-    getPixelData(variant: GraphicsRenderVariant): PixelData
-    setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void)): void
-    getImagePass(props: Partial<ImageProps>): ImagePass
-
-    /** Returns a copy of the current Canvas3D instance props */
-    readonly props: Readonly<Canvas3DProps>
-    readonly input: InputObserver
-    readonly stats: RendererStats
-    readonly interaction: Canvas3dInteractionHelper['events']
-
-    dispose(): void
+export type PartialCanvas3DProps = {
+    [K in keyof Canvas3DProps]?: Canvas3DProps[K] extends { name: string, params: any } ? Canvas3DProps[K] : Partial<Canvas3DProps[K]>
 }
 
-const requestAnimationFrame = typeof window !== 'undefined' ? window.requestAnimationFrame : (f: (time: number) => void) => setImmediate(()=>f(Date.now()));
+export { Canvas3DContext };
 
-namespace Canvas3D {
-    export interface HoverEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys }
-    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 }
+/** Can be used to create multiple Canvas3D objects */
+interface Canvas3DContext {
+    readonly canvas: HTMLCanvasElement
+    readonly webgl: WebGLContext
+    readonly input: InputObserver
+    readonly passes: Passes
+    readonly attribs: Readonly<Canvas3DContext.Attribs>
+    readonly contextLost: BehaviorSubject<now.Timestamp>
+    readonly contextRestored: BehaviorSubject<now.Timestamp>
+    dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => void
+}
 
-    export function fromCanvas(canvas: HTMLCanvasElement, props: Partial<Canvas3DProps> = {}) {
+namespace Canvas3DContext {
+    const DefaultAttribs = {
+        /** true by default to avoid issues with Safari (Jan 2021) */
+        antialias: true,
+        /** true to support multiple Canvas3D objects with a single context */
+        preserveDrawingBuffer: true,
+        pixelScale: 1,
+        pickScale: 0.25,
+        enableWboit: true
+    };
+    export type Attribs = typeof DefaultAttribs
+
+    export function fromCanvas(canvas: HTMLCanvasElement, attribs: Partial<Attribs> = {}): Canvas3DContext {
+        const a = { ...DefaultAttribs, ...attribs };
+        const { antialias, preserveDrawingBuffer, pixelScale } = a;
         const gl = getGLContext(canvas, {
-            alpha: true,
-            antialias: true,
-            depth: true,
-            preserveDrawingBuffer: true,
-            premultipliedAlpha: false,
+            antialias,
+            preserveDrawingBuffer,
+            alpha: true, // the renderer requires an alpha channel
+            depth: true, // the renderer requires a depth buffer
+            premultipliedAlpha: true, // the renderer outputs PMA
         });
         if (gl === null) throw new Error('Could not create a WebGL rendering context');
-        const input = InputObserver.fromElement(canvas);
-        const webgl = createContext(gl);
+
+        const input = InputObserver.fromElement(canvas, { pixelScale });
+        const webgl = createContext(gl, { pixelScale });
+        const passes = new Passes(webgl, attribs);
 
         if (isDebugMode) {
             const loseContextExt = gl.getExtension('WEBGL_lose_context');
             if (loseContextExt) {
+                // Hold down shift+ctrl+alt and press any mouse button to call `loseContext`.
+                // After 1 second `restoreContext` will be called.
                 canvas.addEventListener('mousedown', e => {
                     if (webgl.isContextLost) return;
                     if (!e.shiftKey || !e.ctrlKey || !e.altKey) return;
@@ -150,35 +150,130 @@ namespace Canvas3D {
 
         // https://www.khronos.org/webgl/wiki/HandlingContextLost
 
-        canvas.addEventListener('webglcontextlost', e => {
+        const contextLost = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
+
+        const handleWebglContextLost = (e: Event) => {
             webgl.setContextLost();
             e.preventDefault();
             if (isDebugMode) console.log('context lost');
-        }, false);
+            contextLost.next(now());
+        };
 
-        canvas.addEventListener('webglcontextrestored', () => {
+        const handlewWebglContextRestored = () => {
             if (!webgl.isContextLost) return;
-            webgl.handleContextRestored();
+            webgl.handleContextRestored(() => {
+                passes.draw.reset();
+            });
             if (isDebugMode) console.log('context restored');
-        }, false);
+        };
 
-        return Canvas3D.create(webgl, input, props);
+        canvas.addEventListener('webglcontextlost', handleWebglContextLost, false);
+        canvas.addEventListener('webglcontextrestored', handlewWebglContextRestored, false);
+
+        return {
+            canvas,
+            webgl,
+            input,
+            passes,
+            attribs: a,
+            contextLost,
+            contextRestored: webgl.contextRestored,
+            dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => {
+                input.dispose();
+
+                canvas.removeEventListener('webglcontextlost', handleWebglContextLost, false);
+                canvas.removeEventListener('webglcontextrestored', handlewWebglContextRestored, false);
+                webgl.destroy(options);
+            }
+        };
     }
+}
 
-    export function create(webgl: WebGLContext, input: InputObserver, props: Partial<Canvas3DProps> = {}): Canvas3D {
-        const p = { ...DefaultCanvas3DParams, ...props };
+export { Canvas3D };
+
+interface Canvas3D {
+    readonly webgl: WebGLContext,
+
+    add(repr: Representation.Any): void
+    remove(repr: Representation.Any): void
+    /**
+     * This function must be called if animate() is not set up so that add/remove actions take place.
+     */
+    commit(isSynchronous?: boolean): void
+    /**
+     * Funcion for external "animation" control
+     * Calls commit.
+     */
+    tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean }): void
+    update(repr?: Representation.Any, keepBoundingSphere?: boolean): void
+    clear(): void
+    syncVisibility(): void
+
+    requestDraw(force?: boolean): void
+
+    /** Reset the timers, used by "animate" */
+    resetTime(t: number): void
+    animate(): void
+    pause(): void
+    identify(x: number, y: number): PickData | undefined
+    mark(loci: Representation.Loci, action: MarkerAction): void
+    getLoci(pickingId: PickingId | undefined): Representation.Loci
+
+    notifyDidDraw: boolean,
+    readonly didDraw: BehaviorSubject<now.Timestamp>
+    readonly commited: BehaviorSubject<now.Timestamp>
+    readonly reprCount: BehaviorSubject<number>
+    readonly resized: BehaviorSubject<any>
+
+    handleResize(): void
+    /** performs handleResize on the next animation frame */
+    requestResize(): void
+    /** Focuses camera on scene's bounding sphere, centered and zoomed. */
+    requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
+    readonly camera: Camera
+    readonly boundingSphere: Readonly<Sphere3D>
+    setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void), doNotRequestDraw?: boolean /* = false */): void
+    getImagePass(props: Partial<ImageProps>): ImagePass
+
+    /** Returns a copy of the current Canvas3D instance props */
+    readonly props: Readonly<Canvas3DProps>
+    readonly input: InputObserver
+    readonly stats: RendererStats
+    readonly interaction: Canvas3dInteractionHelper['events']
+
+    dispose(): void
+}
+
+const requestAnimationFrame = typeof window !== 'undefined'
+    ? window.requestAnimationFrame
+    : (f: (time: number) => void) => setImmediate(() => f(Date.now())) as unknown as number;
+const cancelAnimationFrame = typeof window !== 'undefined'
+    ? window.cancelAnimationFrame
+    : (handle: number) => clearImmediate(handle as unknown as NodeJS.Immediate);
+
+namespace Canvas3D {
+    export interface HoverEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
+    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 create({ webgl, input, passes, attribs }: Canvas3DContext, props: Partial<Canvas3DProps> = {}): Canvas3D {
+        const p: Canvas3DProps = { ...DefaultCanvas3DParams, ...props };
 
         const reprRenderObjects = new Map<Representation.Any, Set<GraphicsRenderObject>>();
         const reprUpdatedSubscriptions = new Map<Representation.Any, Subscription>();
         const reprCount = new BehaviorSubject(0);
 
-        const startTime = now();
+        let startTime = now();
         const didDraw = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
+        const commited = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
 
         const { gl, contextRestored } = webgl;
 
-        let width = gl.drawingBufferWidth;
-        let height = gl.drawingBufferHeight;
+        let x = 0;
+        let y = 0;
+        let width = 128;
+        let height = 128;
+        updateViewport();
 
         const scene = Scene.create(webgl);
 
@@ -187,40 +282,41 @@ namespace Canvas3D {
             mode: p.camera.mode,
             fog: p.cameraFog.name === 'on' ? p.cameraFog.params.intensity : 0,
             clipFar: p.cameraClipping.far
-        });
+        }, { x, y, width, height }, { pixelScale: attribs.pixelScale });
+        const stereoCamera = new StereoCamera(camera, p.camera.stereo.params);
 
         const controls = TrackballControls.create(input, camera, p.trackball);
         const renderer = Renderer.create(webgl, p.renderer);
-        const debugHelper = new BoundingSphereHelper(webgl, scene, p.debug);
-        const handleHelper = new HandleHelper(webgl, p.handle);
-        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input);
+        const helper = new Helper(webgl, scene, p);
 
-        const drawPass = new DrawPass(webgl, renderer, scene, camera, debugHelper, handleHelper, {
-            cameraHelper: p.camera.helper
-        });
-        const pickPass = new PickPass(webgl, renderer, scene, camera, handleHelper, 0.5);
-        const postprocessing = new PostprocessingPass(webgl, camera, drawPass, p.postprocessing);
-        const multiSample = new MultiSamplePass(webgl, camera, drawPass, postprocessing, p.multiSample);
+        const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height });
+        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera);
+        const multiSampleHelper = new MultiSampleHelper(passes.multiSample);
 
         let drawPending = false;
         let cameraResetRequested = false;
         let nextCameraResetDuration: number | undefined = void 0;
         let nextCameraResetSnapshot: Partial<Camera.Snapshot> | undefined = void 0;
+        let resizeRequested = false;
 
-        function getLoci(pickingId: PickingId) {
+        let notifyDidDraw = true;
+
+        function getLoci(pickingId: PickingId | undefined) {
             let loci: Loci = EmptyLoci;
             let repr: Representation.Any = Representation.Empty;
-            loci = handleHelper.getLoci(pickingId);
-            reprRenderObjects.forEach((_, _repr) => {
-                const _loci = _repr.getLoci(pickingId);
-                if (!isEmptyLoci(_loci)) {
-                    if (!isEmptyLoci(loci)) {
-                        console.warn('found another loci, this should not happen');
+            if (pickingId) {
+                loci = helper.handle.getLoci(pickingId);
+                reprRenderObjects.forEach((_, _repr) => {
+                    const _loci = _repr.getLoci(pickingId);
+                    if (!isEmptyLoci(_loci)) {
+                        if (!isEmptyLoci(loci)) {
+                            console.warn('found another loci, this should not happen');
+                        }
+                        loci = _loci;
+                        repr = _repr;
                     }
-                    loci = _loci;
-                    repr = _repr;
-                }
-            });
+                });
+            }
             return { loci, repr };
         }
 
@@ -230,36 +326,50 @@ namespace Canvas3D {
             if (repr) {
                 changed = repr.mark(loci, action);
             } else {
-                changed = handleHelper.mark(loci, action);
+                changed = helper.handle.mark(loci, action);
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
             if (changed) {
                 scene.update(void 0, true);
-                handleHelper.scene.update(void 0, true);
-                const prevPickDirty = pickPass.pickDirty;
+                helper.handle.scene.update(void 0, true);
+                const prevPickDirty = pickHelper.dirty;
                 draw(true);
-                pickPass.pickDirty = prevPickDirty; // marking does not change picking buffers
+                pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
             }
         }
 
         function render(force: boolean) {
             if (webgl.isContextLost) return false;
 
+            let resized = false;
+            if (resizeRequested) {
+                handleResize(false);
+                resizeRequested = false;
+                resized = true;
+            }
+
+            if (x > gl.drawingBufferWidth || x + width < 0 ||
+                y > gl.drawingBufferHeight || y + height < 0
+            ) return false;
+
             let didRender = false;
             controls.update(currentTime);
-            Viewport.set(camera.viewport, 0, 0, width, height);
             const cameraChanged = camera.update();
-            multiSample.update(force || cameraChanged, currentTime);
+            const multiSampleChanged = multiSampleHelper.update(force || cameraChanged, p.multiSample);
 
-            if (force || cameraChanged || multiSample.enabled) {
-                renderer.setViewport(0, 0, width, height);
-                if (multiSample.enabled) {
-                    multiSample.render(true, p.transparentBackground);
-                } else {
-                    drawPass.render(!postprocessing.enabled, p.transparentBackground);
-                    if (postprocessing.enabled) postprocessing.render(true);
+            if (resized || force || cameraChanged || multiSampleChanged) {
+                let cam: Camera | StereoCamera = camera;
+                if (p.camera.stereo.name === 'on') {
+                    stereoCamera.update();
+                    cam = stereoCamera;
                 }
-                pickPass.pickDirty = true;
+
+                if (MultiSamplePass.isEnabled(p.multiSample)) {
+                    multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                } else {
+                    passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing);
+                }
+                pickHelper.dirty = true;
                 didRender = true;
             }
 
@@ -271,7 +381,7 @@ namespace Canvas3D {
         let currentTime = 0;
 
         function draw(force?: boolean) {
-            if (render(!!force || forceNextDraw)) {
+            if (render(!!force || forceNextDraw) && notifyDidDraw) {
                 didDraw.next(now() - startTime as now.Timestamp);
             }
             forceNextDraw = false;
@@ -284,20 +394,46 @@ namespace Canvas3D {
             forceNextDraw = !!force;
         }
 
-        function animate() {
-            currentTime = now();
-            commit();
+        let animationFrameHandle = 0;
+
+        function tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean }) {
+            currentTime = t;
+            commit(options?.isSynchronous);
             camera.transition.tick(currentTime);
 
+            if (options?.manualDraw) {
+                return;
+            }
+
             draw(false);
             if (!camera.transition.inTransition && !webgl.isContextLost) {
                 interactionHelper.tick(currentTime);
             }
-            requestAnimationFrame(animate);
         }
 
-        function identify(x: number, y: number): PickingId | undefined {
-            return webgl.isContextLost ? undefined : pickPass.identify(x, y);
+        function _animate() {
+            tick(now());
+            animationFrameHandle = requestAnimationFrame(_animate);
+        }
+
+        function resetTime(t: now.Timestamp) {
+            startTime = t;
+            controls.start(t);
+        }
+
+        function animate() {
+            controls.start(now());
+            if (animationFrameHandle === 0) _animate();
+        }
+
+        function pause() {
+            cancelAnimationFrame(animationFrameHandle);
+            animationFrameHandle = 0;
+        }
+
+        function identify(x: number, y: number): PickData | undefined {
+            const cam = p.camera.stereo.name === 'on' ? stereoCamera : camera;
+            return webgl.isContextLost ? undefined : pickHelper.identify(x, y, cam);
         }
 
         function commit(isSynchronous: boolean = false) {
@@ -306,10 +442,11 @@ namespace Canvas3D {
             if (allCommited) {
                 resolveCameraReset();
                 if (forceDrawAfterAllCommited) {
-                    if (debugHelper.isEnabled) debugHelper.update();
+                    if (helper.debug.isEnabled) helper.debug.update();
                     draw(true);
                     forceDrawAfterAllCommited = false;
                 }
+                commited.next(now());
             }
         }
 
@@ -321,7 +458,7 @@ namespace Canvas3D {
                 const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration;
                 const focus = camera.getFocus(center, radius);
                 const snapshot = nextCameraResetSnapshot ? { ...focus, ...nextCameraResetSnapshot } : focus;
-                camera.setState(snapshot, duration);
+                camera.setState({ ...snapshot, radiusMax: scene.boundingSphere.radius }, duration);
             }
 
             nextCameraResetDuration = void 0;
@@ -348,7 +485,8 @@ 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;
             }
 
@@ -364,8 +502,8 @@ namespace Canvas3D {
 
             if (!scene.commit(isSynchronous ? void 0 : sceneCommitTimeoutMs)) return false;
 
-            if (debugHelper.isEnabled) debugHelper.update();
-            if (reprCount.value === 0 || shouldResetCamera()) {
+            if (helper.debug.isEnabled) helper.debug.update();
+            if (!p.camera.manualReset && (reprCount.value === 0 || shouldResetCamera())) {
                 cameraResetRequested = true;
             }
             if (oldBoundingSphereVisible.radius === 0) nextCameraResetDuration = 0;
@@ -382,7 +520,16 @@ namespace Canvas3D {
                 drawCount: r.values.drawCount.ref.value,
                 instanceCount: r.values.instanceCount.ref.value,
                 materialId: r.materialId,
+                renderItemId: r.id,
             })));
+            console.log(webgl.stats);
+
+            const { texture, attribute, elements } = webgl.resources.getByteCounts();
+            console.log({
+                texture: `${(texture / 1024 / 1024).toFixed(3)} MiB`,
+                attribute: `${(attribute / 1024 / 1024).toFixed(3)} MiB`,
+                elements: `${(elements / 1024 / 1024).toFixed(3)} MiB`,
+            });
         }
 
         function add(repr: Representation.Any) {
@@ -414,7 +561,6 @@ namespace Canvas3D {
             if (renderObjects) {
                 renderObjects.forEach(o => scene.remove(o));
                 reprRenderObjects.delete(repr);
-                scene.update(repr.renderObjects, false, true);
                 forceDrawAfterAllCommited = true;
                 if (isDebugMode) consoleStats();
             }
@@ -444,7 +590,9 @@ namespace Canvas3D {
             return {
                 camera: {
                     mode: camera.state.mode,
-                    helper: { ...drawPass.props.cameraHelper }
+                    helper: { ...helper.camera.props },
+                    stereo: { ...p.camera.stereo },
+                    manualReset: !!p.camera.manualReset
                 },
                 cameraFog: camera.state.fog > 0
                     ? { name: 'on' as const, params: { intensity: camera.state.fog } }
@@ -452,23 +600,36 @@ namespace Canvas3D {
                 cameraClipping: { far: camera.state.clipFar, radius },
                 cameraResetDurationMs: p.cameraResetDurationMs,
                 transparentBackground: p.transparentBackground,
+                viewport: p.viewport,
 
-                postprocessing: { ...postprocessing.props },
-                multiSample: { ...multiSample.props },
+                postprocessing: { ...p.postprocessing },
+                multiSample: { ...p.multiSample },
                 renderer: { ...renderer.props },
                 trackball: { ...controls.props },
-                debug: { ...debugHelper.props },
-                handle: { ...handleHelper.props },
+                debug: { ...helper.debug.props },
+                handle: { ...helper.handle.props },
             };
         }
 
-        handleResize();
-
         const contextRestoredSub = contextRestored.subscribe(() => {
-            pickPass.pickDirty = true;
+            pickHelper.dirty = true;
+            draw(true);
+            // Unclear why, but in Chrome with wboit enabled the first `draw` only clears
+            // the drawingBuffer. Note that in Firefox the drawingBuffer is preserved after
+            // context loss so it is unclear if it behaves the same.
             draw(true);
         });
 
+        const resized = new BehaviorSubject<any>(0);
+
+        function handleResize(draw = true) {
+            passes.updateSize();
+            updateViewport();
+            syncViewport();
+            if (draw) requestDraw(true);
+            resized.next(+new Date());
+        }
+
         return {
             webgl,
 
@@ -489,7 +650,7 @@ namespace Canvas3D {
                 reprUpdatedSubscriptions.clear();
                 reprRenderObjects.clear();
                 scene.clear();
-                debugHelper.clear();
+                helper.debug.clear();
                 requestDraw(true);
                 reprCount.next(reprRenderObjects.size);
             },
@@ -500,19 +661,24 @@ namespace Canvas3D {
                 }
 
                 if (scene.syncVisibility()) {
-                    if (debugHelper.isEnabled) debugHelper.update();
+                    if (helper.debug.isEnabled) helper.debug.update();
                 }
                 requestDraw(true);
             },
 
-            // draw,
             requestDraw,
+            tick,
             animate,
+            resetTime,
+            pause,
             identify,
             mark,
             getLoci,
 
             handleResize,
+            requestResize: () => {
+                resizeRequested = true;
+            },
             requestCameraReset: options => {
                 nextCameraResetDuration = options?.durationMs;
                 nextCameraResetSnapshot = options?.snapshot;
@@ -520,18 +686,13 @@ namespace Canvas3D {
             },
             camera,
             boundingSphere: scene.boundingSphere,
-            getPixelData: (variant: GraphicsRenderVariant) => {
-                switch (variant) {
-                    case 'color': return webgl.getDrawingBufferPixelData();
-                    case 'pickObject': return pickPass.objectPickTarget.getPixelData();
-                    case 'pickInstance': return pickPass.instancePickTarget.getPixelData();
-                    case 'pickGroup': return pickPass.groupPickTarget.getPixelData();
-                    case 'depth': return readTexture(webgl, drawPass.depthTexture) as PixelData;
-                }
-            },
+            get notifyDidDraw() { return notifyDidDraw; },
+            set notifyDidDraw(v: boolean) { notifyDidDraw = v; },
             didDraw,
+            commited,
             reprCount,
-            setProps: (properties) => {
+            resized,
+            setProps: (properties, doNotRequestDraw = false) => {
                 const props: PartialCanvas3DProps = typeof properties === 'function'
                     ? produce(getProps(), properties)
                     : properties;
@@ -558,47 +719,43 @@ namespace Canvas3D {
                 }
                 if (Object.keys(cameraState).length > 0) camera.setState(cameraState);
 
-                if (props.camera?.helper) drawPass.setProps({ cameraHelper: props.camera.helper });
+                if (props.camera?.helper) helper.camera.setProps(props.camera.helper);
+                if (props.camera?.manualReset !== undefined) p.camera.manualReset = props.camera.manualReset;
+                if (props.camera?.stereo !== undefined) Object.assign(p.camera.stereo, props.camera.stereo);
                 if (props.cameraResetDurationMs !== undefined) p.cameraResetDurationMs = props.cameraResetDurationMs;
                 if (props.transparentBackground !== undefined) p.transparentBackground = props.transparentBackground;
+                if (props.viewport !== undefined) {
+                    const doNotUpdate = p.viewport === props.viewport ||
+                        (p.viewport.name === props.viewport.name && shallowEqual(p.viewport.params, props.viewport.params));
 
-                if (props.postprocessing) postprocessing.setProps(props.postprocessing);
-                if (props.multiSample) multiSample.setProps(props.multiSample);
+                    if (!doNotUpdate) {
+                        p.viewport = props.viewport;
+                        updateViewport();
+                        syncViewport();
+                    }
+                }
+
+                if (props.postprocessing) Object.assign(p.postprocessing, props.postprocessing);
+                if (props.multiSample) Object.assign(p.multiSample, props.multiSample);
                 if (props.renderer) renderer.setProps(props.renderer);
                 if (props.trackball) controls.setProps(props.trackball);
-                if (props.debug) debugHelper.setProps(props.debug);
-                if (props.handle) handleHelper.setProps(props.handle);
+                if (props.debug) helper.debug.setProps(props.debug);
+                if (props.handle) helper.handle.setProps(props.handle);
 
-                requestDraw(true);
+                if (cameraState.mode === 'orthographic') {
+                    p.camera.stereo.name = 'off';
+                }
+
+                if (!doNotRequestDraw) {
+                    requestDraw(true);
+                }
             },
             getImagePass: (props: Partial<ImageProps> = {}) => {
-                return new ImagePass(webgl, renderer, scene, camera, debugHelper, handleHelper, props);
+                return new ImagePass(webgl, renderer, scene, camera, helper, passes.draw.wboitEnabled, props);
             },
 
             get props() {
-                const radius = scene.boundingSphere.radius > 0
-                    ? 100 - Math.round((camera.transition.target.radius / scene.boundingSphere.radius) * 100)
-                    : 0;
-
-                return {
-                    camera: {
-                        mode: camera.state.mode,
-                        helper: { ...drawPass.props.cameraHelper }
-                    },
-                    cameraFog: camera.state.fog > 0
-                        ? { name: 'on' as const, params: { intensity: camera.state.fog } }
-                        : { name: 'off' as const, params: {} },
-                    cameraClipping: { far: camera.state.clipFar, radius },
-                    cameraResetDurationMs: p.cameraResetDurationMs,
-                    transparentBackground: p.transparentBackground,
-
-                    postprocessing: { ...postprocessing.props },
-                    multiSample: { ...multiSample.props },
-                    renderer: { ...renderer.props },
-                    trackball: { ...controls.props },
-                    debug: { ...debugHelper.props },
-                    handle: { ...handleHelper.props },
-                };
+                return getProps();
             },
             get input() {
                 return input;
@@ -613,28 +770,32 @@ namespace Canvas3D {
                 contextRestoredSub.unsubscribe();
 
                 scene.clear();
-                debugHelper.clear();
-                input.dispose();
+                helper.debug.clear();
                 controls.dispose();
                 renderer.dispose();
                 interactionHelper.dispose();
             }
         };
 
-        function handleResize() {
-            width = gl.drawingBufferWidth;
-            height = gl.drawingBufferHeight;
+        function updateViewport() {
+            if (p.viewport.name === 'canvas') {
+                x = 0;
+                y = 0;
+                width = gl.drawingBufferWidth;
+                height = gl.drawingBufferHeight;
+            } else {
+                x = p.viewport.params.x * webgl.pixelRatio;
+                y = p.viewport.params.y * webgl.pixelRatio;
+                width = p.viewport.params.width * webgl.pixelRatio;
+                height = p.viewport.params.height * webgl.pixelRatio;
+            }
+        }
 
-            renderer.setViewport(0, 0, width, height);
-            Viewport.set(camera.viewport, 0, 0, width, height);
-            Viewport.set(controls.viewport, 0, 0, width, height);
-
-            drawPass.setSize(width, height);
-            pickPass.setSize(width, height);
-            postprocessing.setSize(width, height);
-            multiSample.setSize(width, height);
-
-            requestDraw(true);
+        function syncViewport() {
+            pickHelper.setViewport(x, y, width, height);
+            renderer.setViewport(x, y, width, height);
+            Viewport.set(camera.viewport, x, y, width, height);
+            Viewport.set(controls.viewport, x, y, width, height);
         }
     }
 }

src/mol-canvas3d/controls/object.ts

@@ -44,9 +44,8 @@ export namespace ObjectControls {
         const height = 2 * Math.tan(camera.state.fov / 2) * dist;
         const zoom = camera.viewport.height / height;
 
-        const dpr = window.devicePixelRatio;
-        panMouseChange[0] *= (1 / zoom) * camera.viewport.width * dpr;
-        panMouseChange[1] *= (1 / zoom) * camera.viewport.height * dpr;
+        panMouseChange[0] *= (1 / zoom) * camera.viewport.width * camera.pixelRatio;
+        panMouseChange[1] *= (1 / zoom) * camera.viewport.height * camera.pixelRatio;
 
         Vec3.cross(panOffset, Vec3.copy(panOffset, eye), camera.up);
         Vec3.setMagnitude(panOffset, panOffset, panMouseChange[0]);

src/mol-canvas3d/controls/trackball.ts

@@ -10,7 +10,7 @@
 
 import { Quat, Vec2, Vec3, EPSILON } from '../../mol-math/linear-algebra';
 import { Viewport } from '../camera/util';
-import InputObserver, { DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
+import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera } from '../camera';
 import { absMax } from '../../mol-math/misc';
@@ -36,8 +36,8 @@ export const DefaultTrackballBindings = {
 export const TrackballControlsParams = {
     noScroll: PD.Boolean(true, { isHidden: true }),
 
-    rotateSpeed: PD.Numeric(3.0, { min: 0.1, max: 10, step: 0.1 }),
-    zoomSpeed: PD.Numeric(6.0, { min: 0.1, max: 10, step: 0.1 }),
+    rotateSpeed: PD.Numeric(5.0, { min: 1, max: 10, step: 1 }),
+    zoomSpeed: PD.Numeric(7.0, { min: 1, max: 15, step: 1 }),
     panSpeed: PD.Numeric(1.0, { min: 0.1, max: 5, step: 0.1 }),
 
     spin: PD.Boolean(false, { description: 'Spin the 3D scene around the x-axis in view space' }),
@@ -60,6 +60,7 @@ interface TrackballControls {
     readonly props: Readonly<TrackballControlsProps>
     setProps: (props: Partial<TrackballControlsProps>) => void
 
+    start: (t: number) => void
     update: (t: number) => void
     reset: () => void
     dispose: () => void
@@ -68,7 +69,7 @@ namespace TrackballControls {
     export function create(input: InputObserver, camera: Camera, props: Partial<TrackballControlsProps> = {}): TrackballControls {
         const p = { ...PD.getDefaultValues(TrackballControlsParams), ...props };
 
-        const viewport = Viewport();
+        const viewport = Viewport.clone(camera.viewport);
 
         let disposed = false;
 
@@ -137,7 +138,8 @@ namespace TrackballControls {
             const dy = _rotCurr[1] - _rotPrev[1];
             Vec3.set(rotMoveDir, dx, dy, 0);
 
-            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed;
+            const aspectRatio = input.width / input.height;
+            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed * input.pixelRatio * aspectRatio;
 
             if (angle) {
                 Vec3.sub(_eye, camera.position, camera.target);
@@ -227,7 +229,7 @@ namespace TrackballControls {
             Vec2.sub(panMouseChange, Vec2.copy(panMouseChange, _panEnd), _panStart);
 
             if (Vec2.squaredMagnitude(panMouseChange)) {
-                const factor = window.devicePixelRatio * p.panSpeed;
+                const factor = input.pixelRatio * p.panSpeed;
                 panMouseChange[0] *= (1 / camera.zoom) * camera.viewport.width * factor;
                 panMouseChange[1] *= (1 / camera.zoom) * camera.viewport.height * factor;
 
@@ -271,11 +273,22 @@ namespace TrackballControls {
             }
         }
 
+        function outsideViewport(x: number, y: number) {
+            x *= input.pixelRatio;
+            y *= input.pixelRatio;
+            return (
+                x > viewport.x + viewport.width ||
+                input.height - y > viewport.y + viewport.height ||
+                x < viewport.x ||
+                input.height - y < viewport.y
+            );
+        }
+
         let lastUpdated = -1;
         /** Update the object's position, direction and up vectors */
         function update(t: number) {
             if (lastUpdated === t) return;
-            if (p.spin) spin(t - lastUpdated);
+            if (p.spin && lastUpdated > 0) spin(t - lastUpdated);
 
             Vec3.sub(_eye, camera.position, camera.target);
 
@@ -307,7 +320,12 @@ namespace TrackballControls {
 
         // listeners
 
-        function onDrag({ pageX, pageY, buttons, modifiers, isStart }: DragInput) {
+        function onDrag({ x, y, pageX, pageY, buttons, modifiers, isStart }: DragInput) {
+            const isOutside = outsideViewport(x, y);
+
+            if (isStart && isOutside) return;
+            if (!isStart && !_isInteracting) return;
+
             _isInteracting = true;
 
             const dragRotate = Binding.match(p.bindings.dragRotate, buttons, modifiers);
@@ -358,7 +376,9 @@ namespace TrackballControls {
             _isInteracting = false;
         }
 
-        function onWheel({ dx, dy, dz, buttons, modifiers }: WheelInput) {
+        function onWheel({ x, y, dx, dy, dz, buttons, modifiers }: WheelInput) {
+            if (outsideViewport(x, y)) return;
+
             const delta = absMax(dx, dy, dz);
             if (Binding.match(p.bindings.scrollZoom, buttons, modifiers)) {
                 _zoomEnd[1] += delta * 0.0001;
@@ -387,13 +407,17 @@ namespace TrackballControls {
 
         const _spinSpeed = Vec2.create(0.005, 0);
         function spin(deltaT: number) {
+            if (p.spinSpeed === 0) return;
+
             const frameSpeed = (p.spinSpeed || 0) / 1000;
             _spinSpeed[0] = 60 * Math.min(Math.abs(deltaT), 1000 / 8) / 1000 * frameSpeed;
             if (!_isInteracting) Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
         }
 
-        // force an update at start
-        update(0);
+        function start(t: number) {
+            lastUpdated = -1;
+            update(t);
+        }
 
         return {
             viewport,
@@ -403,6 +427,7 @@ namespace TrackballControls {
                 Object.assign(p, props);
             },
 
+            start,
             update,
             reset,
             dispose

src/mol-canvas3d/helper/bounding-sphere-helper.ts

@@ -9,7 +9,7 @@ import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
 import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import Scene from '../../mol-gl/scene';
+import { Scene } from '../../mol-gl/scene';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Sphere3D } from '../../mol-math/geometry';
 import { Color } from '../../mol-util/color';
@@ -67,6 +67,7 @@ export class BoundingSphereHelper {
                 uInstanceCount: ro.values.uInstanceCount,
                 instanceCount: ro.values.instanceCount,
                 aInstance: ro.values.aInstance,
+                hasReflection: ro.values.hasReflection,
             });
             if (newInstanceData) this.instancesData.set(ro, newInstanceData);
         });
@@ -131,7 +132,7 @@ function updateBoundingSphereData(scene: Scene, boundingSphere: Sphere3D, data:
         const mesh = createBoundingSphereMesh(boundingSphere, data && data.mesh);
         const renderObject = data ? data.renderObject : createBoundingSphereRenderObject(mesh, color, materialId, transform);
         if (data) {
-            ValueCell.update(renderObject.values.drawCount, Geometry.getDrawCount(mesh));
+            ValueCell.updateIfChanged(renderObject.values.drawCount, Geometry.getDrawCount(mesh));
         } else {
             scene.add(renderObject);
         }
@@ -159,5 +160,5 @@ const instanceMaterialId = getNextMaterialId();
 
 function createBoundingSphereRenderObject(mesh: Mesh, color: Color, materialId: number, transform?: TransformData) {
     const values = Mesh.Utils.createValuesSimple(mesh, { alpha: 0.1, doubleSided: false }, color, 1, transform);
-    return createRenderObject('mesh', values, { visible: true, alphaFactor: 1, pickable: false, opaque: false, writeDepth: false }, materialId);
+    return createRenderObject('mesh', values, { disposed: false, visible: true, alphaFactor: 1, pickable: false, colorOnly: false, opaque: false, writeDepth: false, noClip: false }, materialId);
 }

src/mol-canvas3d/helper/camera-helper.ts

@@ -5,8 +5,8 @@
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
-import Scene from '../../mol-gl/scene';
-import { Camera } from '../camera';
+import { Scene } from '../../mol-gl/scene';
+import { Camera, ICamera } from '../camera';
 import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
@@ -15,7 +15,6 @@ import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
 import { ColorNames } from '../../mol-util/color/names';
 import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
 import { Viewport } from '../camera/util';
-import { ValueCell } from '../../mol-util';
 import { Sphere3D } from '../../mol-math/geometry';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import produce from 'immer';
@@ -71,6 +70,7 @@ export class CameraHelper {
                     this.scene.clear();
                     const params = { ...props.axes.params, scale: props.axes.params.scale * this.webgl.pixelRatio };
                     this.renderObject = createAxesRenderObject(params);
+                    this.renderObject.state.noClip = true;
                     this.scene.add(this.renderObject);
                     this.scene.commit();
 
@@ -87,43 +87,47 @@ export class CameraHelper {
         return this.props.axes.name === 'on';
     }
 
-    update(camera: Camera) {
+    update(camera: ICamera) {
         if (!this.renderObject) return;
 
-        updateCamera(this.camera, camera.viewport);
-
-        const m = this.renderObject.values.aTransform.ref.value as unknown as Mat4;
-        Mat4.extractRotation(m, camera.view);
+        updateCamera(this.camera, camera.viewport, camera.viewOffset);
+        Mat4.extractRotation(this.scene.view, camera.view);
 
         const r = this.renderObject.values.boundingSphere.ref.value.radius;
-        Mat4.setTranslation(m, Vec3.create(
+        Mat4.setTranslation(this.scene.view, Vec3.create(
             -camera.viewport.width / 2 + r,
             -camera.viewport.height / 2 + r,
             0
         ));
-
-        ValueCell.update(this.renderObject.values.aTransform, this.renderObject.values.aTransform.ref.value);
-        this.scene.update([this.renderObject], true);
     }
 }
 
-function updateCamera(camera: Camera, viewport: Viewport) {
+function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.ViewOffset) {
     const { near, far } = camera;
 
-    const fullLeft = -(viewport.width - viewport.x) / 2;
-    const fullRight = (viewport.width - viewport.x) / 2;
-    const fullTop = (viewport.height - viewport.y) / 2;
-    const fullBottom = -(viewport.height - viewport.y) / 2;
+    const fullLeft = -viewport.width / 2;
+    const fullRight = viewport.width / 2;
+    const fullTop = viewport.height / 2;
+    const fullBottom = -viewport.height / 2;
 
     const dx = (fullRight - fullLeft) / 2;
     const dy = (fullTop - fullBottom) / 2;
     const cx = (fullRight + fullLeft) / 2;
     const cy = (fullTop + fullBottom) / 2;
 
-    const left = cx - dx;
-    const right = cx + dx;
-    const top = cy + dy;
-    const bottom = cy - dy;
+    let left = cx - dx;
+    let right = cx + dx;
+    let top = cy + dy;
+    let bottom = cy - dy;
+
+    if (viewOffset.enabled) {
+        const scaleW = (fullRight - fullLeft) / viewOffset.width;
+        const scaleH = (fullTop - fullBottom) / viewOffset.height;
+        left += scaleW * viewOffset.offsetX;
+        right = left + scaleW * viewOffset.width;
+        top -= scaleH * viewOffset.offsetY;
+        bottom = top - scaleH * viewOffset.height;
+    }
 
     Mat4.ortho(camera.projection, left, right, top, bottom, near, far);
 }

src/mol-canvas3d/helper/handle-helper.ts

@@ -5,7 +5,7 @@
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
-import Scene from '../../mol-gl/scene';
+import { Scene } from '../../mol-gl/scene';
 import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
 import { Vec3, Mat4, Mat3 } from '../../mol-math/linear-algebra';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
@@ -72,6 +72,7 @@ export class HandleHelper {
                     this.scene.clear();
                     const params = { ...props.handle.params, scale: props.handle.params.scale * this.webgl.pixelRatio };
                     this.renderObject = createHandleRenderObject(params);
+                    this.renderObject.state.noClip = true;
                     this.scene.add(this.renderObject);
                     this.scene.commit();
 

src/mol-canvas3d/helper/helper.ts

@@ -0,0 +1,37 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Scene } from '../../mol-gl/scene';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { BoundingSphereHelper, DebugHelperParams } from './bounding-sphere-helper';
+import { CameraHelper, CameraHelperParams } from './camera-helper';
+import { HandleHelper, HandleHelperParams } from './handle-helper';
+
+export const HelperParams = {
+    debug: PD.Group(DebugHelperParams),
+    camera: PD.Group({
+        helper: PD.Group(CameraHelperParams)
+    }),
+    handle: PD.Group(HandleHelperParams),
+};
+export const DefaultHelperProps = PD.getDefaultValues(HelperParams);
+export type HelperProps = PD.Values<typeof HelperParams>
+
+
+export class Helper {
+    readonly debug: BoundingSphereHelper
+    readonly camera: CameraHelper
+    readonly handle: HandleHelper
+
+    constructor(webgl: WebGLContext, scene: Scene, props: Partial<HelperProps> = {}) {
+        const p = { ...DefaultHelperProps, ...props };
+
+        this.debug = new BoundingSphereHelper(webgl, scene, p.debug);
+        this.camera = new CameraHelper(webgl, p.camera.helper);
+        this.handle = new HandleHelper(webgl, p.handle);
+    }
+}

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

@@ -7,9 +7,10 @@
 
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { Representation } from '../../mol-repr/representation';
-import InputObserver, { ModifiersKeys, ButtonsType } from '../../mol-util/input/input-observer';
+import { InputObserver, ModifiersKeys, ButtonsType } from '../../mol-util/input/input-observer';
 import { RxEventHelper } from '../../mol-util/rx-event-helper';
-import { Vec2 } from '../../mol-math/linear-algebra';
+import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
+import { Camera } from '../camera';
 
 type Canvas3D = import('../canvas3d').Canvas3D
 type HoverEvent = import('../canvas3d').Canvas3D.HoverEvent
@@ -33,6 +34,7 @@ export class Canvas3dInteractionHelper {
     private endY = -1;
 
     private id: PickingId | undefined = void 0;
+    private position: Vec3 | undefined = void 0;
 
     private currentIdentifyT = 0;
     private isInteracting = false;
@@ -60,33 +62,25 @@ export class Canvas3dInteractionHelper {
         }
 
         if (xyChanged) {
-            this.id = this.canvasIdentify(this.endX, this.endY);
+            const pickData = this.canvasIdentify(this.endX, this.endY);
+            this.id = pickData?.id;
+            this.position = pickData?.position;
             this.startX = this.endX;
             this.startY = this.endY;
         }
 
-        if (!this.id) {
-            this.prevLoci = Representation.Loci.Empty;
-            return;
-        }
-
         if (e === InputEvent.Click) {
             const loci = this.getLoci(this.id);
-            this.events.click.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers });
+            this.events.click.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
             this.prevLoci = loci;
             return;
         }
 
-        if (!this.inside || this.currentIdentifyT !== t) {
-            return;
-        }
+        if (!this.inside || this.currentIdentifyT !== t || !xyChanged || this.outsideViewport(this.endX, this.endY)) return;
 
         const loci = this.getLoci(this.id);
-        // only broadcast the latest hover
-        if (!Representation.Loci.areEqual(this.prevLoci, loci)) {
-            this.events.hover.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers });
-            this.prevLoci = loci;
-        }
+        this.events.hover.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
+        this.prevLoci = loci;
     }
 
     tick(t: number) {
@@ -97,15 +91,15 @@ export class Canvas3dInteractionHelper {
         }
     }
 
-    leave() {
+    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 });
         }
     }
 
-    move(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
+    private move(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
         this.inside = true;
         this.buttons = buttons;
         this.button = button;
@@ -114,7 +108,7 @@ export class Canvas3dInteractionHelper {
         this.endY = y;
     }
 
-    click(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
+    private click(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
         this.endX = x;
         this.endY = y;
         this.buttons = buttons;
@@ -123,7 +117,7 @@ export class Canvas3dInteractionHelper {
         this.identify(InputEvent.Click, 0);
     }
 
-    drag(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
+    private drag(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
         this.endX = x;
         this.endY = y;
         this.buttons = buttons;
@@ -132,17 +126,29 @@ export class Canvas3dInteractionHelper {
         this.identify(InputEvent.Drag, 0);
     }
 
-    modify(modifiers: ModifiersKeys) {
-        if (Representation.Loci.isEmpty(this.prevLoci) || ModifiersKeys.areEqual(modifiers, this.modifiers)) return;
+    private modify(modifiers: ModifiersKeys) {
+        if (ModifiersKeys.areEqual(modifiers, this.modifiers)) return;
         this.modifiers = modifiers;
-        this.events.hover.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers });
+        this.events.hover.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
+    }
+
+    private outsideViewport(x: number, y: number) {
+        const { input, camera: { viewport } } = this;
+        x *= input.pixelRatio;
+        y *= input.pixelRatio;
+        return (
+            x > viewport.x + viewport.width ||
+            input.height - y > viewport.y + viewport.height ||
+            x < viewport.x ||
+            input.height - y < viewport.y
+        );
     }
 
     dispose() {
         this.ev.dispose();
     }
 
-    constructor(private canvasIdentify: Canvas3D['identify'], private getLoci: Canvas3D['getLoci'], input: InputObserver, private maxFps: number = 30) {
+    constructor(private canvasIdentify: Canvas3D['identify'], private getLoci: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, private maxFps: number = 30) {
         input.drag.subscribe(({x, y, buttons, button, modifiers }) => {
             this.isInteracting = true;
             // console.log('drag');
@@ -161,6 +167,7 @@ export class Canvas3dInteractionHelper {
         });
 
         input.click.subscribe(({x, y, buttons, button, modifiers }) => {
+            if (this.outsideViewport(x, y)) return;
             // console.log('click');
             this.click(x, y, buttons, button, modifiers);
         });
@@ -170,6 +177,9 @@ export class Canvas3dInteractionHelper {
             this.isInteracting = false;
         });
 
-        input.modifiers.subscribe(modifiers => this.modify(modifiers));
+        input.modifiers.subscribe(modifiers => {
+            // console.log('modifiers');
+            this.modify(modifiers);
+        });
     }
 }

src/mol-canvas3d/passes/draw.ts

@@ -1,107 +1,356 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
-import { RenderTarget } from '../../mol-gl/webgl/render-target';
-import Renderer from '../../mol-gl/renderer';
-import Scene from '../../mol-gl/scene';
-import { BoundingSphereHelper } from '../helper/bounding-sphere-helper';
+import { createNullRenderTarget, RenderTarget } from '../../mol-gl/webgl/render-target';
+import { Renderer } from '../../mol-gl/renderer';
+import { Scene } from '../../mol-gl/scene';
 import { Texture } from '../../mol-gl/webgl/texture';
-import { Camera } from '../camera';
-import { CameraHelper, CameraHelperParams } from '../helper/camera-helper';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { HandleHelper } from '../helper/handle-helper';
+import { Camera, ICamera } from '../camera';
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { DefineSpec, TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { ValueCell } from '../../mol-util';
+import { Vec2 } from '../../mol-math/linear-algebra';
+import { Helper } from '../helper/helper';
 
-export const DrawPassParams = {
-    cameraHelper: PD.Group(CameraHelperParams)
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { depthMerge_frag } from '../../mol-gl/shader/depth-merge.frag';
+import { copy_frag } from '../../mol-gl/shader/copy.frag';
+import { StereoCamera } from '../camera/stereo';
+import { WboitPass } from './wboit';
+import { AntialiasingPass, PostprocessingPass, PostprocessingProps } from './postprocessing';
+
+const DepthMergeSchema = {
+    ...QuadSchema,
+    tDepthPrimitives: TextureSpec('texture', 'depth', 'ushort', 'nearest'),
+    tDepthVolumes: TextureSpec('texture', 'depth', 'ushort', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+    dPackedDepth: DefineSpec('boolean'),
 };
-export const DefaultDrawPassProps = PD.getDefaultValues(DrawPassParams);
-export type DrawPassProps = PD.Values<typeof DrawPassParams>
+const DepthMergeShaderCode = ShaderCode('depth-merge', quad_vert, depthMerge_frag);
+type DepthMergeRenderable = ComputeRenderable<Values<typeof DepthMergeSchema>>
+
+function getDepthMergeRenderable(ctx: WebGLContext, depthTexturePrimitives: Texture, depthTextureVolumes: Texture, packedDepth: boolean): DepthMergeRenderable {
+    const values: Values<typeof DepthMergeSchema> = {
+        ...QuadValues,
+        tDepthPrimitives: ValueCell.create(depthTexturePrimitives),
+        tDepthVolumes: ValueCell.create(depthTextureVolumes),
+        uTexSize: ValueCell.create(Vec2.create(depthTexturePrimitives.getWidth(), depthTexturePrimitives.getHeight())),
+        dPackedDepth: ValueCell.create(packedDepth),
+    };
+
+    const schema = { ...DepthMergeSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', DepthMergeShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+const CopySchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+};
+const  CopyShaderCode = ShaderCode('copy', quad_vert, copy_frag);
+type  CopyRenderable = ComputeRenderable<Values<typeof CopySchema>>
+
+function getCopyRenderable(ctx: WebGLContext, colorTexture: Texture): CopyRenderable {
+    const values: Values<typeof CopySchema> = {
+        ...QuadValues,
+        tColor: ValueCell.create(colorTexture),
+        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+    };
+
+    const schema = { ...CopySchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', CopyShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
 
 export class DrawPass {
-    colorTarget: RenderTarget
-    depthTexture: Texture
-    packedDepth: boolean
+    private readonly drawTarget: RenderTarget
 
-    cameraHelper: CameraHelper
+    readonly colorTarget: RenderTarget
+    readonly depthTexture: Texture
+    readonly depthTexturePrimitives: Texture
 
-    private depthTarget: RenderTarget | null
+    readonly packedDepth: boolean
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private debugHelper: BoundingSphereHelper, private handleHelper: HandleHelper, props: Partial<DrawPassProps> = {}) {
-        const { gl, extensions, resources } = webgl;
-        const width = gl.drawingBufferWidth;
-        const height = gl.drawingBufferHeight;
-        this.colorTarget = webgl.createRenderTarget(width, height);
+    private depthTarget: RenderTarget
+    private depthTargetPrimitives: RenderTarget | null
+    private depthTargetVolumes: RenderTarget | null
+    private depthTextureVolumes: Texture
+    private depthMerge: DepthMergeRenderable
+
+    private copyFboTarget: CopyRenderable
+    private copyFboPostprocessing: CopyRenderable
+
+    private wboit: WboitPass | undefined
+    readonly postprocessing: PostprocessingPass
+    private readonly antialiasing: AntialiasingPass
+
+    get wboitEnabled() {
+        return !!this.wboit?.supported;
+    }
+
+    constructor(private webgl: WebGLContext, width: number, height: number, enableWboit: boolean) {
+        const { extensions, resources, isWebGL2 } = webgl;
+
+        this.drawTarget = createNullRenderTarget(webgl.gl);
+
+        this.colorTarget = webgl.createRenderTarget(width, height, true, 'uint8', 'linear');
         this.packedDepth = !extensions.depthTexture;
-        this.depthTarget = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
-        this.depthTexture = this.depthTarget ? this.depthTarget.texture : resources.texture('image-depth', 'depth', 'ushort', 'nearest');
-        if (!this.packedDepth) {
-            this.depthTexture.define(width, height);
-            this.depthTexture.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-        }
 
-        const p = { ...DefaultDrawPassProps, ...props };
-        this.cameraHelper = new CameraHelper(webgl, p.cameraHelper);
+        this.depthTarget = webgl.createRenderTarget(width, height);
+        this.depthTexture = this.depthTarget.texture;
+
+        this.depthTargetPrimitives = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
+        this.depthTargetVolumes = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
+
+        this.depthTexturePrimitives = this.depthTargetPrimitives ? this.depthTargetPrimitives.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
+        this.depthTextureVolumes = this.depthTargetVolumes ? this.depthTargetVolumes.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
+        if (!this.packedDepth) {
+            this.depthTexturePrimitives.define(width, height);
+            this.depthTextureVolumes.define(width, height);
+        }
+        this.depthMerge = getDepthMergeRenderable(webgl, this.depthTexturePrimitives, this.depthTextureVolumes, this.packedDepth);
+
+        this.wboit = enableWboit ? new WboitPass(webgl, width, height) : undefined;
+        this.postprocessing = new PostprocessingPass(webgl, this);
+        this.antialiasing = new AntialiasingPass(webgl, this);
+
+        this.copyFboTarget = getCopyRenderable(webgl, this.colorTarget.texture);
+        this.copyFboPostprocessing = getCopyRenderable(webgl, this.postprocessing.target.texture);
+    }
+
+    reset() {
+        this.wboit?.reset();
     }
 
     setSize(width: number, height: number) {
-        this.colorTarget.setSize(width, height);
-        if (this.depthTarget) {
+        const w = this.colorTarget.getWidth();
+        const h = this.colorTarget.getHeight();
+
+        if (width !== w || height !== h) {
+            this.colorTarget.setSize(width, height);
             this.depthTarget.setSize(width, height);
-        } else {
-            this.depthTexture.define(width, height);
+
+            if (this.depthTargetPrimitives) {
+                this.depthTargetPrimitives.setSize(width, height);
+            } else {
+                this.depthTexturePrimitives.define(width, height);
+            }
+
+            if (this.depthTargetVolumes) {
+                this.depthTargetVolumes.setSize(width, height);
+            } else {
+                this.depthTextureVolumes.define(width, height);
+            }
+
+            ValueCell.update(this.depthMerge.values.uTexSize, Vec2.set(this.depthMerge.values.uTexSize.ref.value, width, height));
+
+            ValueCell.update(this.copyFboTarget.values.uTexSize, Vec2.set(this.copyFboTarget.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.copyFboPostprocessing.values.uTexSize, Vec2.set(this.copyFboPostprocessing.values.uTexSize.ref.value, width, height));
+
+            if (this.wboit?.supported) {
+                this.wboit.setSize(width, height);
+            }
+
+            this.postprocessing.setSize(width, height);
+            this.antialiasing.setSize(width, height);
         }
     }
 
-    setProps(props: Partial<DrawPassProps>) {
-        if (props.cameraHelper) this.cameraHelper.setProps(props.cameraHelper);
+    private _depthMerge() {
+        const { state, gl } = this.webgl;
+
+        this.depthMerge.update();
+        this.depthTarget.bind();
+        state.disable(gl.BLEND);
+        state.disable(gl.DEPTH_TEST);
+        state.disable(gl.CULL_FACE);
+        state.depthMask(false);
+        state.clearColor(1, 1, 1, 1);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+        this.depthMerge.render();
     }
 
-    get props(): DrawPassProps {
-        return {
-            cameraHelper: { ...this.cameraHelper.props }
-        };
-    }
+    private _renderWboit(renderer: Renderer, camera: ICamera, scene: Scene, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+        if (!this.wboit?.supported) throw new Error('expected wboit to be supported');
 
-    render(toDrawingBuffer: boolean, transparentBackground: boolean) {
-        const { webgl, renderer, colorTarget, depthTarget } = this;
-        if (toDrawingBuffer) {
-            webgl.unbindFramebuffer();
+        this.colorTarget.bind();
+        renderer.clear(true);
+
+        // render opaque primitives
+        this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+        this.colorTarget.bind();
+        renderer.clearDepth();
+        renderer.renderWboitOpaque(scene.primitives, camera, null);
+
+        // render opaque volumes
+        this.depthTextureVolumes.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+        this.colorTarget.bind();
+        renderer.clearDepth();
+        renderer.renderWboitOpaque(scene.volumes, camera, this.depthTexturePrimitives);
+
+        // merge depth of opaque primitives and volumes
+        this._depthMerge();
+
+        if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
+        }
+
+        // render transparent primitives and volumes
+        this.wboit.bind();
+        renderer.renderWboitTransparent(scene.primitives, camera, this.depthTexture);
+        renderer.renderWboitTransparent(scene.volumes, camera, this.depthTexture);
+
+        // evaluate wboit
+        if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            this.depthTexturePrimitives.attachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
+            this.postprocessing.target.bind();
         } else {
-            colorTarget.bind();
+            this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+            this.colorTarget.bind();
+        }
+        this.wboit.render();
+    }
+
+    private _renderBlended(renderer: Renderer, camera: ICamera, scene: Scene, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+        if (toDrawingBuffer) {
+            this.drawTarget.bind();
+        } else {
+            this.colorTarget.bind();
             if (!this.packedDepth) {
-                // TODO unlcear why it is not enough to call `attachFramebuffer` in `Texture.reset`
-                this.depthTexture.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+                this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
             }
         }
 
-        renderer.setViewport(0, 0, colorTarget.getWidth(), colorTarget.getHeight());
-        this.renderInternal('color', transparentBackground);
+        renderer.clear(true);
+        renderer.renderBlendedOpaque(scene.primitives, camera, null);
 
-        // do a depth pass if not rendering to drawing buffer and
-        // extensions.depthTexture is unsupported (i.e. depthTarget is set)
-        if (!toDrawingBuffer && depthTarget) {
-            depthTarget.bind();
-            this.renderInternal('depth', transparentBackground);
+        if (!toDrawingBuffer) {
+            // do a depth pass if not rendering to drawing buffer and
+            // extensions.depthTexture is unsupported (i.e. depthTarget is set)
+            if (this.depthTargetPrimitives) {
+                this.depthTargetPrimitives.bind();
+                renderer.clear(false);
+                // TODO: this should only render opaque
+                renderer.renderDepth(scene.primitives, camera, null);
+                this.colorTarget.bind();
+            }
+
+            // do direct-volume rendering
+            if (!this.packedDepth) {
+                this.depthTextureVolumes.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+                renderer.clearDepth(); // from previous frame
+            }
+            renderer.renderBlendedVolumeOpaque(scene.volumes, camera, this.depthTexturePrimitives);
+
+            // do volume depth pass if extensions.depthTexture is unsupported (i.e. depthTarget is set)
+            if (this.depthTargetVolumes) {
+                this.depthTargetVolumes.bind();
+                renderer.clear(false);
+                renderer.renderDepth(scene.volumes, camera, this.depthTexturePrimitives);
+                this.colorTarget.bind();
+            }
+
+            // merge depths from primitive and volume rendering
+            this._depthMerge();
+            this.colorTarget.bind();
+
+            if (PostprocessingPass.isEnabled(postprocessingProps)) {
+                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
+            }
+            renderer.renderBlendedVolumeTransparent(scene.volumes, camera, this.depthTexturePrimitives);
+
+            const target = PostprocessingPass.isEnabled(postprocessingProps)
+                ? this.postprocessing.target : this.colorTarget;
+            if (!this.packedDepth) {
+                this.depthTexturePrimitives.attachFramebuffer(target.framebuffer, 'depth');
+            }
+            target.bind();
+        }
+
+        renderer.renderBlendedTransparent(scene.primitives, camera, null);
+    }
+
+    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+        const volumeRendering = scene.volumes.renderables.length > 0;
+        const postprocessingEnabled = PostprocessingPass.isEnabled(postprocessingProps);
+        const antialiasingEnabled = AntialiasingPass.isEnabled(postprocessingProps);
+
+        const { x, y, width, height } = camera.viewport;
+        renderer.setViewport(x, y, width, height);
+        renderer.update(camera);
+
+        if (this.wboitEnabled) {
+            this._renderWboit(renderer, camera, scene, transparentBackground, postprocessingProps);
+        } else {
+            this._renderBlended(renderer, camera, scene, !volumeRendering && !postprocessingEnabled && !antialiasingEnabled && toDrawingBuffer, transparentBackground, postprocessingProps);
+        }
+
+        if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            this.postprocessing.target.bind();
+        } else if (!toDrawingBuffer || volumeRendering || this.wboitEnabled) {
+            this.colorTarget.bind();
+        } else {
+            this.drawTarget.bind();
+        }
+
+        if (helper.debug.isEnabled) {
+            helper.debug.syncVisibility();
+            renderer.renderBlended(helper.debug.scene, camera, null);
+        }
+        if (helper.handle.isEnabled) {
+            renderer.renderBlended(helper.handle.scene, camera, null);
+        }
+        if (helper.camera.isEnabled) {
+            helper.camera.update(camera);
+            renderer.update(helper.camera.camera);
+            renderer.renderBlended(helper.camera.scene, helper.camera.camera, null);
+        }
+
+        if (antialiasingEnabled) {
+            this.antialiasing.render(camera, toDrawingBuffer, postprocessingProps);
+        } else if (toDrawingBuffer) {
+            this.drawTarget.bind();
+
+            this.webgl.state.disable(this.webgl.gl.DEPTH_TEST);
+            if (PostprocessingPass.isEnabled(postprocessingProps)) {
+                this.copyFboPostprocessing.render();
+            } else if (volumeRendering || this.wboitEnabled) {
+                this.copyFboTarget.render();
+            }
+        }
+
+        this.webgl.gl.flush();
+    }
+
+    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+        renderer.setTransparentBackground(transparentBackground);
+        renderer.setDrawingBufferSize(this.colorTarget.getWidth(), this.colorTarget.getHeight());
+
+        if (StereoCamera.is(camera)) {
+            this._render(renderer, camera.left, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps);
+            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps);
+        } else {
+            this._render(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps);
         }
     }
 
-    private renderInternal(variant: 'color' | 'depth', transparentBackground: boolean) {
-        const { renderer, scene, camera, debugHelper, cameraHelper, handleHelper } = this;
-        renderer.render(scene, camera, variant, true, transparentBackground);
-        if (debugHelper.isEnabled) {
-            debugHelper.syncVisibility();
-            renderer.render(debugHelper.scene, camera, variant, false, transparentBackground);
-        }
-        if (handleHelper.isEnabled) {
-            renderer.render(handleHelper.scene, camera, variant, false, transparentBackground);
-        }
-        if (cameraHelper.isEnabled) {
-            cameraHelper.update(camera);
-            renderer.render(cameraHelper.scene, cameraHelper.camera, variant, false, transparentBackground);
+    getColorTarget(postprocessingProps: PostprocessingProps): RenderTarget {
+        if (AntialiasingPass.isEnabled(postprocessingProps)) {
+            return this.antialiasing.target;
+        } else if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            return this.postprocessing.target;
         }
+        return this.colorTarget;
     }
 }

src/mol-canvas3d/passes/fxaa.ts

@@ -0,0 +1,130 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { TextureSpec, UniformSpec, DefineSpec, Values } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { Vec2 } from '../../mol-math/linear-algebra';
+import { ValueCell } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { fxaa_frag } from '../../mol-gl/shader/fxaa.frag';
+import { Viewport } from '../camera/util';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+
+export const FxaaParams = {
+    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: 16, step: 1 }, { description: 'Number of edge exploration steps.' }),
+    subpixelQuality: PD.Numeric(0.30, { min: 0.00, max: 1.00, step: 0.01 }, { description: 'Choose the amount of sub-pixel aliasing removal.' }),
+};
+export type FxaaProps = PD.Values<typeof FxaaParams>
+
+export class FxaaPass {
+    private readonly renderable: FxaaRenderable
+
+    constructor(private webgl: WebGLContext, input: Texture) {
+        this.renderable = getFxaaRenderable(webgl, input);
+    }
+
+    private updateState(viewport: Viewport) {
+        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 } = 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);
+    }
+
+    setSize(width: number, height: number) {
+        ValueCell.update(this.renderable.values.uTexSizeInv, Vec2.set(this.renderable.values.uTexSizeInv.ref.value, 1 / width, 1 / height));
+    }
+
+    update(input: Texture, props: FxaaProps) {
+        const { values } = this.renderable;
+        const { edgeThresholdMin, edgeThresholdMax, iterations, subpixelQuality } = props;
+
+        let needsUpdate = false;
+
+        if (values.tColor.ref.value !== input) {
+            ValueCell.update(this.renderable.values.tColor, input);
+            needsUpdate = true;
+        }
+
+        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.renderable.update();
+        }
+    }
+
+    render(viewport: Viewport, target: RenderTarget | undefined) {
+        if (target) {
+            target.bind();
+        } else {
+            this.webgl.unbindFramebuffer();
+        }
+        this.updateState(viewport);
+        this.renderable.render();
+    }
+}
+
+//
+
+const FxaaSchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    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(0.3),
+    };
+
+    const schema = { ...FxaaSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', FxaaShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-canvas3d/passes/image.ts

@@ -6,51 +6,59 @@
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
-import Renderer from '../../mol-gl/renderer';
-import Scene from '../../mol-gl/scene';
-import { BoundingSphereHelper } from '../helper/bounding-sphere-helper';
+import { Renderer } from '../../mol-gl/renderer';
+import { Scene } from '../../mol-gl/scene';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { DrawPass, DrawPassParams } from './draw';
-import { PostprocessingPass, PostprocessingParams } from './postprocessing';
-import { MultiSamplePass, MultiSampleParams } from './multi-sample';
+import { DrawPass } from './draw';
+import { PostprocessingParams } from './postprocessing';
+import { MultiSamplePass, MultiSampleParams, MultiSampleHelper } from './multi-sample';
 import { Camera } from '../camera';
 import { Viewport } from '../camera/util';
-import { HandleHelper } from '../helper/handle-helper';
+import { PixelData } from '../../mol-util/image';
+import { Helper } from '../helper/helper';
+import { CameraHelper, CameraHelperParams } from '../helper/camera-helper';
 
 export const ImageParams = {
     transparentBackground: PD.Boolean(false),
     multiSample: PD.Group(MultiSampleParams),
     postprocessing: PD.Group(PostprocessingParams),
-    drawPass: PD.Group(DrawPassParams),
+
+    cameraHelper: PD.Group(CameraHelperParams),
 };
 export type ImageProps = PD.Values<typeof ImageParams>
 
 export class ImagePass {
-    private _width = 1024
-    private _height = 768
+    private _width = 0
+    private _height = 0
     private _camera = new Camera()
-    private _transparentBackground = false
+
+    readonly props: ImageProps
 
     private _colorTarget: RenderTarget
     get colorTarget() { return this._colorTarget; }
 
-    readonly drawPass: DrawPass
-    private readonly postprocessing: PostprocessingPass
-    private readonly multiSample: MultiSamplePass
+    private readonly drawPass: DrawPass
+    private readonly multiSamplePass: MultiSamplePass
+    private readonly multiSampleHelper: MultiSampleHelper
+    private readonly helper: Helper
 
     get width() { return this._width; }
     get height() { return this._height; }
 
-    constructor(webgl: WebGLContext, private renderer: Renderer, scene: Scene, private camera: Camera, debugHelper: BoundingSphereHelper, handleHelper: HandleHelper, props: Partial<ImageProps>) {
-        const p = { ...PD.getDefaultValues(ImageParams), ...props };
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, helper: Helper, enableWboit: boolean, props: Partial<ImageProps>) {
+        this.props = { ...PD.getDefaultValues(ImageParams), ...props };
 
-        this._transparentBackground = p.transparentBackground;
+        this.drawPass = new DrawPass(webgl, 128, 128, enableWboit);
+        this.multiSamplePass = new MultiSamplePass(webgl, this.drawPass);
+        this.multiSampleHelper = new MultiSampleHelper(this.multiSamplePass);
 
-        this.drawPass = new DrawPass(webgl, renderer, scene, this._camera, debugHelper, handleHelper, p.drawPass);
-        this.postprocessing = new PostprocessingPass(webgl, this._camera, this.drawPass, p.postprocessing);
-        this.multiSample = new MultiSamplePass(webgl, this._camera, this.drawPass, this.postprocessing, p.multiSample);
+        this.helper = {
+            camera: new CameraHelper(webgl, this.props.cameraHelper),
+            debug: helper.debug,
+            handle: helper.handle,
+        };
 
-        this.setSize(this._width, this._height);
+        this.setSize(1024, 768);
     }
 
     setSize(width: number, height: number) {
@@ -60,24 +68,12 @@ export class ImagePass {
         this._height = height;
 
         this.drawPass.setSize(width, height);
-        this.postprocessing.setSize(width, height);
-        this.multiSample.setSize(width, height);
+        this.multiSamplePass.syncSize();
     }
 
     setProps(props: Partial<ImageProps> = {}) {
-        if (props.transparentBackground !== undefined) this._transparentBackground = props.transparentBackground;
-        if (props.postprocessing) this.postprocessing.setProps(props.postprocessing);
-        if (props.multiSample) this.multiSample.setProps(props.multiSample);
-        if (props.drawPass) this.drawPass.setProps(props.drawPass);
-    }
-
-    get props(): ImageProps {
-        return {
-            transparentBackground: this._transparentBackground,
-            postprocessing: this.postprocessing.props,
-            multiSample: this.multiSample.props,
-            drawPass: this.drawPass.props
-        };
+        Object.assign(this.props, props);
+        if (props.cameraHelper) this.helper.camera.setProps(props.cameraHelper);
     }
 
     render() {
@@ -85,26 +81,29 @@ export class ImagePass {
         Viewport.set(this._camera.viewport, 0, 0, this._width, this._height);
         this._camera.update();
 
-        this.renderer.setViewport(0, 0, this._width, this._height);
-
-        if (this.multiSample.enabled) {
-            this.multiSample.render(false, this._transparentBackground);
-            this._colorTarget = this.multiSample.colorTarget;
+        if (MultiSamplePass.isEnabled(this.props.multiSample)) {
+            this.multiSampleHelper.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props);
+            this._colorTarget = this.multiSamplePass.colorTarget;
         } else {
-            this.drawPass.render(false, this._transparentBackground);
-            if (this.postprocessing.enabled) {
-                this.postprocessing.render(false);
-                this._colorTarget = this.postprocessing.target;
-            } else {
-                this._colorTarget = this.drawPass.colorTarget;
-            }
+            this.drawPass.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props.postprocessing);
+            this._colorTarget = this.drawPass.getColorTarget(this.props.postprocessing);
         }
     }
 
-    getImageData(width: number, height: number) {
+    getImageData(width: number, height: number, viewport?: Viewport) {
         this.setSize(width, height);
         this.render();
-        const pd = this.colorTarget.getPixelData();
-        return new ImageData(new Uint8ClampedArray(pd.array), pd.width, pd.height);
+        this.colorTarget.bind();
+
+        const w = viewport?.width ?? width, h = viewport?.height ?? height;
+
+        const array = new Uint8Array(w * h * 4);
+        if (!viewport) {
+            this.webgl.readPixels(0, 0, w, h, array);
+        } else {
+            this.webgl.readPixels(viewport.x, height - viewport.y - viewport.height, w, h, array);
+        }
+        PixelData.flipY({ array, width: w, height: h });
+        return new ImageData(new Uint8ClampedArray(array), w, h);
     }
 }

src/mol-canvas3d/passes/multi-sample.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -16,11 +16,15 @@ import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/rendera
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { Camera } from '../../mol-canvas3d/camera';
-import { PostprocessingPass } from './postprocessing';
+import { PostprocessingProps } from './postprocessing';
 import { DrawPass } from './draw';
+import { Renderer } from '../../mol-gl/renderer';
+import { Scene } from '../../mol-gl/scene';
+import { Helper } from '../helper/helper';
+import { StereoCamera } from '../camera/stereo';
 
-import quad_vert from '../../mol-gl/shader/quad.vert';
-import compose_frag from '../../mol-gl/shader/compose.frag';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { compose_frag } from '../../mol-gl/shader/compose.frag';
 
 const ComposeSchema = {
     ...QuadSchema,
@@ -28,7 +32,7 @@ const ComposeSchema = {
     uTexSize: UniformSpec('v2'),
     uWeight: UniformSpec('f'),
 };
-
+const ComposeShaderCode = ShaderCode('compose', quad_vert, compose_frag);
 type ComposeRenderable = ComputeRenderable<Values<typeof ComposeSchema>>
 
 function getComposeRenderable(ctx: WebGLContext, colorTexture: Texture): ComposeRenderable {
@@ -40,8 +44,7 @@ function getComposeRenderable(ctx: WebGLContext, colorTexture: Texture): Compose
     };
 
     const schema = { ...ComposeSchema };
-    const shaderCode = ShaderCode('compose', quad_vert, compose_frag);
-    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', ComposeShaderCode, schema, values);
 
     return createComputeRenderable(renderItem, values);
 }
@@ -52,69 +55,63 @@ export const MultiSampleParams = {
 };
 export type MultiSampleProps = PD.Values<typeof MultiSampleParams>
 
+type Props = { multiSample: MultiSampleProps, postprocessing: PostprocessingProps }
+
 export class MultiSamplePass {
-    props: MultiSampleProps
+    static isEnabled(props: MultiSampleProps) {
+        return props.mode !== 'off';
+    }
+
     colorTarget: RenderTarget
 
     private composeTarget: RenderTarget
     private holdTarget: RenderTarget
     private compose: ComposeRenderable
 
-    private sampleIndex = -1
-    private currentTime = 0
-    private lastRenderTime = 0
-
-    constructor(private webgl: WebGLContext, private camera: Camera, private drawPass: DrawPass, private postprocessing: PostprocessingPass, props: Partial<MultiSampleProps>) {
-        const { gl } = webgl;
-        this.colorTarget = webgl.createRenderTarget(gl.drawingBufferWidth, gl.drawingBufferHeight);
-        this.composeTarget = webgl.createRenderTarget(gl.drawingBufferWidth, gl.drawingBufferHeight);
-        this.holdTarget = webgl.createRenderTarget(gl.drawingBufferWidth, gl.drawingBufferHeight);
+    constructor(private webgl: WebGLContext, private drawPass: DrawPass) {
+        const { colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat } = webgl.extensions;
+        const width = drawPass.colorTarget.getWidth();
+        const height = drawPass.colorTarget.getHeight();
+        this.colorTarget = webgl.createRenderTarget(width, height, false);
+        const type = colorBufferHalfFloat && textureHalfFloat ? 'fp16' :
+            colorBufferFloat && textureFloat ? 'float32' : 'uint8';
+        this.composeTarget = webgl.createRenderTarget(width, height, false, type);
+        this.holdTarget = webgl.createRenderTarget(width, height, false);
         this.compose = getComposeRenderable(webgl, drawPass.colorTarget.texture);
-        this.props = { ...PD.getDefaultValues(MultiSampleParams), ...props };
     }
 
-    get enabled() {
-        if (this.props.mode === 'temporal') {
-            if (this.currentTime - this.lastRenderTime > 200) {
-                return this.sampleIndex !== -1;
-            } else {
-                this.sampleIndex = 0;
-                return false;
-            }
-        } else if (this.props.mode === 'on') {
-            return true;
-        } else {
-            return false;
+    syncSize() {
+        const width = this.drawPass.colorTarget.getWidth();
+        const height = this.drawPass.colorTarget.getHeight();
+
+        const [w, h] = this.compose.values.uTexSize.ref.value;
+        if (width !== w || height !== h) {
+            this.colorTarget.setSize(width, height);
+            this.composeTarget.setSize(width, height);
+            this.holdTarget.setSize(width, height);
+            ValueCell.update(this.compose.values.uTexSize, Vec2.set(this.compose.values.uTexSize.ref.value, width, height));
         }
     }
 
-    update(changed: boolean, currentTime: number) {
-        if (changed) this.lastRenderTime = currentTime;
-        this.currentTime = currentTime;
-    }
-
-    setSize(width: number, height: number) {
-        this.colorTarget.setSize(width, height);
-        this.composeTarget.setSize(width, height);
-        this.holdTarget.setSize(width, height);
-        ValueCell.update(this.compose.values.uTexSize, Vec2.set(this.compose.values.uTexSize.ref.value, width, height));
-    }
-
-    setProps(props: Partial<MultiSampleProps>) {
-        if (props.mode !== undefined) this.props.mode = props.mode;
-        if (props.sampleLevel !== undefined) this.props.sampleLevel = props.sampleLevel;
-    }
-
-    render(toDrawingBuffer: boolean, transparentBackground: boolean) {
-        if (this.props.mode === 'temporal') {
-            this.renderTemporalMultiSample(toDrawingBuffer, transparentBackground);
+    render(sampleIndex: number, renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
+        if (props.multiSample.mode === 'temporal') {
+            return this.renderTemporalMultiSample(sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
         } else {
-            this.renderMultiSample(toDrawingBuffer, transparentBackground);
+            this.renderMultiSample(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+            return sampleIndex;
         }
     }
 
-    private renderMultiSample(toDrawingBuffer: boolean, transparentBackground: boolean) {
-        const { camera, compose, composeTarget, drawPass, postprocessing, webgl } = this;
+    private bindOutputTarget(toDrawingBuffer: boolean) {
+        if (toDrawingBuffer) {
+            this.webgl.unbindFramebuffer();
+        } else {
+            this.colorTarget.bind();
+        }
+    }
+
+    private renderMultiSample(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
+        const { compose, composeTarget, drawPass, webgl } = this;
         const { gl, state } = webgl;
 
         // based on the Multisample Anti-Aliasing Render Pass
@@ -122,18 +119,16 @@ export class MultiSamplePass {
         //
         // This manual approach to MSAA re-renders the scene once for
         // each sample with camera jitter and accumulates the results.
-        const offsetList = JitterVectors[ Math.max(0, Math.min(this.props.sampleLevel, 5)) ];
+        const offsetList = JitterVectors[ Math.max(0, Math.min(props.multiSample.sampleLevel, 5)) ];
 
+        const { x, y, width, height } = camera.viewport;
         const baseSampleWeight = 1.0 / offsetList.length;
         const roundingRange = 1 / 32;
 
         camera.viewOffset.enabled = true;
-        ValueCell.update(compose.values.tColor, postprocessing.enabled ? postprocessing.target.texture : drawPass.colorTarget.texture);
+        ValueCell.update(compose.values.tColor, drawPass.getColorTarget(props.postprocessing).texture);
         compose.update();
 
-        const width = drawPass.colorTarget.getWidth();
-        const height = drawPass.colorTarget.getHeight();
-
         // render the scene multiple times, each slightly jitter offset
         // from the last and accumulate the results.
         for (let i = 0; i < offsetList.length; ++i) {
@@ -148,19 +143,18 @@ export class MultiSamplePass {
             const sampleWeight = baseSampleWeight + roundingRange * uniformCenteredDistribution;
             ValueCell.update(compose.values.uWeight, sampleWeight);
 
-            // render scene and optionally postprocess
-            drawPass.render(false, transparentBackground);
-            if (postprocessing.enabled) postprocessing.render(false);
+            // render scene
+            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing);
 
             // compose rendered scene with compose target
             composeTarget.bind();
-            gl.viewport(0, 0, width, height);
             state.enable(gl.BLEND);
             state.blendEquationSeparate(gl.FUNC_ADD, gl.FUNC_ADD);
             state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ONE, gl.ONE);
             state.disable(gl.DEPTH_TEST);
-            state.disable(gl.SCISSOR_TEST);
             state.depthMask(false);
+            gl.viewport(x, y, width, height);
+            gl.scissor(x, y, width, height);
             if (i === 0) {
                 state.clearColor(0, 0, 0, 0);
                 gl.clear(gl.COLOR_BUFFER_BIT);
@@ -172,12 +166,10 @@ export class MultiSamplePass {
         ValueCell.update(compose.values.tColor, composeTarget.texture);
         compose.update();
 
-        if (toDrawingBuffer) {
-            webgl.unbindFramebuffer();
-        } else {
-            this.colorTarget.bind();
-        }
-        gl.viewport(0, 0, width, height);
+        this.bindOutputTarget(toDrawingBuffer);
+        gl.viewport(x, y, width, height);
+        gl.scissor(x, y, width, height);
+
         state.disable(gl.BLEND);
         compose.render();
 
@@ -185,8 +177,8 @@ export class MultiSamplePass {
         camera.update();
     }
 
-    private renderTemporalMultiSample(toDrawingBuffer: boolean, transparentBackground: boolean) {
-        const { camera, compose, composeTarget, holdTarget, postprocessing, drawPass, webgl } = this;
+    private renderTemporalMultiSample(sampleIndex: number, renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
+        const { compose, composeTarget, holdTarget, drawPass, webgl } = this;
         const { gl, state } = webgl;
 
         // based on the Multisample Anti-Aliasing Render Pass
@@ -194,79 +186,73 @@ export class MultiSamplePass {
         //
         // This manual approach to MSAA re-renders the scene once for
         // each sample with camera jitter and accumulates the results.
-        const offsetList = JitterVectors[ Math.max(0, Math.min(this.props.sampleLevel, 5)) ];
+        const offsetList = JitterVectors[ Math.max(0, Math.min(props.multiSample.sampleLevel, 5)) ];
 
-        if (this.sampleIndex === -1) return;
-        if (this.sampleIndex >= offsetList.length) {
-            this.sampleIndex = -1;
-            return;
-        }
+        if (sampleIndex === -2 || sampleIndex >= offsetList.length) return -2;
 
-        const i = this.sampleIndex;
+        const { x, y, width, height } = camera.viewport;
+        const sampleWeight = 1.0 / offsetList.length;
 
-        if (i === 0) {
-            drawPass.render(false, transparentBackground);
-            if (postprocessing.enabled) postprocessing.render(false);
+        if (sampleIndex === -1) {
+            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing);
             ValueCell.update(compose.values.uWeight, 1.0);
-            ValueCell.update(compose.values.tColor, postprocessing.enabled ? postprocessing.target.texture : drawPass.colorTarget.texture);
+            ValueCell.update(compose.values.tColor, drawPass.getColorTarget(props.postprocessing).texture);
             compose.update();
 
             holdTarget.bind();
             state.disable(gl.BLEND);
-            compose.render();
-        }
-
-        const sampleWeight = 1.0 / offsetList.length;
-
-        camera.viewOffset.enabled = true;
-        ValueCell.update(compose.values.tColor, postprocessing.enabled ? postprocessing.target.texture : drawPass.colorTarget.texture);
-        ValueCell.update(compose.values.uWeight, sampleWeight);
-        compose.update();
-
-        const width = drawPass.colorTarget.getWidth();
-        const height = drawPass.colorTarget.getHeight();
-
-        // render the scene multiple times, each slightly jitter offset
-        // from the last and accumulate the results.
-        const numSamplesPerFrame = Math.pow(2, this.props.sampleLevel);
-        for (let i = 0; i < numSamplesPerFrame; ++i) {
-            const offset = offsetList[this.sampleIndex];
-            Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height);
-            camera.update();
-
-            // render scene and optionally postprocess
-            drawPass.render(false, transparentBackground);
-            if (postprocessing.enabled) postprocessing.render(false);
-
-            // compose rendered scene with compose target
-            composeTarget.bind();
-            state.enable(gl.BLEND);
-            state.blendEquationSeparate(gl.FUNC_ADD, gl.FUNC_ADD);
-            state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ONE, gl.ONE);
             state.disable(gl.DEPTH_TEST);
-            state.disable(gl.SCISSOR_TEST);
             state.depthMask(false);
-            if (this.sampleIndex === 0) {
-                state.clearColor(0, 0, 0, 0);
-                gl.clear(gl.COLOR_BUFFER_BIT);
-            }
+            gl.viewport(x, y, width, height);
+            gl.scissor(x, y, width, height);
             compose.render();
+            sampleIndex += 1;
+        } else {
+            camera.viewOffset.enabled = true;
+            ValueCell.update(compose.values.tColor, drawPass.getColorTarget(props.postprocessing).texture);
+            ValueCell.update(compose.values.uWeight, sampleWeight);
+            compose.update();
 
-            this.sampleIndex += 1;
-            if (this.sampleIndex >= offsetList.length ) break;
+            // render the scene multiple times, each slightly jitter offset
+            // from the last and accumulate the results.
+            const numSamplesPerFrame = Math.pow(2, Math.max(0, props.multiSample.sampleLevel - 2));
+            for (let i = 0; i < numSamplesPerFrame; ++i) {
+                const offset = offsetList[sampleIndex];
+                Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height);
+                camera.update();
+
+                // render scene
+                drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing);
+
+                // compose rendered scene with compose target
+                composeTarget.bind();
+                state.enable(gl.BLEND);
+                state.blendEquationSeparate(gl.FUNC_ADD, gl.FUNC_ADD);
+                state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ONE, gl.ONE);
+                state.disable(gl.DEPTH_TEST);
+                state.depthMask(false);
+                gl.viewport(x, y, width, height);
+                gl.scissor(x, y, width, height);
+                if (sampleIndex === 0) {
+                    state.clearColor(0, 0, 0, 0);
+                    gl.clear(gl.COLOR_BUFFER_BIT);
+                }
+                compose.render();
+
+                sampleIndex += 1;
+                if (sampleIndex >= offsetList.length ) break;
+            }
         }
 
-        const accumulationWeight = this.sampleIndex * sampleWeight;
+        this.bindOutputTarget(toDrawingBuffer);
+        gl.viewport(x, y, width, height);
+        gl.scissor(x, y, width, height);
+
+        const accumulationWeight = sampleIndex * sampleWeight;
         if (accumulationWeight > 0) {
             ValueCell.update(compose.values.uWeight, 1.0);
             ValueCell.update(compose.values.tColor, composeTarget.texture);
             compose.update();
-            if (toDrawingBuffer) {
-                webgl.unbindFramebuffer();
-            } else {
-                this.colorTarget.bind();
-            }
-            gl.viewport(0, 0, width, height);
             state.disable(gl.BLEND);
             compose.render();
         }
@@ -274,12 +260,6 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, 1.0 - accumulationWeight);
             ValueCell.update(compose.values.tColor, holdTarget.texture);
             compose.update();
-            if (toDrawingBuffer) {
-                webgl.unbindFramebuffer();
-            } else {
-                this.colorTarget.bind();
-            }
-            gl.viewport(0, 0, width, height);
             if (accumulationWeight === 0) state.disable(gl.BLEND);
             else state.enable(gl.BLEND);
             compose.render();
@@ -287,7 +267,8 @@ export class MultiSamplePass {
 
         camera.viewOffset.enabled = false;
         camera.update();
-        if (this.sampleIndex >= offsetList.length) this.sampleIndex = -1;
+
+        return sampleIndex >= offsetList.length ? -2 : sampleIndex;
     }
 }
 
@@ -329,4 +310,21 @@ JitterVectors.forEach(offsetList => {
         offset[0] *= 0.0625;
         offset[1] *= 0.0625;
     });
-});
+});
+
+export class MultiSampleHelper {
+    private sampleIndex = -2
+
+    update(changed: boolean, props: MultiSampleProps) {
+        if (changed) this.sampleIndex = -1;
+        return props.mode === 'temporal' ? this.sampleIndex !== -2 : false;
+    }
+
+    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
+        this.sampleIndex = this.multiSamplePass.render(this.sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+    }
+
+    constructor(private multiSamplePass: MultiSamplePass) {
+
+    }
+}

src/mol-canvas3d/passes/passes.ts

@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { DrawPass } from './draw';
+import { PickPass } from './pick';
+import { MultiSamplePass } from './multi-sample';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+
+export class Passes {
+    readonly draw: DrawPass
+    readonly pick: PickPass
+    readonly multiSample: MultiSamplePass
+
+    constructor(private webgl: WebGLContext, attribs: Partial<{ pickScale: number, enableWboit: boolean }> = {}) {
+        const { gl } = webgl;
+        this.draw = new DrawPass(webgl, gl.drawingBufferWidth, gl.drawingBufferHeight, attribs.enableWboit || false);
+        this.pick = new PickPass(webgl, this.draw, attribs.pickScale || 0.25);
+        this.multiSample = new MultiSamplePass(webgl, this.draw);
+    }
+
+    updateSize() {
+        const { gl } = this.webgl;
+        this.draw.setSize(gl.drawingBufferWidth, gl.drawingBufferHeight);
+        this.pick.syncSize();
+        this.multiSample.syncSize();
+    }
+}

src/mol-canvas3d/passes/pick.ts

@@ -1,131 +1,251 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { WebGLContext } from '../../mol-gl/webgl/context';
-import { RenderTarget } from '../../mol-gl/webgl/render-target';
-import Renderer from '../../mol-gl/renderer';
-import Scene from '../../mol-gl/scene';
 import { PickingId } from '../../mol-geo/geometry/picking';
-import { decodeFloatRGB } from '../../mol-util/float-packing';
-import { Camera } from '../camera';
-import { HandleHelper } from '../helper/handle-helper';
+import { Renderer } from '../../mol-gl/renderer';
+import { Scene } from '../../mol-gl/scene';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { GraphicsRenderVariant } from '../../mol-gl/webgl/render-item';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { decodeFloatRGB, unpackRGBAToDepth } from '../../mol-util/float-packing';
+import { Camera, ICamera } from '../camera';
+import { StereoCamera } from '../camera/stereo';
+import { cameraUnproject } from '../camera/util';
+import { Viewport } from '../camera/util';
+import { Helper } from '../helper/helper';
+import { DrawPass } from './draw';
+
+const NullId = Math.pow(2, 24) - 2;
+
+export type PickData = { id: PickingId, position: Vec3 }
 
 export class PickPass {
-    pickDirty = true
+    readonly objectPickTarget: RenderTarget
+    readonly instancePickTarget: RenderTarget
+    readonly groupPickTarget: RenderTarget
+    readonly depthPickTarget: RenderTarget
 
-    objectPickTarget: RenderTarget
-    instancePickTarget: RenderTarget
-    groupPickTarget: RenderTarget
-
-    private objectBuffer: Uint8Array
-    private instanceBuffer: Uint8Array
-    private groupBuffer: Uint8Array
-
-    private pickScale: number
     private pickWidth: number
     private pickHeight: number
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private handleHelper: HandleHelper, private pickBaseScale: number) {
-        const { gl } = webgl;
-        const width = gl.drawingBufferWidth;
-        const height = gl.drawingBufferHeight;
-
-        this.pickScale = pickBaseScale / webgl.pixelRatio;
-        this.pickWidth = Math.round(width * this.pickScale);
-        this.pickHeight = Math.round(height * this.pickScale);
+    constructor(private webgl: WebGLContext, private drawPass: DrawPass, readonly pickBaseScale: number) {
+        const pickScale = pickBaseScale / webgl.pixelRatio;
+        this.pickWidth = Math.ceil(drawPass.colorTarget.getWidth() * pickScale);
+        this.pickHeight = Math.ceil(drawPass.colorTarget.getHeight() * pickScale);
 
         this.objectPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
         this.instancePickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
         this.groupPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
-
-        this.setupBuffers();
+        this.depthPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
     }
 
+    get drawingBufferHeight() {
+        return this.drawPass.colorTarget.getHeight();
+    }
+
+    syncSize() {
+        const pickScale = this.pickBaseScale / this.webgl.pixelRatio;
+        const pickWidth = Math.ceil(this.drawPass.colorTarget.getWidth() * pickScale);
+        const pickHeight = Math.ceil(this.drawPass.colorTarget.getHeight() * pickScale);
+
+        if (pickWidth !== this.pickWidth || pickHeight !== this.pickHeight) {
+            this.pickWidth = pickWidth;
+            this.pickHeight = pickHeight;
+
+            this.objectPickTarget.setSize(this.pickWidth, this.pickHeight);
+            this.instancePickTarget.setSize(this.pickWidth, this.pickHeight);
+            this.groupPickTarget.setSize(this.pickWidth, this.pickHeight);
+            this.depthPickTarget.setSize(this.pickWidth, this.pickHeight);
+        }
+    }
+
+    private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: GraphicsRenderVariant) {
+        const depth = this.drawPass.depthTexturePrimitives;
+        renderer.clear(false);
+        renderer.renderPick(scene.primitives, camera, variant, null);
+        renderer.renderPick(scene.volumes, camera, variant, depth);
+        renderer.renderPick(helper.handle.scene, camera, variant, null);
+    }
+
+    render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper) {
+        renderer.update(camera);
+
+        this.objectPickTarget.bind();
+        this.renderVariant(renderer, camera, scene, helper, 'pickObject');
+
+        this.instancePickTarget.bind();
+        this.renderVariant(renderer, camera, scene, helper, 'pickInstance');
+
+        this.groupPickTarget.bind();
+        this.renderVariant(renderer, camera, scene, helper, 'pickGroup');
+
+        this.depthPickTarget.bind();
+        this.renderVariant(renderer, camera, scene, helper, 'depth');
+    }
+}
+
+export class PickHelper {
+    dirty = true
+
+    private objectBuffer: Uint8Array
+    private instanceBuffer: Uint8Array
+    private groupBuffer: Uint8Array
+    private depthBuffer: Uint8Array
+
+    private viewport = Viewport()
+
+    private pickScale: number
+    private pickX: number
+    private pickY: number
+    private pickWidth: number
+    private pickHeight: number
+    private halfPickWidth: number
+
     private setupBuffers() {
         const bufferSize = this.pickWidth * this.pickHeight * 4;
         if (!this.objectBuffer || this.objectBuffer.length !== bufferSize) {
             this.objectBuffer = new Uint8Array(bufferSize);
             this.instanceBuffer = new Uint8Array(bufferSize);
             this.groupBuffer = new Uint8Array(bufferSize);
+            this.depthBuffer = new Uint8Array(bufferSize);
         }
     }
 
-    setSize(width: number, height: number) {
-        this.pickScale = this.pickBaseScale / this.webgl.pixelRatio;
-        this.pickWidth = Math.round(width * this.pickScale);
-        this.pickHeight = Math.round(height * this.pickScale);
+    setViewport(x: number, y: number, width: number, height: number) {
+        Viewport.set(this.viewport, x, y, width, height);
 
-        this.objectPickTarget.setSize(this.pickWidth, this.pickHeight);
-        this.instancePickTarget.setSize(this.pickWidth, this.pickHeight);
-        this.groupPickTarget.setSize(this.pickWidth, this.pickHeight);
+        this.pickScale = this.pickPass.pickBaseScale / this.webgl.pixelRatio;
+        this.pickX = Math.ceil(x * this.pickScale);
+        this.pickY = Math.ceil(y * this.pickScale);
 
-        this.setupBuffers();
-    }
+        const pickWidth = Math.ceil(width * this.pickScale);
+        const pickHeight = Math.ceil(height * this.pickScale);
 
-    render() {
-        const { renderer, scene, camera, handleHelper: { scene: handleScene } } = this;
-        renderer.setViewport(0, 0, this.pickWidth, this.pickHeight);
+        if (pickWidth !== this.pickWidth || pickHeight !== this.pickHeight) {
+            this.pickWidth = pickWidth;
+            this.pickHeight = pickHeight;
+            this.halfPickWidth = Math.floor(this.pickWidth / 2);
 
-        this.objectPickTarget.bind();
-        renderer.render(scene, camera, 'pickObject', true, false);
-        renderer.render(handleScene, camera, 'pickObject', false, false);
-        this.instancePickTarget.bind();
-        renderer.render(scene, camera, 'pickInstance', true, false);
-        renderer.render(handleScene, camera, 'pickInstance', false, false);
-        this.groupPickTarget.bind();
-        renderer.render(scene, camera, 'pickGroup', true, false);
-        renderer.render(handleScene, camera, 'pickGroup', false, false);
-
-        this.pickDirty = false;
+            this.setupBuffers();
+        }
     }
 
     private syncBuffers() {
-        const { webgl } = this;
+        const { pickX, pickY, pickWidth, pickHeight } = this;
 
-        this.objectPickTarget.bind();
-        webgl.readPixels(0, 0, this.pickWidth, this.pickHeight, this.objectBuffer);
+        this.pickPass.objectPickTarget.bind();
+        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.objectBuffer);
 
-        this.instancePickTarget.bind();
-        webgl.readPixels(0, 0, this.pickWidth, this.pickHeight, this.instanceBuffer);
+        this.pickPass.instancePickTarget.bind();
+        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.instanceBuffer);
 
-        this.groupPickTarget.bind();
-        webgl.readPixels(0, 0, this.pickWidth, this.pickHeight, this.groupBuffer);
+        this.pickPass.groupPickTarget.bind();
+        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.groupBuffer);
+
+        this.pickPass.depthPickTarget.bind();
+        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.depthBuffer);
+    }
+
+    private getBufferIdx(x: number, y: number): number {
+        return (y * this.pickWidth + x) * 4;
+    }
+
+    private getDepth(x: number, y: number): number {
+        const idx = this.getBufferIdx(x, y);
+        const b = this.depthBuffer;
+        return unpackRGBAToDepth(b[idx], b[idx + 1], b[idx + 2], b[idx + 3]);
     }
 
     private getId(x: number, y: number, buffer: Uint8Array) {
-        const idx = (y * this.pickWidth + x) * 4;
+        const idx = this.getBufferIdx(x, y);
         return decodeFloatRGB(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
     }
 
-    identify(x: number, y: number): PickingId | undefined {
+    private render(camera: Camera | StereoCamera) {
+        const { pickX, pickY, pickWidth, pickHeight, halfPickWidth } = this;
+        const { renderer, scene, helper } = this;
+
+        renderer.setTransparentBackground(false);
+        renderer.setDrawingBufferSize(this.pickPass.objectPickTarget.getWidth(), this.pickPass.objectPickTarget.getHeight());
+
+        if (StereoCamera.is(camera)) {
+            renderer.setViewport(pickX, pickY, halfPickWidth, pickHeight);
+            this.pickPass.render(renderer, camera.left, scene, helper);
+
+            renderer.setViewport(pickX + halfPickWidth, pickY, pickWidth - halfPickWidth, pickHeight);
+            this.pickPass.render(renderer, camera.right, scene, helper);
+        } else {
+            renderer.setViewport(pickX, pickY, pickWidth, pickHeight);
+            this.pickPass.render(renderer, camera, scene, helper);
+        }
+
+        this.dirty = false;
+    }
+
+    identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
         const { webgl, pickScale } = this;
         if (webgl.isContextLost) return;
 
-        const { gl } = webgl;
-        if (this.pickDirty) {
-            this.render();
+        x *= webgl.pixelRatio;
+        y *= webgl.pixelRatio;
+        y = this.pickPass.drawingBufferHeight - y; // flip y
+
+        const { viewport } = this;
+
+        // check if within viewport
+        if (x < viewport.x ||
+            y < viewport.y ||
+            x > viewport.x + viewport.width ||
+            y > viewport.y + viewport.height
+        ) return;
+
+        if (this.dirty) {
+            this.render(camera);
             this.syncBuffers();
         }
 
-        x *= webgl.pixelRatio;
-        y *= webgl.pixelRatio;
-        y = gl.drawingBufferHeight - y; // flip y
+        const xv = x - viewport.x;
+        const yv = y - viewport.y;
 
-        const xp = Math.round(x * pickScale);
-        const yp = Math.round(y * pickScale);
+        const xp = Math.floor(xv * pickScale);
+        const yp = Math.floor(yv * pickScale);
 
         const objectId = this.getId(xp, yp, this.objectBuffer);
-        if (objectId === -1) return;
+        // console.log('objectId', objectId);
+        if (objectId === -1 || objectId === NullId) return;
 
         const instanceId = this.getId(xp, yp, this.instanceBuffer);
-        if (instanceId === -1) return;
+        // console.log('instanceId', instanceId);
+        if (instanceId === -1 || instanceId === NullId) return;
 
         const groupId = this.getId(xp, yp, this.groupBuffer);
-        if (groupId === -1) return;
+        // console.log('groupId', groupId);
+        if (groupId === -1 || groupId === NullId) return;
 
-        return { objectId, instanceId, groupId };
+        const z = this.getDepth(xp, yp);
+        const position = Vec3.create(x, viewport.height - y, z);
+        if (StereoCamera.is(camera)) {
+            const halfWidth = Math.floor(viewport.width / 2);
+            if (x > viewport.x + halfWidth) {
+                position[0] = viewport.x + (xv - halfWidth) * 2;
+                cameraUnproject(position, position, viewport, camera.right.inverseProjectionView);
+            } else {
+                position[0] = viewport.x + xv * 2;
+                cameraUnproject(position, position, viewport, camera.left.inverseProjectionView);
+            }
+        } else {
+            cameraUnproject(position, position, viewport, camera.inverseProjectionView);
+        }
+
+        // console.log({ { objectId, instanceId, groupId }, position} );
+        return { id: { objectId, instanceId, groupId }, position };
+    }
+
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport) {
+        this.setViewport(viewport.x, viewport.y, viewport.width, viewport.height);
     }
 }

src/mol-canvas3d/passes/postprocessing.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
  */
 
 import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
@@ -12,20 +13,174 @@ import { Texture } from '../../mol-gl/webgl/texture';
 import { ValueCell } from '../../mol-util';
 import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
 import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
-import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
+import { Mat4, Vec2, Vec3 } from '../../mol-math/linear-algebra';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { DrawPass } from './draw';
-import { Camera } from '../../mol-canvas3d/camera';
-import { produce } from 'immer';
+import { ICamera } from '../../mol-canvas3d/camera';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { outlines_frag } from '../../mol-gl/shader/outlines.frag';
+import { ssao_frag } from '../../mol-gl/shader/ssao.frag';
+import { ssaoBlur_frag } from '../../mol-gl/shader/ssao-blur.frag';
+import { postprocessing_frag } from '../../mol-gl/shader/postprocessing.frag';
+import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
+import { Color } from '../../mol-util/color';
+import { FxaaParams, FxaaPass } from './fxaa';
+import { SmaaParams, SmaaPass } from './smaa';
 
-import quad_vert from '../../mol-gl/shader/quad.vert';
-import postprocessing_frag from '../../mol-gl/shader/postprocessing.frag';
+const OutlinesSchema = {
+    ...QuadSchema,
+    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+
+    uMaxPossibleViewZDiff: UniformSpec('f'),
+};
+type OutlinesRenderable = ComputeRenderable<Values<typeof OutlinesSchema>>
+
+function getOutlinesRenderable(ctx: WebGLContext, depthTexture: Texture): OutlinesRenderable {
+    const values: Values<typeof OutlinesSchema> = {
+        ...QuadValues,
+        tDepth: ValueCell.create(depthTexture),
+        uTexSize: ValueCell.create(Vec2.create(depthTexture.getWidth(), depthTexture.getHeight())),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+
+        uMaxPossibleViewZDiff: ValueCell.create(0.5),
+    };
+
+    const schema = { ...OutlinesSchema };
+    const shaderCode = ShaderCode('outlines', quad_vert, outlines_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+const SsaoSchema = {
+    ...QuadSchema,
+    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+
+    uSamples: UniformSpec('v3[]'),
+    dNSamples: DefineSpec('number'),
+
+    uProjection: UniformSpec('m4'),
+    uInvProjection: UniformSpec('m4'),
+
+    uTexSize: UniformSpec('v2'),
+
+    uRadius: UniformSpec('f'),
+    uBias: UniformSpec('f'),
+};
+
+type SsaoRenderable = ComputeRenderable<Values<typeof SsaoSchema>>
+
+function getSsaoRenderable(ctx: WebGLContext, depthTexture: Texture): SsaoRenderable {
+    const values: Values<typeof SsaoSchema> = {
+        ...QuadValues,
+        tDepth: ValueCell.create(depthTexture),
+
+        uSamples: ValueCell.create([0.0, 0.0, 1.0]),
+        dNSamples: ValueCell.create(1),
+
+        uProjection: ValueCell.create(Mat4.identity()),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+
+        uTexSize: ValueCell.create(Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)),
+
+        uRadius: ValueCell.create(8.0),
+        uBias: ValueCell.create(0.025),
+    };
+
+    const schema = { ...SsaoSchema };
+    const shaderCode = ShaderCode('ssao', quad_vert, ssao_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+const SsaoBlurSchema = {
+    ...QuadSchema,
+    tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    uKernel: UniformSpec('f[]'),
+    dOcclusionKernelSize: DefineSpec('number'),
+
+    uBlurDirectionX: UniformSpec('f'),
+    uBlurDirectionY: UniformSpec('f'),
+
+    uMaxPossibleViewZDiff: UniformSpec('f'),
+
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+    dOrthographic: DefineSpec('number'),
+};
+
+type SsaoBlurRenderable = ComputeRenderable<Values<typeof SsaoBlurSchema>>
+
+function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, direction: 'horizontal' | 'vertical'): SsaoBlurRenderable {
+    const values: Values<typeof SsaoBlurSchema> = {
+        ...QuadValues,
+        tSsaoDepth: ValueCell.create(ssaoDepthTexture),
+        uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())),
+
+        uKernel: ValueCell.create([0.0]),
+        dOcclusionKernelSize: ValueCell.create(1),
+
+        uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0),
+        uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0),
+
+        uMaxPossibleViewZDiff: ValueCell.create(0.5),
+
+        uNear: ValueCell.create(0.0),
+        uFar: ValueCell.create(10000.0),
+        dOrthographic: ValueCell.create(0),
+    };
+
+    const schema = { ...SsaoBlurSchema };
+    const shaderCode = ShaderCode('ssao_blur', quad_vert, ssaoBlur_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+function getBlurKernel(kernelSize: number): number[] {
+    let sigma = kernelSize / 3.0;
+    let halfKernelSize = Math.floor((kernelSize + 1) / 2);
+
+    let kernel = [];
+    for (let x = 0; x < halfKernelSize; x++) {
+        kernel.push((1.0 / ((Math.sqrt(2 * Math.PI)) * sigma)) * Math.exp(-x * x / (2 * sigma * sigma)));
+    }
+
+    return kernel;
+}
+
+function getSamples(vectorSamples: Vec3[], nSamples: number): number[] {
+    let samples = [];
+    for (let i = 0; i < nSamples; i++) {
+        let scale = (i * i + 2.0 * i + 1) / (nSamples * nSamples);
+        scale = 0.1 + scale * (1.0 - 0.1);
+
+        samples.push(vectorSamples[i][0] * scale);
+        samples.push(vectorSamples[i][1] * scale);
+        samples.push(vectorSamples[i][2] * scale);
+    }
+
+    return samples;
+}
 
 const PostprocessingSchema = {
     ...QuadSchema,
+    tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tOutlines: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     uTexSize: UniformSpec('v2'),
 
     dOrthographic: DefineSpec('number'),
@@ -34,46 +189,25 @@ const PostprocessingSchema = {
     uFogNear: UniformSpec('f'),
     uFogFar: UniformSpec('f'),
     uFogColor: UniformSpec('v3'),
+    uTransparentBackground: UniformSpec('b'),
+
+    uMaxPossibleViewZDiff: UniformSpec('f'),
 
     dOcclusionEnable: DefineSpec('boolean'),
-    dOcclusionKernelSize: DefineSpec('number'),
-    uOcclusionBias: UniformSpec('f'),
-    uOcclusionRadius: UniformSpec('f'),
 
     dOutlineEnable: DefineSpec('boolean'),
-    uOutlineScale: UniformSpec('f'),
+    dOutlineScale: DefineSpec('number'),
     uOutlineThreshold: UniformSpec('f'),
-
-    dPackedDepth: DefineSpec('boolean'),
 };
-
-export const PostprocessingParams = {
-    occlusion: PD.MappedStatic('off', {
-        on: PD.Group({
-            kernelSize: PD.Numeric(4, { min: 1, max: 32, step: 1 }),
-            bias: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
-            radius: PD.Numeric(64, { min: 0, max: 256, step: 1 }),
-        }),
-        off: PD.Group({})
-    }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
-    outline: PD.MappedStatic('off', {
-        on: PD.Group({
-            scale: PD.Numeric(1, { min: 0, max: 10, step: 1 }),
-            threshold: PD.Numeric(0.8, { min: 0, max: 5, step: 0.01 }),
-        }),
-        off: PD.Group({})
-    }, { cycle: true, description: 'Draw outline around 3D objects' })
-};
-export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
-
 type PostprocessingRenderable = ComputeRenderable<Values<typeof PostprocessingSchema>>
 
-function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTexture: Texture, packedDepth: boolean, props: Partial<PostprocessingProps>): PostprocessingRenderable {
-    const p = { ...PD.getDefaultValues(PostprocessingParams), ...props };
+function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTexture: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture): PostprocessingRenderable {
     const values: Values<typeof PostprocessingSchema> = {
         ...QuadValues,
+        tSsaoDepth: ValueCell.create(ssaoDepthTexture),
         tColor: ValueCell.create(colorTexture),
         tDepth: ValueCell.create(depthTexture),
+        tOutlines: ValueCell.create(outlinesTexture),
         uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
 
         dOrthographic: ValueCell.create(0),
@@ -82,17 +216,15 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
         uFogNear: ValueCell.create(10000),
         uFogFar: ValueCell.create(10000),
         uFogColor: ValueCell.create(Vec3.create(1, 1, 1)),
+        uTransparentBackground: ValueCell.create(false),
 
-        dOcclusionEnable: ValueCell.create(p.occlusion.name === 'on'),
-        dOcclusionKernelSize: ValueCell.create(p.occlusion.name === 'on' ? p.occlusion.params.kernelSize : 4),
-        uOcclusionBias: ValueCell.create(p.occlusion.name === 'on' ? p.occlusion.params.bias : 0.5),
-        uOcclusionRadius: ValueCell.create(p.occlusion.name === 'on' ? p.occlusion.params.radius : 64),
+        uMaxPossibleViewZDiff: ValueCell.create(0.5),
 
-        dOutlineEnable: ValueCell.create(p.outline.name === 'on'),
-        uOutlineScale: ValueCell.create((p.outline.name === 'on' ? p.outline.params.scale : 1) * ctx.pixelRatio),
-        uOutlineThreshold: ValueCell.create(p.outline.name === 'on' ? p.outline.params.threshold : 0.8),
+        dOcclusionEnable: ValueCell.create(false),
 
-        dPackedDepth: ValueCell.create(packedDepth),
+        dOutlineEnable: ValueCell.create(false),
+        dOutlineScale: ValueCell.create(1),
+        uOutlineThreshold: ValueCell.create(0.33),
     };
 
     const schema = { ...PostprocessingSchema };
@@ -102,73 +234,334 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
     return createComputeRenderable(renderItem, values);
 }
 
-export class PostprocessingPass {
-    target: RenderTarget
-    props: PostprocessingProps
-    renderable: PostprocessingRenderable
+export const PostprocessingParams = {
+    occlusion: PD.MappedStatic('on', {
+        on: PD.Group({
+            samples: PD.Numeric(32, {min: 1, max: 256, step: 1}),
+            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final radius is 2^x.' }),
+            bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
+            blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
+        }),
+        off: PD.Group({})
+    }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
+    outline: PD.MappedStatic('off', {
+        on: PD.Group({
+            scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
+            threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
+        }),
+        off: PD.Group({})
+    }, { cycle: true, description: 'Draw outline around 3D objects' }),
+    antialiasing: PD.MappedStatic('smaa', {
+        fxaa: PD.Group(FxaaParams),
+        smaa: PD.Group(SmaaParams),
+        off: PD.Group({})
+    }, { options: [['fxaa', 'FXAA'], ['smaa', 'SMAA'], ['off', 'Off']], description: 'Smooth pixel edges' }),
+};
+export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
 
-    constructor(private webgl: WebGLContext, private camera: Camera, drawPass: DrawPass, props: Partial<PostprocessingProps>) {
-        const { gl } = webgl;
-        this.target = webgl.createRenderTarget(gl.drawingBufferWidth, gl.drawingBufferHeight);
-        this.props = { ...PD.getDefaultValues(PostprocessingParams), ...props };
-        const { colorTarget, depthTexture, packedDepth } = drawPass;
-        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture, packedDepth, this.props);
+export class PostprocessingPass {
+    static isEnabled(props: PostprocessingProps) {
+        return props.occlusion.name === 'on' || props.outline.name === 'on';
     }
 
-    get enabled() {
-        return this.props.occlusion.name === 'on' || this.props.outline.name === 'on';
+    readonly target: RenderTarget
+
+    private readonly outlinesTarget: RenderTarget
+    private readonly outlinesRenderable: OutlinesRenderable
+
+    private readonly randomHemisphereVector: Vec3[]
+    private readonly ssaoFramebuffer: Framebuffer
+    private readonly ssaoBlurFirstPassFramebuffer: Framebuffer
+    private readonly ssaoBlurSecondPassFramebuffer: Framebuffer
+
+    private readonly ssaoDepthTexture: Texture
+    private readonly ssaoDepthBlurProxyTexture: Texture
+
+    private readonly ssaoRenderable: SsaoRenderable
+    private readonly ssaoBlurFirstPassRenderable: SsaoBlurRenderable
+    private readonly ssaoBlurSecondPassRenderable: SsaoBlurRenderable
+
+    private nSamples: number
+    private blurKernelSize: number
+
+    private readonly renderable: PostprocessingRenderable
+
+    private scale: number
+
+    constructor(private webgl: WebGLContext, drawPass: DrawPass) {
+        this.scale = 1 / this.webgl.pixelRatio;
+
+        const { colorTarget, depthTexture } = drawPass;
+        const width = colorTarget.getWidth();
+        const height = colorTarget.getHeight();
+
+        this.nSamples = 1;
+        this.blurKernelSize = 1;
+
+        this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
+
+        this.outlinesTarget = webgl.createRenderTarget(width, height, false);
+        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTexture);
+
+        this.randomHemisphereVector = [];
+        for (let i = 0; i < 256; i++) {
+            let v = Vec3();
+            v[0] = Math.random() * 2.0 - 1.0;
+            v[1] = Math.random() * 2.0 - 1.0;
+            v[2] = Math.random();
+            Vec3.normalize(v, v);
+            Vec3.scale(v, v, Math.random());
+            this.randomHemisphereVector.push(v);
+        }
+        this.ssaoFramebuffer = webgl.resources.framebuffer();
+        this.ssaoBlurFirstPassFramebuffer = webgl.resources.framebuffer();
+        this.ssaoBlurSecondPassFramebuffer = webgl.resources.framebuffer();
+
+        const sw = Math.floor(width * this.scale);
+        const sh = Math.floor(height * this.scale);
+
+        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+        this.ssaoDepthTexture.define(sw, sh);
+        this.ssaoDepthTexture.attachFramebuffer(this.ssaoFramebuffer, 'color0');
+
+        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+        this.ssaoDepthBlurProxyTexture.define(sw, sh);
+        this.ssaoDepthBlurProxyTexture.attachFramebuffer(this.ssaoBlurFirstPassFramebuffer, 'color0');
+
+        this.ssaoDepthTexture.attachFramebuffer(this.ssaoBlurSecondPassFramebuffer, 'color0');
+
+        this.ssaoRenderable = getSsaoRenderable(webgl, depthTexture);
+        this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
+        this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
+        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture, this.outlinesTarget.texture, this.ssaoDepthTexture);
     }
 
     setSize(width: number, height: number) {
-        this.target.setSize(width, height);
-        ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        if (width !== w || height !== h) {
+            const sw = Math.floor(width * this.scale);
+            const sh = Math.floor(height * this.scale);
+            this.target.setSize(width, height);
+            this.outlinesTarget.setSize(width, height);
+            this.ssaoDepthTexture.define(sw, sh);
+            this.ssaoDepthBlurProxyTexture.define(sw, sh);
+
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
+        }
     }
 
-    setProps(props: Partial<PostprocessingProps>) {
-        this.props = produce(this.props, p => {
-            if (props.occlusion !== undefined) {
-                p.occlusion.name = props.occlusion.name;
-                ValueCell.updateIfChanged(this.renderable.values.dOcclusionEnable, props.occlusion.name === 'on');
-                if (props.occlusion.name === 'on') {
-                    p.occlusion.params = { ...props.occlusion.params };
-                    ValueCell.updateIfChanged(this.renderable.values.dOcclusionKernelSize, props.occlusion.params.kernelSize);
-                    ValueCell.updateIfChanged(this.renderable.values.uOcclusionBias, props.occlusion.params.bias);
-                    ValueCell.updateIfChanged(this.renderable.values.uOcclusionRadius, props.occlusion.params.radius);
-                }
+    private updateState(camera: ICamera, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
+        let needsUpdateMain = false;
+        let needsUpdateSsao = false;
+        let needsUpdateSsaoBlur = false;
+
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+        const outlinesEnabled = props.outline.name === 'on';
+        const occlusionEnabled = props.occlusion.name === 'on';
+
+        let invProjection = Mat4.identity();
+        Mat4.invert(invProjection, camera.projection);
+
+        if (props.occlusion.name === 'on') {
+            ValueCell.updateIfChanged(this.ssaoRenderable.values.uProjection, camera.projection);
+            ValueCell.updateIfChanged(this.ssaoRenderable.values.uInvProjection, invProjection);
+
+            ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.uNear, camera.near);
+            ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.uNear, camera.near);
+
+            ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.uFar, camera.far);
+            ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.uFar, camera.far);
+
+            if (this.ssaoBlurFirstPassRenderable.values.dOrthographic.ref.value !== orthographic) { needsUpdateSsaoBlur = true; }
+            ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.dOrthographic, orthographic);
+            ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.dOrthographic, orthographic);
+
+            if (this.nSamples !== props.occlusion.params.samples) {
+                needsUpdateSsao = true;
+
+                this.nSamples = props.occlusion.params.samples;
+                ValueCell.updateIfChanged(this.ssaoRenderable.values.uSamples, getSamples(this.randomHemisphereVector, this.nSamples));
+                ValueCell.updateIfChanged(this.ssaoRenderable.values.dNSamples, this.nSamples);
+            }
+            ValueCell.updateIfChanged(this.ssaoRenderable.values.uRadius, Math.pow(2, props.occlusion.params.radius));
+            ValueCell.updateIfChanged(this.ssaoRenderable.values.uBias, props.occlusion.params.bias);
+
+            if (this.blurKernelSize !== props.occlusion.params.blurKernelSize) {
+                needsUpdateSsaoBlur = true;
+
+                this.blurKernelSize = props.occlusion.params.blurKernelSize;
+                let kernel = getBlurKernel(this.blurKernelSize);
+
+                ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.uKernel, kernel);
+                ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.uKernel, kernel);
+                ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
+                ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
             }
 
-            if (props.outline !== undefined) {
-                p.outline.name = props.outline.name;
-                ValueCell.updateIfChanged(this.renderable.values.dOutlineEnable, props.outline.name === 'on');
-                if (props.outline.name === 'on') {
-                    p.outline.params = { ...props.outline.params };
-                    ValueCell.updateIfChanged(this.renderable.values.uOutlineScale, props.outline.params.scale);
-                    ValueCell.updateIfChanged(this.renderable.values.uOutlineThreshold, props.outline.params.threshold);
-                }
-            }
-        });
+        }
 
-        this.renderable.update();
-    }
+        if (props.outline.name === 'on') {
+            const factor = Math.pow(1000, props.outline.params.threshold) / 1000;
+            const maxPossibleViewZDiff = factor * (camera.far - camera.near);
+            const outlineScale = props.outline.params.scale - 1;
 
-    render(toDrawingBuffer: boolean) {
-        ValueCell.update(this.renderable.values.uFar, this.camera.far);
-        ValueCell.update(this.renderable.values.uNear, this.camera.near);
-        ValueCell.update(this.renderable.values.uFogFar, this.camera.fogFar);
-        ValueCell.update(this.renderable.values.uFogNear, this.camera.fogNear);
-        ValueCell.update(this.renderable.values.dOrthographic, this.camera.state.mode === 'orthographic' ? 1 : 0);
+            ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
+            ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
+            ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
+
+            ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
+            ValueCell.updateIfChanged(this.renderable.values.uOutlineThreshold, props.outline.params.threshold);
+            if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) { needsUpdateMain = true; }
+            ValueCell.updateIfChanged(this.renderable.values.dOutlineScale, outlineScale);
+        }
+
+        ValueCell.updateIfChanged(this.renderable.values.uFar, camera.far);
+        ValueCell.updateIfChanged(this.renderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.renderable.values.uFogFar, camera.fogFar);
+        ValueCell.updateIfChanged(this.renderable.values.uFogNear, camera.fogNear);
+        ValueCell.update(this.renderable.values.uFogColor, Color.toVec3Normalized(this.renderable.values.uFogColor.ref.value, backgroundColor));
+        ValueCell.updateIfChanged(this.renderable.values.uTransparentBackground, transparentBackground);
+        if (this.renderable.values.dOrthographic.ref.value !== orthographic) { needsUpdateMain = true; }
+        ValueCell.updateIfChanged(this.renderable.values.dOrthographic, orthographic);
+        if (this.renderable.values.dOutlineEnable.ref.value !== outlinesEnabled) { needsUpdateMain = true; }
+        ValueCell.updateIfChanged(this.renderable.values.dOutlineEnable, outlinesEnabled);
+        if (this.renderable.values.dOcclusionEnable.ref.value !== occlusionEnabled) { needsUpdateMain = true; }
+        ValueCell.updateIfChanged(this.renderable.values.dOcclusionEnable, occlusionEnabled);
+
+        if (needsUpdateSsao) {
+            this.ssaoRenderable.update();
+        }
+
+        if (needsUpdateSsaoBlur) {
+            this.ssaoBlurFirstPassRenderable.update();
+            this.ssaoBlurSecondPassRenderable.update();
+        }
+
+        if (needsUpdateMain) {
+            this.renderable.update();
+        }
 
         const { gl, state } = this.webgl;
-        if (toDrawingBuffer) {
-            this.webgl.unbindFramebuffer();
-            gl.viewport(0, 0, gl.drawingBufferWidth, gl.drawingBufferHeight);
-        } else {
-            this.target.bind();
-        }
-        state.disable(gl.SCISSOR_TEST);
+
+        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);
+    }
+
+    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
+        this.updateState(camera, transparentBackground, backgroundColor, props);
+
+        if (props.outline.name === 'on') {
+            this.outlinesTarget.bind();
+            this.outlinesRenderable.render();
+        }
+
+        if (props.occlusion.name === 'on') {
+            const { x, y, width, height } = camera.viewport;
+            const sx = Math.floor(x * this.scale);
+            const sy = Math.floor(y * this.scale);
+            const sw = Math.floor(width * this.scale);
+            const sh = Math.floor(height * this.scale);
+            this.webgl.gl.viewport(sx, sy, sw, sh);
+            this.webgl.gl.scissor(sx, sy, sw, sh);
+
+            this.ssaoFramebuffer.bind();
+            this.ssaoRenderable.render();
+
+            this.ssaoBlurFirstPassFramebuffer.bind();
+            this.ssaoBlurFirstPassRenderable.render();
+
+            this.ssaoBlurSecondPassFramebuffer.bind();
+            this.ssaoBlurSecondPassRenderable.render();
+
+            this.webgl.gl.viewport(x, y, width, height);
+            this.webgl.gl.scissor(x, y, width, height);
+        }
+
+        if (toDrawingBuffer) {
+            this.webgl.unbindFramebuffer();
+        } else {
+            this.target.bind();
+        }
+
+        const { gl, state } = this.webgl;
+        state.clearColor(0, 0, 0, 1);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
         this.renderable.render();
     }
-}
+}
+
+export class AntialiasingPass {
+    static isEnabled(props: PostprocessingProps) {
+        return props.antialiasing.name !== 'off';
+    }
+
+    readonly target: RenderTarget
+    private readonly fxaa: FxaaPass
+    private readonly smaa: SmaaPass
+
+    constructor(webgl: WebGLContext, private drawPass: DrawPass) {
+        const { colorTarget } = drawPass;
+        const width = colorTarget.getWidth();
+        const height = colorTarget.getHeight();
+
+        this.target = webgl.createRenderTarget(width, height, false);
+        this.fxaa = new FxaaPass(webgl, this.target.texture);
+        this.smaa = new SmaaPass(webgl, this.target.texture);
+    }
+
+    setSize(width: number, height: number) {
+        const w = this.target.texture.getWidth();
+        const h = this.target.texture.getHeight();
+
+        if (width !== w || height !== h) {
+            this.target.setSize(width, height);
+            this.fxaa.setSize(width, height);
+            if (this.smaa.supported) this.smaa.setSize(width, height);
+        }
+    }
+
+    private _renderFxaa(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
+        if (props.antialiasing.name !== 'fxaa') return;
+
+        const input = PostprocessingPass.isEnabled(props)
+            ? this.drawPass.postprocessing.target.texture
+            : this.drawPass.colorTarget.texture;
+        this.fxaa.update(input, props.antialiasing.params);
+        this.fxaa.render(camera.viewport, toDrawingBuffer ? undefined : this.target);
+    }
+
+    private _renderSmaa(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
+        if (props.antialiasing.name !== 'smaa') return;
+
+        const input = PostprocessingPass.isEnabled(props)
+            ? this.drawPass.postprocessing.target.texture
+            : this.drawPass.colorTarget.texture;
+        this.smaa.update(input, props.antialiasing.params);
+        this.smaa.render(camera.viewport, toDrawingBuffer ? undefined : this.target);
+    }
+
+    render(camera: ICamera, toDrawingBuffer: boolean, props: PostprocessingProps) {
+        if (props.antialiasing.name === 'off') return;
+
+        if (props.antialiasing.name === 'fxaa') {
+            this._renderFxaa(camera, toDrawingBuffer, props);
+        } else if (props.antialiasing.name === 'smaa') {
+            if (!this.smaa.supported) {
+                throw new Error('SMAA not supported, missing "HTMLImageElement"');
+            }
+            this._renderSmaa(camera, toDrawingBuffer, props);
+        }
+    }
+}
+

src/mol-canvas3d/passes/wboit.ts

@@ -0,0 +1,143 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { ValueCell } from '../../mol-util';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { evaluateWboit_frag } from '../../mol-gl/shader/evaluate-wboit.frag';
+import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
+import { Vec2 } from '../../mol-math/linear-algebra';
+import { isDebugMode } from '../../mol-util/debug';
+
+const EvaluateWboitSchema = {
+    ...QuadSchema,
+    tWboitA: TextureSpec('texture', 'rgba', 'float', 'nearest'),
+    tWboitB: TextureSpec('texture', 'rgba', 'float', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+};
+const EvaluateWboitShaderCode = ShaderCode('evaluate-wboit', quad_vert, evaluateWboit_frag);
+type EvaluateWboitRenderable = ComputeRenderable<Values<typeof EvaluateWboitSchema>>
+
+function getEvaluateWboitRenderable(ctx: WebGLContext, wboitATexture: Texture, wboitBTexture: Texture): EvaluateWboitRenderable {
+    const values: Values<typeof EvaluateWboitSchema> = {
+        ...QuadValues,
+        tWboitA: ValueCell.create(wboitATexture),
+        tWboitB: ValueCell.create(wboitBTexture),
+        uTexSize: ValueCell.create(Vec2.create(wboitATexture.getWidth(), wboitATexture.getHeight())),
+    };
+
+    const schema = { ...EvaluateWboitSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', EvaluateWboitShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+//
+
+export class WboitPass {
+    private readonly renderable: EvaluateWboitRenderable
+
+    private readonly framebuffer: Framebuffer
+    private readonly textureA: Texture
+    private readonly textureB: Texture
+
+    private _supported = false;
+    get supported() {
+        return this._supported;
+    }
+
+    bind() {
+        const { state, gl } = this.webgl;
+
+        this.framebuffer.bind();
+
+        state.clearColor(0, 0, 0, 1);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        state.disable(gl.DEPTH_TEST);
+
+        state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ZERO, gl.ONE_MINUS_SRC_ALPHA);
+        state.enable(gl.BLEND);
+    }
+
+    render() {
+        const { state, gl } = this.webgl;
+
+        state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
+        state.enable(gl.BLEND);
+
+        this.renderable.update();
+        this.renderable.render();
+    }
+
+    setSize(width: number, height: number) {
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        if (width !== w || height !== h) {
+            this.textureA.define(width, height);
+            this.textureB.define(width, height);
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    reset() {
+        if (this._supported) this._init();
+    }
+
+    private _init() {
+        const { extensions: { drawBuffers } } = this.webgl;
+
+        this.framebuffer.bind();
+        drawBuffers!.drawBuffers([
+            drawBuffers!.COLOR_ATTACHMENT0,
+            drawBuffers!.COLOR_ATTACHMENT1,
+        ]);
+
+        this.textureA.attachFramebuffer(this.framebuffer, 'color0');
+        this.textureB.attachFramebuffer(this.framebuffer, 'color1');
+    }
+
+    static isSupported(webgl: WebGLContext) {
+        const { extensions: { drawBuffers, textureFloat, colorBufferFloat, depthTexture } } = webgl;
+        if (!textureFloat || !colorBufferFloat || !depthTexture || !drawBuffers) {
+            if (isDebugMode) {
+                const missing: string[] = [];
+                if (!textureFloat) missing.push('textureFloat');
+                if (!colorBufferFloat) missing.push('colorBufferFloat');
+                if (!depthTexture) missing.push('depthTexture');
+                if (!drawBuffers) missing.push('drawBuffers');
+                console.log(`Missing "${missing.join('", "')}" extensions required for "wboit"`);
+            }
+            return false;
+        } else {
+            return true;
+        }
+    }
+
+    constructor(private webgl: WebGLContext, width: number, height: number) {
+        if (!WboitPass.isSupported(webgl)) return;
+
+        const { resources } = webgl;
+
+        this.textureA = resources.texture('image-float32', 'rgba', 'float', 'nearest');
+        this.textureA.define(width, height);
+
+        this.textureB = resources.texture('image-float32', 'rgba', 'float', 'nearest');
+        this.textureB.define(width, height);
+
+        this.renderable = getEvaluateWboitRenderable(webgl, this.textureA, this.textureB);
+        this.framebuffer = resources.framebuffer();
+
+        this._supported = true;
+        this._init();
+    }
+}

src/mol-canvas3d/util.ts

@@ -5,14 +5,14 @@
  */
 
 /** Set canvas size taking `devicePixelRatio` into account */
-export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height: number) {
-    canvas.width = Math.round(window.devicePixelRatio * width);
-    canvas.height = Math.round(window.devicePixelRatio * height);
+export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height: number, scale = 1) {
+    canvas.width = Math.round(window.devicePixelRatio * scale * width);
+    canvas.height = Math.round(window.devicePixelRatio * scale * height);
     Object.assign(canvas.style, { width: `${width}px`, height: `${height}px` });
 }
 
 /** Resize canvas to container element taking `devicePixelRatio` into account */
-export function resizeCanvas (canvas: HTMLCanvasElement, container: Element) {
+export function resizeCanvas (canvas: HTMLCanvasElement, container: Element, scale = 1) {
     let width = window.innerWidth;
     let height = window.innerHeight;
     if (container !== document.body) {
@@ -20,7 +20,7 @@ export function resizeCanvas (canvas: HTMLCanvasElement, container: Element) {
         width = bounds.right - bounds.left;
         height = bounds.bottom - bounds.top;
     }
-    setCanvasSize(canvas, width, height);
+    setCanvasSize(canvas, width, height, scale);
 }
 
 function _canvasToBlob(canvas: HTMLCanvasElement, callback: BlobCallback, type?: string, quality?: any) {

src/mol-data/_spec/iterators.spec.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Iterator from '../iterator';
+import { Iterator } from '../iterator';
 
 function iteratorToArray<T>(it: Iterator<T>): T[] {
     const ret = [];

src/mol-data/db.ts

@@ -5,9 +5,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import Database from './db/database';
-import Table from './db/table';
-import Column from './db/column';
+import { Database } from './db/database';
+import { Table } from './db/table';
+import { Column } from './db/column';
 import * as ColumnHelpers from './db/column-helpers';
 
 type DatabaseCollection<T extends Database.Schema> = { [name: string]: Database<T> }

src/mol-data/db/_spec/table.spec.ts

@@ -6,8 +6,8 @@
  */
 
 import * as ColumnHelpers from '../column-helpers';
-import Column from '../column';
-import Table from '../table';
+import { Column } from '../column';
+import { Table } from '../table';
 
 describe('column', () => {
     const cc = Column.ofConst(10, 2, Column.Schema.int);

src/mol-data/db/column-helpers.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Column from './column';
+import { Column } from './column';
 
 export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams<any>) {
     const start = params && typeof params.start !== 'undefined' ? Math.max(Math.min(params.start, rowCount - 1), 0) : 0;

src/mol-data/db/column.ts

@@ -230,7 +230,7 @@ namespace Column {
     }
 }
 
-export default Column;
+export { Column };
 
 function createFirstIndexMapOfColumn<T>(c: Column<T>): Map<T, number> {
     const map = new Map<T, number>();
@@ -364,7 +364,7 @@ function isIdentity(map: ArrayLike<number>, rowCount: number) {
 }
 
 function columnView<T>(c: Column<T>, map: ArrayLike<number>, checkIdentity: boolean): Column<T> {
-    if (!c.isDefined || c.rowCount === 0) return c;
+    if (c.rowCount === 0) return c;
     if (checkIdentity && isIdentity(map, c.rowCount)) return c;
     if (!!c.__array && typeof c.value(0) === typeof c.__array[0]) return arrayView(c, map);
     return viewFull(c, map);

src/mol-data/db/database.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Table from './table';
+import { Table } from './table';
 
 /** A collection of tables */
 type Database<Schema extends Database.Schema> = {
@@ -41,4 +41,4 @@ namespace Database {
     }
 }
 
-export default Database;
+export { Database };

src/mol-data/db/table.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Column from './column';
+import { Column } from './column';
 import { sortArray } from '../util/sort';
 import { StringBuilder } from '../../mol-util';
 
@@ -280,4 +280,4 @@ namespace Table {
     }
 }
 
-export default Table;
+export { Table };

src/mol-data/index.ts

@@ -6,7 +6,7 @@
 
 import * as DB from './db';
 import * as Int from './int';
-import Iterator from './iterator';
+import { Iterator } from './iterator';
 import * as Util from './util';
 import * as Generic from './generic';
 

src/mol-data/int.ts

@@ -4,13 +4,13 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Interval from './int/interval';
-import OrderedSet from './int/ordered-set';
-import Segmentation from './int/segmentation';
-import SortedArray from './int/sorted-array';
-import Tuple from './int/tuple';
-import LinkedIndex from './int/linked-index';
-import IntMap from './int/map';
-import Iterator from './iterator';
+import { Interval } from './int/interval';
+import { OrderedSet } from './int/ordered-set';
+import { Segmentation } from './int/segmentation';
+import { SortedArray } from './int/sorted-array';
+import { IntTuple as Tuple } from './int/tuple';
+import { LinkedIndex } from './int/linked-index';
+import { IntMap } from './int/map';
+import { Iterator } from './iterator';
 
 export { Interval, OrderedSet, Segmentation, SortedArray, Tuple, LinkedIndex, IntMap, Iterator };

src/mol-data/int/_spec/interval.spec.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Interval from '../interval';
+import { Interval } from '../interval';
 
 describe('interval', () => {
     function testI(name: string, a: Interval, b: Interval) {

src/mol-data/int/_spec/linked-index.spec.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import LinkedIndex from '../linked-index';
+import { LinkedIndex } from '../linked-index';
 
 describe('linked-index', () => {
     it('initial state', () => {

src/mol-data/int/_spec/ordered-set.spec.ts

@@ -4,9 +4,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import OrderedSet from '../ordered-set';
-import Interval from '../interval';
-import SortedArray from '../sorted-array';
+import { OrderedSet } from '../ordered-set';
+import { Interval } from '../interval';
+import { SortedArray } from '../sorted-array';
 
 describe('ordered set', () => {
     function ordSetToArray(set: OrderedSet) {

src/mol-data/int/_spec/segmentation.spec.ts

@@ -4,9 +4,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import OrderedSet from '../ordered-set';
-import Interval from '../interval';
-import Segmentation from '../segmentation';
+import { OrderedSet } from '../ordered-set';
+import { Interval } from '../interval';
+import { Segmentation } from '../segmentation';
 
 describe('segments', () => {
     const data = OrderedSet.ofSortedArray([4, 9, 10, 11, 14, 15, 16]);