1.3.2

.eslintrc.json

@@ -31,14 +31,7 @@
         "no-unsafe-finally": "warn",
         "no-var": "error",
         "spaced-comment": "error",
-        "semi": "warn",
-        "no-restricted-syntax": [
-            "error",
-            {
-                "selector": "ExportDefaultDeclaration",
-                "message": "Default exports are not allowed"
-            }
-        ]
+        "semi": "warn"
     },
     "overrides": [
         {

.npmignore

@@ -1 +1 @@
-tsconfig.commonjs.tsbuildinfo
+tsconfig.commonjs.buildinfo

README.md

@@ -5,12 +5,15 @@
 
 # Mol*
 
-The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as a basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open-source and available to anyone who wants to use it for developing visualization tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
 
+This particular project is the implementation of this technology (still under development).
 
-## Project Structure Overview
+*If you are looking for the "MOLeculAR structure annoTator", that package is now available on NPM as [MolArt](https://www.npmjs.com/package/molart).*
 
-The core of Mol* consists of these modules (see under `src/`):
+## Project Overview
+
+The core of Mol* currently consists of these modules (see under `src/`):
 
 - `mol-task` Computation abstraction with progress tracking and cancellation support.
 - `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
@@ -26,6 +29,7 @@ The core of Mol* consists of these modules (see under `src/`):
 - `mol-gl` A wrapper around WebGL.
 - `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
 - `mol-state` State representation tree with state saving and automatic updates.
+- `mol-app` Components for building UIs.
 - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
 - `mol-plugin-state` State transformations, builders, and managers.
 - `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
@@ -37,7 +41,7 @@ Moreover, the project contains the implementation of `servers`, including
 - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
 - `servers/plugin-state` A basic server to store Mol* Plugin states.
 
-The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
 
 ## Previous Work
 This project builds on experience from previous solutions:
@@ -165,9 +169,12 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 ## Contributing
 Just open an issue or make a pull request. All contributions are welcome.
 
+## Roadmap
+Continually develop this prototype project. As individual modules become stable, make them into standalone libraries.
+
 ## Funding
 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)
+* [EntosAI](https://www.entos.ai) (``alpha-orbitals`` extension)

docs/interesting-pdb-entries.md

@@ -26,5 +26,3 @@
     * Protein (1BRR, 5Z6Y)
     * DNA (5D3G)
 * Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
-* Long linear sugar chain (4HG6)
-* Anisotropic B-factors/Ellipsoids (1EJG)

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.2",
+  "version": "1.3.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -14,7 +14,6 @@
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
     "test": "npm run lint && jest",
-    "jest": "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",
     "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
@@ -116,7 +115,7 @@
     "simple-git": "^2.25.0",
     "style-loader": "^2.0.0",
     "ts-jest": "^26.4.4",
-    "typescript": "^4.2.3",
+    "typescript": "^4.1.2",
     "webpack": "^4.44.1",
     "webpack-cli": "^3.3.12",
     "webpack-version-file-plugin": "^0.4.0"
@@ -138,14 +137,14 @@
     "cors": "^2.8.5",
     "express": "^4.17.1",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^8.0.1",
+    "immer": "^8.0.0",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.1",
     "react": "^17.0.1",
     "react-dom": "^17.0.1",
-    "rxjs": "^6.6.6",
+    "rxjs": "^6.6.3",
     "swagger-ui-dist": "^3.37.2",
-    "tslib": "^2.1.0",
+    "tslib": "^2.0.3",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

src/apps/docking-viewer/index.ts

@@ -5,32 +5,30 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Structure } from '../../mol-model/structure';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
-import { createPlugin } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
-import { PluginBehaviors } from '../../mol-plugin/behavior';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginConfig } from '../../mol-plugin/config';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { StateObject } from '../../mol-state';
-import { Task } from '../../mol-task';
-import { Color } from '../../mol-util/color';
-import { ColorNames } from '../../mol-util/color/names';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import '../../mol-util/polyfill';
-import { ObjectKeys } from '../../mol-util/type-helpers';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import './index.html';
-import { ShowButtons, StructurePreset, ViewportComponent } from './viewport';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { PluginConfig } from '../../mol-plugin/config';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { Structure } from '../../mol-model/structure';
+import { PluginStateTransform, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Task } from '../../mol-task';
+import { StateObject } from '../../mol-state';
+import { ViewportComponent, StructurePreset, ShowButtons } from './viewport';
+import { PluginBehaviors } from '../../mol-plugin/behavior';
+import { ColorNames } from '../../mol-util/color/names';
+import { Color } from '../../mol-util/color';
 
 require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
-export { Viewer as DockingViewer };
+export { setProductionMode, setDebugMode } from '../../mol-util/debug';
 
 const DefaultViewerOptions = {
     extensions: ObjectKeys({}),
@@ -54,7 +52,7 @@ const DefaultViewerOptions = {
 };
 
 class Viewer {
-    plugin: PluginUIContext
+    plugin: PluginContext
 
     constructor(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
         const o = { ...DefaultViewerOptions, ...{
@@ -71,10 +69,9 @@ class Viewer {
             viewportShowSelectionMode: false,
             viewportShowAnimation: false,
         } };
-        const defaultSpec = DefaultPluginUISpec();
 
-        const spec: PluginUISpec = {
-            actions: defaultSpec.actions,
+        const spec: PluginSpec = {
+            actions: [...DefaultPluginSpec.actions],
             behaviors: [
                 PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
                 PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
@@ -84,23 +81,23 @@ class Viewer {
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
             ],
-            animations: defaultSpec.animations,
-            customParamEditors: defaultSpec.customParamEditors,
+            animations: [...DefaultPluginSpec.animations || []],
+            customParamEditors: DefaultPluginSpec.customParamEditors,
             layout: {
                 initial: {
                     isExpanded: o.layoutIsExpanded,
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
                 },
-            },
-            components: {
-                ...defaultSpec.components,
                 controls: {
-                    ...defaultSpec.components?.controls,
+                    ...DefaultPluginSpec.layout && DefaultPluginSpec.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',
                 viewport: {
                     view: ViewportComponent
@@ -211,3 +208,4 @@ const MergeStructures = PluginStateTransform.BuiltIn({
 });
 
 (window as any).DockingViewer = Viewer;
+export { Viewer as DockingViewer };

src/apps/docking-viewer/viewport.tsx

@@ -4,23 +4,24 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import * as React from 'react';
+import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
+import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
+import { LociLabels } from '../../mol-plugin-ui/controls';
+import { Toasts } from '../../mol-plugin-ui/toast';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { StateObjectRef } from '../../mol-state';
+import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { InteractionsRepresentationProvider } from '../../mol-model-props/computed/representations/interactions';
 import { InteractionTypeColorThemeProvider } from '../../mol-model-props/computed/themes/interaction-type';
-import { presetStaticComponent, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
-import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
-import { PluginUIComponent } from '../../mol-plugin-ui/base';
-import { LociLabels } from '../../mol-plugin-ui/controls';
-import { Button } from '../../mol-plugin-ui/controls/common';
-import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
-import { Toasts } from '../../mol-plugin-ui/toast';
-import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginConfig } from '../../mol-plugin/config';
 import { PluginContext } from '../../mol-plugin/context';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { StateObjectRef } from '../../mol-state';
+import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
 import { Color } from '../../mol-util/color';
+import { PluginConfig } from '../../mol-plugin/config';
 
 function shinyStyle(plugin: PluginContext) {
     return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {

src/apps/viewer/index.html

@@ -48,14 +48,18 @@
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
             if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
+            var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
+            var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
+            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
-            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').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,
-                collapseLeftPanel: collapseLeftPanel,
                 pdbProvider: pdbProvider || 'pdbe',
                 emdbProvider: emdbProvider || 'pdbe',
             });

src/apps/viewer/index.ts

@@ -5,43 +5,42 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
-import { CellPack } from '../../extensions/cellpack';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
-import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { Mp4Export } from '../../extensions/mp4-export';
-import { PDBeStructureQualityReport } from '../../extensions/pdbe';
-import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
-import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
-import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
-import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
-import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createPlugin } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginConfig } from '../../mol-plugin/config';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { PluginState } from '../../mol-plugin/state';
-import { StateObjectSelector } from '../../mol-state';
-import { Asset } from '../../mol-util/assets';
-import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
-import { ObjectKeys } from '../../mol-util/type-helpers';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import './index.html';
 import './embedded.html';
 import './favicon.ico';
-import './index.html';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { PluginConfig } from '../../mol-plugin/config';
+import { CellPack } from '../../extensions/cellpack';
+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { Asset } from '../../mol-util/assets';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import { PluginState } from '../../mol-plugin/state';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+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');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { setProductionMode, setDebugMode } from '../../mol-util/debug';
 
 const CustomFormats = [
     ['g3d', G3dProvider] as const
@@ -68,7 +67,6 @@ const DefaultViewerOptions = {
     layoutShowSequence: true,
     layoutShowLog: true,
     layoutShowLeftPanel: true,
-    collapseLeftPanel: false,
     disableAntialiasing: false,
     pixelScale: 1,
     enableWboit: true,
@@ -87,42 +85,35 @@ const DefaultViewerOptions = {
 type ViewerOptions = typeof DefaultViewerOptions;
 
 export class Viewer {
-    plugin: PluginUIContext
+    plugin: PluginContext
 
     constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
         const o = { ...DefaultViewerOptions, ...options };
-        const defaultSpec = DefaultPluginUISpec();
 
-        const spec: PluginUISpec = {
-            actions: defaultSpec.actions,
+        const spec: PluginSpec = {
+            actions: [...DefaultPluginSpec.actions],
             behaviors: [
-                ...defaultSpec.behaviors,
+                ...DefaultPluginSpec.behaviors,
                 ...o.extensions.map(e => Extensions[e]),
             ],
-            animations: [...defaultSpec.animations || []],
-            customParamEditors: defaultSpec.customParamEditors,
+            animations: [...DefaultPluginSpec.animations || []],
+            customParamEditors: DefaultPluginSpec.customParamEditors,
             customFormats: o?.customFormats,
             layout: {
                 initial: {
                     isExpanded: o.layoutIsExpanded,
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
-                    regionState: {
-                        bottom: 'full',
-                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
-                        right: 'full',
-                        top: 'full',
-                    }
                 },
-            },
-            components: {
-                ...defaultSpec.components,
                 controls: {
-                    ...defaultSpec.components?.controls,
+                    ...DefaultPluginSpec.layout && DefaultPluginSpec.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',
             },
             config: [

src/cli/cif2bcif/converter.ts

@@ -70,7 +70,7 @@ function classify(name: string, field: CifField): CifWriter.Field {
     }
 }
 
-export function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
+export default 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 { parseCifText } from '../../mol-io/reader/cif/text/parser';
+import parseText 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 parseCifText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
+    const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
     if (mmcifDic.isError) throw mmcifDic;
 
     await ensureIhmDicAvailable();
-    const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
+    const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
     if (ihmDic.isError) throw ihmDic;
 
     await ensureCarbBranchDicAvailable();
-    const carbBranchDic = await parseCifText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
+    const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
     if (carbBranchDic.isError) throw carbBranchDic;
 
     await ensureCarbCompDicAvailable();
-    const carbCompDic = await parseCifText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
+    const carbCompDic = await parseText(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 parseCifText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
+    const cifCoreDic = await parseText(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 parseCifText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
+                const dic = await parseText(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 parseCifText(fs.readFileSync(dicPath, 'utf8')).run();
+    const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
     if (dic.isError) throw dic;
 
     const dicVersion = getDicVersion(dic.result.blocks[0]);

src/cli/state-docs/index.ts

@@ -18,6 +18,7 @@ _.StateTransforms.Data.Download.id;
 
 // Empty plugin context
 const ctx = new PluginContext({
+    actions: [],
     behaviors: []
 });
 

src/examples/alpha-orbitals/controls.tsx

@@ -4,6 +4,7 @@
  * @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';

src/examples/alpha-orbitals/index.html

@@ -22,23 +22,7 @@
                 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>
@@ -46,14 +30,6 @@
     <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>

src/examples/alpha-orbitals/index.ts

@@ -4,25 +4,24 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { BehaviorSubject } from 'rxjs';
-import { debounceTime, skip } from 'rxjs/operators';
-import { AlphaOrbital, Basis } from '../../extensions/alpha-orbitals/data-model';
 import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
 import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
-import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
+import { createPluginAsync, DefaultPluginSpec } from '../../mol-plugin';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { createPluginAsync } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
-import { PluginCommands } from '../../mol-plugin/commands';
 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 {
@@ -50,26 +49,18 @@ type Selectors = {
 }
 
 export class AlphaOrbitalsExample {
-    plugin: PluginUIContext;
+    plugin: PluginContext;
 
     async init(target: string | HTMLElement) {
-        const defaultSpec = DefaultPluginUISpec();
         this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...defaultSpec,
+            ...DefaultPluginSpec,
             layout: {
                 initial: {
                     isExpanded: false,
                     showControls: false
                 },
-            },
-            components: {
                 controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
             },
-            canvas3d: {
-                camera: {
-                    helper: { axes: { name: 'off', params: { } } }
-                }
-            },
             config: [
                 [PluginConfig.Viewport.ShowExpand, false],
                 [PluginConfig.Viewport.ShowControls, false],
@@ -174,8 +165,7 @@ export class AlphaOrbitalsExample {
             kind,
             relativeIsovalue: this.state.value.isoValue,
             pickable: false,
-            xrayShaded: true,
-            tryUseGpu: false
+            xrayShaded: true
         };
     }
 

src/examples/basic-wrapper/controls.tsx

@@ -5,6 +5,7 @@
  */
 
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import * as React from 'react';
 
 export class CustomToastMessage extends PluginUIComponent {
     render() {

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.targetFps = 30;
+            BasicMolStarWrapper.animate.modelIndex.maxFPS = 30;
 
             addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());

src/examples/basic-wrapper/index.ts

@@ -4,36 +4,38 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 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/model-index';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { createPlugin } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
 import { Script } from '../../mol-script/script';
-import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import { StripedResidues } from './coloring';
 import { CustomToastMessage } from './controls';
 import './index.html';
 import { buildStaticSuperposition, dynamicSuperpositionTest, StaticSuperpositionTestData } from './superposition';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { Asset } from '../../mol-util/assets';
 require('mol-plugin-ui/skin/light.scss');
 
 type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
 
 class BasicWrapper {
-    plugin: PluginUIContext;
+    plugin: PluginContext;
 
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginUISpec(),
+            ...DefaultPluginSpec,
             layout: {
                 initial: {
                     isExpanded: false,
                     showControls: false
+                },
+                controls: {
+                    // left: 'none'
                 }
             },
             components: {
@@ -80,17 +82,13 @@ 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: {
-            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' } } }); },
+            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: {} } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
     }

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 function createMapping(allData: any) {
+export default function create(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;
-                width: 100%;
-                height: 100%;
+                left: 160px;
+                top: 100px;
+                width: 600px;
+                height: 600px;
+                border: 1px solid #ccc;
             }
 
             #controls {
                 position: absolute;
                 width: 150px;
-                bottom: 100px;
-                right: 50px;
-                z-index: 10;
-                font-family: sans-serif;
-                font-size: smaller;
+                top: 100px;
+                left: 780px;
             }
 
             #controls > button {
@@ -46,13 +46,13 @@
         <div id="app"></div>
         <script>
             LightingDemo.init('app')
-            LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3)
+            LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' })
 
             addHeader('Example PDB IDs');
-            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));
+            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' }));
 
             addSeparator()
 

src/examples/lighting/index.ts

@@ -5,13 +5,12 @@
  */
 
 import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { createPlugin } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { Asset } from '../../mol-util/assets';
+import { PluginContext } from '../../mol-plugin/context';
 import './index.html';
+import { Asset } from '../../mol-util/assets';
 require('mol-plugin-ui/skin/light.scss');
 
 type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
@@ -25,11 +24,12 @@ const Canvas3DPresets = {
             mode: 'temporal' as Canvas3DProps['multiSample']['mode']
         },
         postprocessing: {
-            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
-            outline: { name: 'on', params: { scale: 1, threshold: 0.1 } }
+            occlusion: { name: 'on', params: { samples: 64, radius: 8, bias: 1.0, blurKernelSize: 13 } },
+            outline: { name: 'on', params: { scale: 1, threshold: 0.33 } }
         },
         renderer: {
-            style: { name: 'flat', params: {} }
+            ambientIntensity: 1,
+            lightIntensity: 0,
         }
     },
     occlusion: <Preset> {
@@ -37,11 +37,12 @@ const Canvas3DPresets = {
             mode: 'temporal' as Canvas3DProps['multiSample']['mode']
         },
         postprocessing: {
-            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+            occlusion: { name: 'on', params: { samples: 64, radius: 8, bias: 1.0, blurKernelSize: 13 } },
             outline: { name: 'off', params: { } }
         },
         renderer: {
-            style: { name: 'matte', params: {} }
+            ambientIntensity: 0.4,
+            lightIntensity: 0.6,
         }
     },
     standard: <Preset> {
@@ -53,31 +54,25 @@ const Canvas3DPresets = {
             outline: { name: 'off', params: { } }
         },
         renderer: {
-            style: { name: 'matte', params: {} }
+            ambientIntensity: 0.4,
+            lightIntensity: 0.6,
         }
     }
 };
 
-
 type Canvas3DPreset = keyof typeof Canvas3DPresets
 
 class LightingDemo {
-    plugin: PluginUIContext;
-
-    private radius = 5;
-    private bias = 1.1;
-    private preset: Canvas3DPreset = 'illustrative';
+    plugin: PluginContext;
 
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginUISpec(),
+            ...DefaultPluginSpec,
             layout: {
                 initial: {
                     isExpanded: false,
                     showControls: false
                 },
-            },
-            components: {
                 controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
             }
         });
@@ -87,10 +82,6 @@ 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: {
@@ -108,7 +99,7 @@ class LightingDemo {
         }});
     }
 
-    async load({ url, format = 'mmcif', isBinary = true, assemblyId = '' }: LoadParams, radius: number, bias: number) {
+    async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
         await this.plugin.clear();
 
         const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
@@ -120,11 +111,7 @@ 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', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
-
-        this.radius = radius;
-        this.bias = bias;
-        this.setPreset(this.preset);
+        if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick' });
     }
 }
 

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.targetFps = 30;
+            PluginWrapper.animate.modelIndex.maxFPS = 30;
 
             addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());

src/examples/proteopedia-wrapper/index.ts

@@ -6,15 +6,14 @@
 
 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/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';
-import { createPlugin } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
 import { PluginState } from '../../mol-plugin/state';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
@@ -41,13 +40,13 @@ class MolStarProteopediaWrapper {
         modelInfo: this._ev<ModelInfo>()
     };
 
-    plugin: PluginUIContext;
+    plugin: PluginContext;
 
     init(target: string | HTMLElement, options?: {
         customColorList?: number[]
     }) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginUISpec(),
+            ...DefaultPluginSpec,
             animations: [
                 AnimateModelIndex
             ],
@@ -272,17 +271,13 @@ class MolStarProteopediaWrapper {
         resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
     }
 
-    private animateModelIndexTargetFps() {
-        return Math.max(1, this.animate.modelIndex.targetFps | 0);
-    }
-
     animate = {
         modelIndex: {
-            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' } } }); },
+            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: {} } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
     }

src/examples/proteopedia-wrapper/ui/controls.tsx

@@ -4,13 +4,14 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
+import * as React from 'react';
 import * as ReactDOM from 'react-dom';
-import { PluginUIContext } from '../../../mol-plugin-ui/context';
 import { PluginContextContainer } from '../../../mol-plugin-ui/plugin';
 import { TransformUpdaterControl } from '../../../mol-plugin-ui/state/update-transform';
+import { PluginContext } from '../../../mol-plugin/context';
 import { StateElements } from '../helpers';
 
-export function volumeStreamingControls(plugin: PluginUIContext, parent: Element) {
+export function volumeStreamingControls(plugin: PluginContext, parent: Element) {
     ReactDOM.render(<PluginContextContainer plugin={plugin}>
         <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
     </PluginContextContainer>, parent);

src/extensions/alpha-orbitals/transforms.ts

@@ -172,8 +172,7 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
         color: PD.Color(ColorNames.blue),
         alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
         xrayShaded: PD.Boolean(false),
-        pickable: PD.Boolean(true),
-        tryUseGpu: PD.Boolean(true)
+        pickable: PD.Boolean(true)
     }
 })({
     canAutoUpdate() {
@@ -191,7 +190,7 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
             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, sourceData: a.data }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
+            return new PluginStateObject.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
         });
     },
     update({ a, b, newParams: srcParams }, plugin: PluginContext) {
@@ -201,7 +200,6 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
             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.sourceData = a.data;
             b.data.repr.setState({ pickable: srcParams.pickable });
             b.description = VolumeRepresentation3DHelpers.getDescription(props);
             return StateTransformer.UpdateResult.Updated;
@@ -231,7 +229,7 @@ function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Da
         colorParams: { value: params.color }
     } : {
         type: 'isosurface',
-        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded, tryUseGpu: params.tryUseGpu },
+        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);
@@ -328,7 +328,6 @@ 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/behavior.ts

@@ -121,7 +121,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
             await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
             const repr = MembraneOrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => MembraneOrientationParams);
             await repr.createOrUpdate(params, a.data).runInContext(ctx);
-            return new PluginStateObject.Shape.Representation3D({ repr, sourceData: a.data }, { label: 'Membrane Orientation' });
+            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: 'Membrane Orientation' });
         });
     },
     update({ a, b, newParams }, plugin: PluginContext) {
@@ -129,7 +129,6 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
             await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
-            b.data.sourceData = a.data;
             return StateTransformer.UpdateResult.Updated;
         });
     },

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/cellpack/model.ts

@@ -414,7 +414,7 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
         }
 
         if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
-        const structure = Structure.create(units);
+        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 });
         }

src/extensions/g3d/data.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { decodeMsgPack } from '../../mol-io/common/msgpack/decode';
+import msgpackDecode 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 = decodeMsgPack(data.slice(0, last + 1));
+    const header = msgpackDecode(data.slice(0, last + 1));
     return header;
 }
 
@@ -53,7 +53,7 @@ export async function getG3dDataBlock(ctx: PluginContext, header: G3dHeader, url
     return {
         header,
         resolution,
-        data: decodeMsgPack(unzipped)
+        data: msgpackDecode(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';

src/extensions/mp4-export/ui.tsx

@@ -4,6 +4,7 @@
  * @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';

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/behavior.ts

@@ -124,7 +124,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
             const repr = AssemblySymmetryRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => AssemblySymmetryParams);
             await repr.createOrUpdate(params, a.data).runInContext(ctx);
             const { type, kind, symbol } = assemblySymmetry;
-            return new PluginStateObject.Shape.Representation3D({ repr, sourceData: a.data }, { label: kind, description: `${type} (${symbol})` });
+            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: kind, description: `${type} (${symbol})` });
         });
     },
     update({ a, b, newParams }, plugin: PluginContext) {
@@ -138,7 +138,6 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
             }
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
-            b.data.sourceData = a.data;
             const { type, kind, symbol } = assemblySymmetry;
             b.label = kind;
             b.description = `${type} (${symbol})`;

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

@@ -5,7 +5,7 @@
  */
 
 import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphql/types';
-import { symmetry_gql } from '../graphql/symmetry.gql';
+import query 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, symmetry_gql, variables);
+        const result = await client.request(ctx.runtime, query, variables);
         let value: AssemblySymmetryDataValue = [];
 
         if (!result.data.assembly?.rcsb_struct_symmetry) {

src/extensions/rcsb/assembly-symmetry/ui.tsx

@@ -4,6 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import * as React from 'react';
 import { CollapsableState, CollapsableControls } from '../../../mol-plugin-ui/base';
 import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
 import { InitAssemblySymmetry3D, AssemblySymmetry3D, AssemblySymmetryPreset, tryCreateAssemblySymmetry } from './behavior';

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

@@ -1,4 +1,4 @@
-export const symmetry_gql = /* GraphQL */ `
+export default /* 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/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/mol-canvas3d/camera.ts

@@ -9,7 +9,6 @@ import { Mat4, Vec3, Vec4, EPSILON } from '../mol-math/linear-algebra';
 import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
-import { Scene } from '../mol-gl/scene';
 
 export { ICamera, Camera };
 
@@ -127,23 +126,6 @@ class Camera implements ICamera {
         return state;
     }
 
-    getInvariantFocus(target: Vec3, radius: number, up: Vec3, dir: Vec3): Partial<Camera.Snapshot> {
-        const r = Math.max(radius, 0.01);
-        const targetDistance = this.getTargetDistance(r);
-
-        Vec3.copy(this.deltaDirection, dir);
-        Vec3.setMagnitude(this.deltaDirection, this.deltaDirection, targetDistance);
-        Vec3.sub(this.newPosition, target, this.deltaDirection);
-
-        const state = Camera.copySnapshot(Camera.createDefaultSnapshot(), this.state);
-        state.target = Vec3.clone(target);
-        state.radius = r;
-        state.position = Vec3.clone(this.newPosition);
-        Vec3.copy(state.up, up);
-
-        return state;
-    }
-
     focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3) {
         if (radius > 0) {
             this.setState(this.getFocus(target, radius, up, dir), durationMs);
@@ -168,8 +150,6 @@ class Camera implements ICamera {
 namespace Camera {
     export type Mode = 'perspective' | 'orthographic'
 
-    export type SnapshotProvider = Partial<Snapshot> | ((scene: Scene, camera: Camera) => Partial<Snapshot>)
-
     /**
      * Sets an offseted view in a larger frustum. This is useful for
      * - multi-window or multi-monitor/multi-machine setups

src/mol-canvas3d/canvas3d.ts

@@ -8,14 +8,14 @@
 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 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';
@@ -229,12 +229,11 @@ interface Canvas3D {
     /** performs handleResize on the next animation frame */
     requestResize(): void
     /** Focuses camera on scene's bounding sphere, centered and zoomed. */
-    requestCameraReset(options?: { durationMs?: number, snapshot?: Camera.SnapshotProvider }): void
+    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
-    getRenderObjects(): GraphicsRenderObject[]
 
     /** Returns a copy of the current Canvas3D instance props */
     readonly props: Readonly<Canvas3DProps>
@@ -297,7 +296,7 @@ namespace Canvas3D {
         let drawPending = false;
         let cameraResetRequested = false;
         let nextCameraResetDuration: number | undefined = void 0;
-        let nextCameraResetSnapshot: Camera.SnapshotProvider | undefined = void 0;
+        let nextCameraResetSnapshot: Partial<Camera.Snapshot> | undefined = void 0;
         let resizeRequested = false;
 
         let notifyDidDraw = true;
@@ -306,11 +305,7 @@ namespace Canvas3D {
             let loci: Loci = EmptyLoci;
             let repr: Representation.Any = Representation.Empty;
             if (pickingId) {
-                const cameraHelperLoci = helper.camera.getLoci(pickingId);
-                if (cameraHelperLoci !== EmptyLoci) return { loci: cameraHelperLoci, repr };
-
                 loci = helper.handle.getLoci(pickingId);
-
                 reprRenderObjects.forEach((_, _repr) => {
                     const _loci = _repr.getLoci(pickingId);
                     if (!isEmptyLoci(_loci)) {
@@ -332,13 +327,11 @@ namespace Canvas3D {
                 changed = repr.mark(loci, action);
             } else {
                 changed = helper.handle.mark(loci, action);
-                changed = helper.camera.mark(loci, action) || changed;
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
             if (changed) {
                 scene.update(void 0, true);
                 helper.handle.scene.update(void 0, true);
-                helper.camera.scene.update(void 0, true);
                 const prevPickDirty = pickHelper.dirty;
                 draw(true);
                 pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
@@ -460,21 +453,11 @@ namespace Canvas3D {
         function resolveCameraReset() {
             if (!cameraResetRequested) return;
 
-            const boundingSphere = scene.boundingSphereVisible;
-            const { center, radius } = boundingSphere;
-
-            const autoAdjustControls = controls.props.autoAdjustMinMaxDistance;
-            if (autoAdjustControls.name === 'on') {
-                const minDistance = autoAdjustControls.params.minDistanceFactor * radius + autoAdjustControls.params.minDistancePadding;
-                const maxDistance = Math.max(autoAdjustControls.params.maxDistanceFactor * radius, autoAdjustControls.params.maxDistanceMin);
-                controls.setProps({ minDistance, maxDistance });
-            }
-
+            const { center, radius } = scene.boundingSphereVisible;
             if (radius > 0) {
                 const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration;
                 const focus = camera.getFocus(center, radius);
-                const next = typeof nextCameraResetSnapshot === 'function' ? nextCameraResetSnapshot(scene, camera) : nextCameraResetSnapshot;
-                const snapshot = next ? { ...focus, ...next } : focus;
+                const snapshot = nextCameraResetSnapshot ? { ...focus, ...nextCameraResetSnapshot } : focus;
                 camera.setState({ ...snapshot, radiusMax: scene.boundingSphere.radius }, duration);
             }
 
@@ -770,11 +753,6 @@ namespace Canvas3D {
             getImagePass: (props: Partial<ImageProps> = {}) => {
                 return new ImagePass(webgl, renderer, scene, camera, helper, passes.draw.wboitEnabled, props);
             },
-            getRenderObjects(): GraphicsRenderObject[] {
-                const renderObjects: GraphicsRenderObject[] = [];
-                scene.forEach((_, ro) => renderObjects.push(ro));
-                return renderObjects;
-            },
 
             get props() {
                 return getProps();

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';
@@ -49,21 +49,7 @@ export const TrackballControlsParams = {
     minDistance: PD.Numeric(0.01, {}, { isHidden: true }),
     maxDistance: PD.Numeric(1e150, {}, { isHidden: true }),
 
-    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true }),
-
-    /**
-     * minDistance = minDistanceFactor * boundingSphere.radius + minDistancePadding
-     * maxDistance = max(maxDistanceFactor * boundingSphere.radius, maxDistanceMin)
-     */
-    autoAdjustMinMaxDistance: PD.MappedStatic('on', {
-        off: PD.EmptyGroup(),
-        on: PD.Group({
-            minDistanceFactor: PD.Numeric(0),
-            minDistancePadding: PD.Numeric(5),
-            maxDistanceFactor: PD.Numeric(10),
-            maxDistanceMin: PD.Numeric(20)
-        })
-    }, { isHidden: true })
+    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true })
 };
 export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 

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';

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

@@ -1,35 +1,30 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import produce from 'immer';
-import { Interval } from '../../mol-data/int/interval';
-import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
-import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
-import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
-import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
-import { PickingId } from '../../mol-geo/geometry/picking';
-import { GraphicsRenderObject } from '../../mol-gl/render-object';
-import { Scene } from '../../mol-gl/scene';
 import { WebGLContext } from '../../mol-gl/webgl/context';
-import { Sphere3D } from '../../mol-math/geometry';
-import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { DataLoci, EmptyLoci, Loci } from '../../mol-model/loci';
-import { Shape } from '../../mol-model/shape';
-import { Visual } from '../../mol-repr/visual';
-import { ColorNames } from '../../mol-util/color/names';
-import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
+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';
+import { GraphicsRenderObject } from '../../mol-gl/render-object';
+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 { Sphere3D } from '../../mol-math/geometry';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import produce from 'immer';
+import { Shape } from '../../mol-model/shape';
 
 // TODO add scale line/grid
 
 const AxesParams = {
     ...Mesh.Params,
-    alpha: { ...Mesh.Params.alpha, defaultValue: 0.51 },
+    alpha: { ...Mesh.Params.alpha, defaultValue: 0.33 },
     ignoreLight: { ...Mesh.Params.ignoreLight, defaultValue: true },
     colorX: PD.Color(ColorNames.red, { isEssential: true }),
     colorY: PD.Color(ColorNames.green, { isEssential: true }),
@@ -92,32 +87,6 @@ export class CameraHelper {
         return this.props.axes.name === 'on';
     }
 
-    getLoci(pickingId: PickingId) {
-        const { objectId, groupId, instanceId } = pickingId;
-        if (!this.renderObject || objectId !== this.renderObject.id || groupId === CameraHelperAxis.None) return EmptyLoci;
-        return CameraAxesLoci(this, groupId, instanceId);
-    }
-
-    private eachGroup = (loci: Loci, apply: (interval: Interval) => boolean): boolean => {
-        if (!this.renderObject) return false;
-        if (!isCameraAxesLoci(loci)) return false;
-        let changed = false;
-        const groupCount = this.renderObject.values.uGroupCount.ref.value;
-        const { elements } = loci;
-        for (const { groupId, instanceId } of elements) {
-            const idx = instanceId * groupCount + groupId;
-            if (apply(Interval.ofSingleton(idx))) changed = true;
-        }
-        return changed;
-    }
-
-    mark(loci: Loci, action: MarkerAction) {
-        if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
-        if (!isCameraAxesLoci(loci)) return false;
-        if (loci.data !== this) return false;
-        return Visual.mark(this.renderObject, loci, action, this.eachGroup);
-    }
-
     update(camera: ICamera) {
         if (!this.renderObject) return;
 
@@ -133,38 +102,6 @@ export class CameraHelper {
     }
 }
 
-export const enum CameraHelperAxis {
-    None = 0,
-    X,
-    Y,
-    Z,
-    XY,
-    XZ,
-    YZ
-}
-
-function getAxisLabel(axis: number) {
-    switch (axis) {
-        case CameraHelperAxis.X: return 'X Axis';
-        case CameraHelperAxis.Y: return 'Y Axis';
-        case CameraHelperAxis.Z: return 'Z Axis';
-        case CameraHelperAxis.XY: return 'XY Plane';
-        case CameraHelperAxis.XZ: return 'XZ Plane';
-        case CameraHelperAxis.YZ: return 'YZ Plane';
-        default: return 'Axes';
-    }
-}
-
-function CameraAxesLoci(cameraHelper: CameraHelper, groupId: number, instanceId: number) {
-    return DataLoci('camera-axes', cameraHelper, [{ groupId, instanceId }],
-        void 0 /** bounding sphere */,
-        () => getAxisLabel(groupId));
-}
-export type CameraAxesLoci = ReturnType<typeof CameraAxesLoci>
-export function isCameraAxesLoci(x: Loci): x is CameraAxesLoci {
-    return x.kind === 'data-loci' && x.tag === 'camera-axes';
-}
-
 function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.ViewOffset) {
     const { near, far } = camera;
 
@@ -197,52 +134,27 @@ function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.Vie
 
 function createAxesMesh(scale: number, mesh?: Mesh) {
     const state = MeshBuilder.createState(512, 256, mesh);
-    const radius = 0.075 * scale;
+    const radius = 0.05 * scale;
     const x = Vec3.scale(Vec3(), Vec3.unitX, scale);
     const y = Vec3.scale(Vec3(), Vec3.unitY, scale);
     const z = Vec3.scale(Vec3(), Vec3.unitZ, scale);
     const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments: 32 };
 
-    state.currentGroup = CameraHelperAxis.None;
+    state.currentGroup = 0;
     addSphere(state, Vec3.origin, radius, 2);
 
-    state.currentGroup = CameraHelperAxis.X;
+    state.currentGroup = 1;
     addSphere(state, x, radius, 2);
     addCylinder(state, Vec3.origin, x, 1, cylinderProps);
 
-    state.currentGroup = CameraHelperAxis.Y;
+    state.currentGroup = 2;
     addSphere(state, y, radius, 2);
     addCylinder(state, Vec3.origin, y, 1, cylinderProps);
 
-    state.currentGroup = CameraHelperAxis.Z;
+    state.currentGroup = 3;
     addSphere(state, z, radius, 2);
     addCylinder(state, Vec3.origin, z, 1, cylinderProps);
 
-    Vec3.scale(x, x, 0.5);
-    Vec3.scale(y, y, 0.5);
-    Vec3.scale(z, z, 0.5);
-
-    state.currentGroup = CameraHelperAxis.XY;
-    MeshBuilder.addTriangle(state, Vec3.origin, x, y);
-    MeshBuilder.addTriangle(state, Vec3.origin, y, x);
-    const xy = Vec3.add(Vec3(), x, y);
-    MeshBuilder.addTriangle(state, xy, x, y);
-    MeshBuilder.addTriangle(state, xy, y, x);
-
-    state.currentGroup = CameraHelperAxis.XZ;
-    MeshBuilder.addTriangle(state, Vec3.origin, x, z);
-    MeshBuilder.addTriangle(state, Vec3.origin, z, x);
-    const xz = Vec3.add(Vec3(), x, z);
-    MeshBuilder.addTriangle(state, xz, x, z);
-    MeshBuilder.addTriangle(state, xz, z, x);
-
-    state.currentGroup = CameraHelperAxis.YZ;
-    MeshBuilder.addTriangle(state, Vec3.origin, y, z);
-    MeshBuilder.addTriangle(state, Vec3.origin, z, y);
-    const yz = Vec3.add(Vec3(), y, z);
-    MeshBuilder.addTriangle(state, yz, y, z);
-    MeshBuilder.addTriangle(state, yz, z, y);
-
     return MeshBuilder.getMesh(state);
 }
 

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';

src/mol-canvas3d/helper/helper.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Scene } from '../../mol-gl/scene';
+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';

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

@@ -7,7 +7,7 @@
 
 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, Vec3 } from '../../mol-math/linear-algebra';
 import { Camera } from '../camera';

src/mol-canvas3d/passes/draw.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -7,8 +7,8 @@
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { createNullRenderTarget, RenderTarget } from '../../mol-gl/webgl/render-target';
-import { Renderer } from '../../mol-gl/renderer';
-import { Scene } from '../../mol-gl/scene';
+import Renderer from '../../mol-gl/renderer';
+import Scene from '../../mol-gl/scene';
 import { Texture } from '../../mol-gl/webgl/texture';
 import { Camera, ICamera } from '../camera';
 import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
@@ -20,8 +20,8 @@ import { ValueCell } from '../../mol-util';
 import { Vec2 } from '../../mol-math/linear-algebra';
 import { Helper } from '../helper/helper';
 
-import { quad_vert } from '../../mol-gl/shader/quad.vert';
-import { depthMerge_frag } from '../../mol-gl/shader/depth-merge.frag';
+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';
@@ -100,7 +100,7 @@ export class DrawPass {
     }
 
     constructor(private webgl: WebGLContext, width: number, height: number, enableWboit: boolean) {
-        const { extensions, resources, isWebGL2 } = webgl;
+        const { extensions, resources } = webgl;
 
         this.drawTarget = createNullRenderTarget(webgl.gl);
 
@@ -113,8 +113,8 @@ export class DrawPass {
         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');
+        this.depthTexturePrimitives = this.depthTargetPrimitives ? this.depthTargetPrimitives.texture : resources.texture('image-depth', 'depth', 'ushort', 'nearest');
+        this.depthTextureVolumes = this.depthTargetVolumes ? this.depthTargetVolumes.texture : resources.texture('image-depth', 'depth', 'ushort', 'nearest');
         if (!this.packedDepth) {
             this.depthTexturePrimitives.define(width, height);
             this.depthTextureVolumes.define(width, height);

src/mol-canvas3d/passes/fxaa.ts

@@ -14,8 +14,8 @@ 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 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';
 

src/mol-canvas3d/passes/image.ts

@@ -6,8 +6,8 @@
 
 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 Renderer from '../../mol-gl/renderer';
+import Scene from '../../mol-gl/scene';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { DrawPass } from './draw';
 import { PostprocessingParams } from './postprocessing';

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

@@ -18,13 +18,13 @@ import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { Camera } from '../../mol-canvas3d/camera';
 import { PostprocessingProps } from './postprocessing';
 import { DrawPass } from './draw';
-import { Renderer } from '../../mol-gl/renderer';
-import { Scene } from '../../mol-gl/scene';
+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,

src/mol-canvas3d/passes/pick.ts

@@ -5,8 +5,8 @@
  */
 
 import { PickingId } from '../../mol-geo/geometry/picking';
-import { Renderer } from '../../mol-gl/renderer';
-import { Scene } from '../../mol-gl/scene';
+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';
@@ -66,20 +66,14 @@ export class PickPass {
     private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: GraphicsRenderVariant) {
         const depth = this.drawPass.depthTexturePrimitives;
         renderer.clear(false);
-
-        renderer.update(camera);
         renderer.renderPick(scene.primitives, camera, variant, null);
         renderer.renderPick(scene.volumes, camera, variant, depth);
         renderer.renderPick(helper.handle.scene, camera, variant, null);
-
-        if (helper.camera.isEnabled) {
-            helper.camera.update(camera);
-            renderer.update(helper.camera.camera);
-            renderer.renderPick(helper.camera.scene, helper.camera.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');
 

src/mol-canvas3d/passes/postprocessing.ts

@@ -18,11 +18,11 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { DrawPass } from './draw';
 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 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 ssao_blur_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';
@@ -143,7 +143,7 @@ function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, dir
     };
 
     const schema = { ...SsaoBlurSchema };
-    const shaderCode = ShaderCode('ssao_blur', quad_vert, ssaoBlur_frag);
+    const shaderCode = ShaderCode('ssao_blur', quad_vert, ssao_blur_frag);
     const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
 
     return createComputeRenderable(renderItem, values);

src/mol-canvas3d/passes/wboit.ts

@@ -13,8 +13,8 @@ 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 quad_vert from '../../mol-gl/shader/quad.vert';
+import evaluate_wboit_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';
@@ -25,7 +25,7 @@ const EvaluateWboitSchema = {
     tWboitB: TextureSpec('texture', 'rgba', 'float', 'nearest'),
     uTexSize: UniformSpec('v2'),
 };
-const EvaluateWboitShaderCode = ShaderCode('evaluate-wboit', quad_vert, evaluateWboit_frag);
+const EvaluateWboitShaderCode = ShaderCode('evaluate-wboit', quad_vert, evaluate_wboit_frag);
 type EvaluateWboitRenderable = ComputeRenderable<Values<typeof EvaluateWboitSchema>>
 
 function getEvaluateWboitRenderable(ctx: WebGLContext, wboitATexture: Texture, wboitBTexture: Texture): EvaluateWboitRenderable {

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 { Column };
+export default Column;
 
 function createFirstIndexMapOfColumn<T>(c: Column<T>): Map<T, number> {
     const map = new Map<T, number>();

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 { Database };
+export default 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 { Table };
+export default 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 { IntTuple as 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 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]);

src/mol-data/int/_spec/sorted-array.spec.ts

@@ -4,8 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Interval } from '../interval';
-import { SortedArray } from '../sorted-array';
+import Interval from '../interval';
+import SortedArray from '../sorted-array';
 
 describe('sortedArray', () => {
     function testI(name: string, a: Interval, b: Interval) {

src/mol-data/int/_spec/sorted-ranges.spec.ts

@@ -4,9 +4,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { SortedRanges } from '../sorted-ranges';
-import { OrderedSet } from '../ordered-set';
-import { SortedArray } from '../sorted-array';
+import SortedRanges from '../sorted-ranges';
+import OrderedSet from '../ordered-set';
+import SortedArray from '../sorted-array';
 
 describe('rangesArray', () => {
     function test(name: string, a: any, b: any) {

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

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { IntTuple } from '../tuple';
+import IntTuple from '../tuple';
 
 describe('int pair', () => {
     it('works', () => {

src/mol-data/int/impl/interval.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { IntTuple as Tuple } from '../tuple';
+import Tuple from '../tuple';
 
 export const Empty = Tuple.Zero;
 export function ofRange(min: number, max: number) { return max < min ? Tuple.create(min, min) : Tuple.create(min, max + 1); }

src/mol-data/int/impl/ordered-set.ts

@@ -4,8 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { SortedArray as S } from '../sorted-array';
-import { Interval as I } from '../interval';
+import S from '../sorted-array';
+import I from '../interval';
 
 type OrderedSetImpl = I | S
 type Nums = ArrayLike<number>

src/mol-data/int/impl/segmentation.ts

@@ -4,11 +4,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Iterator } from '../../iterator';
-import { OrderedSet } from '../ordered-set';
-import { Interval } from '../interval';
-import { SortedArray } from '../sorted-array';
-import { Segmentation as Segs } from '../segmentation';
+import Iterator from '../../iterator';
+import OrderedSet from '../ordered-set';
+import Interval from '../interval';
+import SortedArray from '../sorted-array';
+import Segs from '../segmentation';
 
 interface Segmentation {
     /** Segments stored as a sorted array */

src/mol-data/int/impl/sorted-array.ts

@@ -5,7 +5,7 @@
  */
 
 import { sortArray, hash3, hash4, createRangeArray } from '../../util';
-import { Interval } from '../interval';
+import Interval from '../interval';
 
 type Nums = ArrayLike<number>
 

src/mol-data/int/interval.ts

@@ -60,4 +60,4 @@ namespace Interval {
 /** Interval describing a range [min, max] of values */
 interface Interval<T extends number = number> { '@type': 'int-interval' }
 
-export { Interval };
+export default Interval;

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

@@ -55,4 +55,4 @@ class LinkedIndexImpl implements LinkedIndex {
     }
 }
 
-export { LinkedIndex };
+export default LinkedIndex;

src/mol-data/int/map.ts

@@ -58,4 +58,4 @@ namespace IntMap {
     }
 }
 
-export { IntMap };
+export default IntMap;

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

@@ -5,8 +5,8 @@
  */
 
 import * as Base from './impl/ordered-set';
-import { Interval } from './interval';
-import { SortedArray } from './sorted-array';
+import Interval from './interval';
+import SortedArray from './sorted-array';
 
 namespace OrderedSet {
     export const Empty: OrderedSet = Base.Empty as any;
@@ -82,4 +82,4 @@ namespace OrderedSet {
 
 type OrderedSet<T extends number = number> = SortedArray<T> | Interval<T>
 
-export { OrderedSet };
+export default OrderedSet;

src/mol-data/int/segmentation.ts

@@ -4,8 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Interval } from './interval';
-import { OrderedSet } from './ordered-set';
+import Interval from './interval';
+import OrderedSet from './ordered-set';
 import * as Impl from './impl/segmentation';
 
 namespace Segmentation {
@@ -33,4 +33,4 @@ interface Segmentation<T extends number = number, I extends number = number> {
     readonly count: number
 }
 
-export { Segmentation };
+export default Segmentation;

src/mol-data/int/sorted-array.ts

@@ -5,7 +5,7 @@
  */
 
 import * as Impl from './impl/sorted-array';
-import { Interval } from './interval';
+import Interval from './interval';
 
 namespace SortedArray {
     export const Empty: SortedArray = Impl.Empty as any;
@@ -54,4 +54,4 @@ namespace SortedArray {
 
 interface SortedArray<T extends number = number> extends ArrayLike<T> { '@type': 'int-sorted-array' }
 
-export { SortedArray };
+export default SortedArray;

src/mol-data/int/sorted-ranges.ts

@@ -5,7 +5,7 @@
  */
 
 import { Segmentation, OrderedSet, SortedArray, Interval } from '../int';
-import { Iterator as _Iterator } from '../iterator';
+import _Iterator from '../iterator';
 
 /** Pairs of min and max indices of sorted, non-overlapping ranges */
 type SortedRanges<T extends number = number> = SortedArray<T>
@@ -115,4 +115,4 @@ namespace SortedRanges {
     }
 }
 
-export { SortedRanges };
+export default SortedRanges;

src/mol-data/int/tuple.ts

@@ -80,4 +80,4 @@ namespace IntTuple {
     }
 }
 
-export { IntTuple };
+export default IntTuple;

src/mol-data/iterator.ts

@@ -117,4 +117,4 @@ namespace Iterator {
     }
 }
 
-export { Iterator };
+export default Iterator;

src/mol-data/util/combination.ts

@@ -6,7 +6,7 @@
 
 // adpated from https://github.com/dankogai/js-combinatorics, MIT 2013-2016 Dan Kogai
 
-import { Iterator } from '../iterator';
+import Iterator from '../iterator';
 
 function P(m: number, n: number) {
     let p = 1;

src/mol-data/util/interval-iterator.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Iterator } from '../iterator';
+import Iterator from '../iterator';
 import { OrderedSet, Interval, Segmentation } from '../int';
 
 /** Emits a segment of length one for each element in the interval that is also in the set */

src/mol-geo/geometry/spheres/spheres.ts

@@ -177,7 +177,7 @@ export namespace Spheres {
 
         const counts = { drawCount: spheres.sphereCount * 2 * 3, vertexCount: spheres.sphereCount * 4, groupCount, instanceCount };
 
-        const padding = spheres.boundingSphere.radius ? getMaxSize(size) * props.sizeFactor : 0;
+        const padding = getMaxSize(size) * props.sizeFactor;
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), spheres.boundingSphere, padding);
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
@@ -222,9 +222,7 @@ export namespace Spheres {
     }
 
     function updateBoundingSphere(values: SpheresValues, spheres: Spheres) {
-        const padding = spheres.boundingSphere.radius
-            ? getMaxSize(values) * values.uSizeFactor.ref.value
-            : 0;
+        const padding = getMaxSize(values) * values.uSizeFactor.ref.value;
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), spheres.boundingSphere, padding);
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
 

src/mol-geo/geometry/texture-mesh/texture-mesh.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
  */
@@ -36,36 +36,11 @@ export interface TextureMesh {
     readonly vertexTexture: ValueCell<Texture>,
     readonly groupTexture: ValueCell<Texture>,
     readonly normalTexture: ValueCell<Texture>,
-    readonly doubleBuffer: TextureMesh.DoubleBuffer
 
     readonly boundingSphere: Sphere3D
 }
 
 export namespace TextureMesh {
-    export class DoubleBuffer {
-        private index = 0;
-        private textures: ({ vertex: Texture, group: Texture, normal: Texture } | undefined)[] = []
-
-        get() {
-            return this.textures[this.index];
-        }
-
-        set(vertex: Texture, group: Texture, normal: Texture) {
-            this.textures[this.index] = Object.assign(this.textures[this.index] || {}, {
-                vertex, group, normal
-            });
-            this.index = (this.index + 1) % 2;
-        }
-
-        destroy() {
-            for (const buffer of this.textures) {
-                buffer!.vertex.destroy();
-                buffer!.group.destroy();
-                buffer!.normal.destroy();
-            }
-        }
-    }
-
     export function create(vertexCount: number, groupCount: number, vertexTexture: Texture, groupTexture: Texture, normalTexture: Texture, boundingSphere: Sphere3D, textureMesh?: TextureMesh): TextureMesh {
         const width = vertexTexture.getWidth();
         const height = vertexTexture.getHeight();
@@ -74,9 +49,7 @@ export namespace TextureMesh {
             textureMesh.groupCount = groupCount;
             ValueCell.update(textureMesh.geoTextureDim, Vec2.set(textureMesh.geoTextureDim.ref.value, width, height));
             ValueCell.update(textureMesh.vertexTexture, vertexTexture);
-            ValueCell.update(textureMesh.groupTexture, groupTexture);
             ValueCell.update(textureMesh.normalTexture, normalTexture);
-            textureMesh.doubleBuffer.set(vertexTexture, groupTexture, normalTexture);
             Sphere3D.copy(textureMesh.boundingSphere, boundingSphere);
             return textureMesh;
         } else {
@@ -88,7 +61,6 @@ export namespace TextureMesh {
                 vertexTexture: ValueCell.create(vertexTexture),
                 groupTexture: ValueCell.create(groupTexture),
                 normalTexture: ValueCell.create(normalTexture),
-                doubleBuffer: new DoubleBuffer(),
                 boundingSphere: Sphere3D.clone(boundingSphere),
             };
         }

src/mol-gl/_spec/renderer.spec.ts

@@ -10,14 +10,14 @@ import { Camera } from '../../mol-canvas3d/camera';
 import { Vec3, Mat4, Vec4 } from '../../mol-math/linear-algebra';
 import { ValueCell } from '../../mol-util';
 
-import { Renderer } from '../renderer';
+import Renderer from '../renderer';
 import { createValueColor } from '../../mol-geo/geometry/color-data';
 import { createValueSize } from '../../mol-geo/geometry/size-data';
 import { createContext } from '../webgl/context';
 import { RenderableState } from '../renderable';
 import { createRenderObject } from '../render-object';
 import { PointsValues } from '../renderable/points';
-import { Scene } from '../scene';
+import Scene from '../scene';
 import { createEmptyMarkers } from '../../mol-geo/geometry/marker-data';
 import { fillSerial } from '../../mol-util/array';
 import { Color } from '../../mol-util/color';

src/mol-gl/compute/grid3d.ts

@@ -7,8 +7,8 @@
 import { RenderableSchema, Values, UnboxedValues, UniformSpec, TextureSpec, DefineSpec, RenderableValues } from '../renderable/schema';
 import { WebGLContext } from '../webgl/context';
 import { getRegularGrid3dDelta, RegularGrid3d } from '../../mol-math/geometry/common';
-import { grid3dTemplate_frag } from '../shader/util/grid3d-template.frag';
-import { quad_vert } from '../shader/quad.vert';
+import shader_template from '../shader/util/grid3d-template.frag';
+import quad_vert from '../shader/quad.vert';
 import { ShaderCode } from '../shader-code';
 import { UUID, ValueCell } from '../../mol-util';
 import { objectForEach } from '../../mol-util/object';
@@ -74,7 +74,7 @@ export function createGrid3dComputeRenderable<S extends RenderableSchema, P, CS>
         if (isBound) uniforms.push(`#endif`);
     });
 
-    const code = grid3dTemplate_frag
+    const code = shader_template
         .replace('{UNIFORMS}', uniforms.join('\n'))
         .replace('{UTILS}', spec.utilCode ?? '')
         .replace('{MAIN}', spec.mainCode)

src/mol-gl/compute/histogram-pyramid/reduction.ts

@@ -16,8 +16,8 @@ import { Vec2, Vec3 } from '../../../mol-math/linear-algebra';
 import { getHistopyramidSum } from './sum';
 import { Framebuffer } from '../../../mol-gl/webgl/framebuffer';
 import { isPowerOfTwo } from '../../../mol-math/misc';
-import { quad_vert } from '../../../mol-gl/shader/quad.vert';
-import { reduction_frag } from '../../../mol-gl/shader/histogram-pyramid/reduction.frag';
+import quad_vert from '../../../mol-gl/shader/quad.vert';
+import reduction_frag from '../../../mol-gl/shader/histogram-pyramid/reduction.frag';
 import { isWebGL2 } from '../../webgl/compat';
 
 const HistopyramidReductionSchema = {

src/mol-gl/compute/histogram-pyramid/sum.ts

@@ -13,8 +13,8 @@ import { ShaderCode } from '../../../mol-gl/shader-code';
 import { ValueCell } from '../../../mol-util';
 import { decodeFloatRGB } from '../../../mol-util/float-packing';
 import { QuadSchema, QuadValues } from '../util';
-import { quad_vert } from '../../../mol-gl/shader/quad.vert';
-import { sum_frag } from '../../../mol-gl/shader/histogram-pyramid/sum.frag';
+import quad_vert from '../../../mol-gl/shader/quad.vert';
+import sum_frag from '../../../mol-gl/shader/histogram-pyramid/sum.frag';
 import { isWebGL2 } from '../../webgl/compat';
 
 const HistopyramidSumSchema = {

src/mol-gl/compute/marching-cubes/active-voxels.ts

@@ -14,8 +14,8 @@ import { ValueCell } from '../../../mol-util';
 import { Vec3, Vec2 } from '../../../mol-math/linear-algebra';
 import { QuadSchema, QuadValues } from '../util';
 import { getTriCount } from './tables';
-import { quad_vert } from '../../../mol-gl/shader/quad.vert';
-import { activeVoxels_frag } from '../../../mol-gl/shader/marching-cubes/active-voxels.frag';
+import quad_vert from '../../../mol-gl/shader/quad.vert';
+import active_voxels_frag from '../../../mol-gl/shader/marching-cubes/active-voxels.frag';
 
 const ActiveVoxelsSchema = {
     ...QuadSchema,
@@ -65,7 +65,7 @@ function createActiveVoxelsRenderable(ctx: WebGLContext, volumeData: Texture, gr
     };
 
     const schema = { ...ActiveVoxelsSchema };
-    const shaderCode = ShaderCode('active-voxels', quad_vert, activeVoxels_frag);
+    const shaderCode = ShaderCode('active-voxels', quad_vert, active_voxels_frag);
     const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
 
     return createComputeRenderable(renderItem, values);

src/mol-gl/compute/marching-cubes/isosurface.ts

@@ -15,8 +15,8 @@ import { Vec3, Vec2, Mat4 } from '../../../mol-math/linear-algebra';
 import { QuadSchema, QuadValues } from '../util';
 import { createHistogramPyramid, HistogramPyramid } from '../histogram-pyramid/reduction';
 import { getTriIndices } from './tables';
-import { quad_vert } from '../../../mol-gl/shader/quad.vert';
-import { isosurface_frag } from '../../../mol-gl/shader/marching-cubes/isosurface.frag';
+import quad_vert from '../../../mol-gl/shader/quad.vert';
+import isosurface_frag from '../../../mol-gl/shader/marching-cubes/isosurface.frag';
 import { calcActiveVoxels } from './active-voxels';
 import { isWebGL2 } from '../../webgl/compat';
 
@@ -32,7 +32,6 @@ const IsosurfaceSchema = {
     uSize: UniformSpec('f'),
     uLevels: UniformSpec('f'),
     uCount: UniformSpec('f'),
-    uInvert: UniformSpec('b'),
 
     uGridDim: UniformSpec('v3'),
     uGridTexDim: UniformSpec('v3'),
@@ -45,7 +44,7 @@ type IsosurfaceValues = Values<typeof IsosurfaceSchema>
 
 const IsosurfaceName = 'isosurface';
 
-function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, invert: boolean, packedGroup: boolean): ComputeRenderable<IsosurfaceValues> {
+function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, packedGroup: boolean): ComputeRenderable<IsosurfaceValues> {
     if (ctx.namedComputeRenderables[IsosurfaceName]) {
         const v = ctx.namedComputeRenderables[IsosurfaceName].values as IsosurfaceValues;
 
@@ -57,7 +56,6 @@ function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture
         ValueCell.updateIfChanged(v.uSize, Math.pow(2, levels));
         ValueCell.updateIfChanged(v.uLevels, levels);
         ValueCell.updateIfChanged(v.uCount, count);
-        ValueCell.updateIfChanged(v.uInvert, invert);
 
         ValueCell.update(v.uGridDim, gridDim);
         ValueCell.update(v.uGridTexDim, gridTexDim);
@@ -68,12 +66,12 @@ function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture
 
         ctx.namedComputeRenderables[IsosurfaceName].update();
     } else {
-        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
+        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, packedGroup);
     }
     return ctx.namedComputeRenderables[IsosurfaceName];
 }
 
-function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, invert: boolean, packedGroup: boolean) {
+function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, packedGroup: boolean) {
     // console.log('uSize', Math.pow(2, levels))
     const values: IsosurfaceValues = {
         ...QuadValues,
@@ -87,7 +85,6 @@ function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Text
         uSize: ValueCell.create(Math.pow(2, levels)),
         uLevels: ValueCell.create(levels),
         uCount: ValueCell.create(count),
-        uInvert: ValueCell.create(invert),
 
         uGridDim: ValueCell.create(gridDim),
         uGridTexDim: ValueCell.create(gridTexDim),
@@ -115,7 +112,7 @@ function setRenderingDefaults(ctx: WebGLContext) {
     state.clearColor(0, 0, 0, 0);
 }
 
-export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
+export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     const { gl, resources, extensions } = ctx;
     const { pyramidTex, height, levels, scale, count } = histogramPyramid;
     const width = pyramidTex.getWidth();
@@ -170,7 +167,7 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
     groupTexture.attachFramebuffer(framebuffer, 1);
     normalTexture.attachFramebuffer(framebuffer, 2);
 
-    const renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
+    const renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, packedGroup);
     ctx.state.currentRenderItemId = -1;
 
     const { drawBuffers } = ctx.extensions;
@@ -188,23 +185,14 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
     gl.clear(gl.COLOR_BUFFER_BIT);
     renderable.render();
 
-    gl.finish();
+    gl.flush();
 
     return { vertexTexture, groupTexture, normalTexture, vertexCount: count };
 }
 
 //
 
-/**
- * GPU isosurface extraction
- *
- * Algorithm from "High‐speed Marching Cubes using HistoPyramids"
- * by C Dyken, G Ziegler, C Theobalt, HP Seidel
- * https://doi.org/10.1111/j.1467-8659.2008.01182.x
- *
- * Implementation based on http://www.miaumiau.cat/2016/10/stream-compaction-in-webgl/
- */
-export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
+export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     // console.time('calcActiveVoxels');
     const activeVoxelsTex = calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);
     // ctx.waitForGpuCommandsCompleteSync();
@@ -216,7 +204,7 @@ export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDi
     // console.timeEnd('createHistogramPyramid');
 
     // console.time('createIsosurfaceBuffers');
-    const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, vertexTexture, groupTexture, normalTexture);
+    const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, packedGroup, vertexTexture, groupTexture, normalTexture);
     // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createIsosurfaceBuffers');
 

src/mol-gl/renderable/schema.ts

@@ -37,7 +37,6 @@ export function splitValues(schema: RenderableSchema, values: RenderableValues)
     const textureValues: TextureValues = {};
     const uniformValues: UniformValues = {};
     const materialUniformValues: UniformValues = {};
-    const bufferedUniformValues: UniformValues = {};
     Object.keys(schema).forEach(k => {
         const spec = schema[k];
         if (spec.type === 'attribute') attributeValues[k] = values[k];
@@ -46,12 +45,11 @@ export function splitValues(schema: RenderableSchema, values: RenderableValues)
         if (spec.type === 'texture' && values[k] !== undefined) textureValues[k] = values[k];
         // check if k exists in values to exclude global uniforms
         if (spec.type === 'uniform' && values[k] !== undefined) {
-            if (spec.variant === 'material') materialUniformValues[k] = values[k];
-            else if (spec.variant === 'buffered') bufferedUniformValues[k] = values[k];
+            if (spec.isMaterial) materialUniformValues[k] = values[k];
             else uniformValues[k] = values[k];
         }
     });
-    return { attributeValues, defineValues, textureValues, uniformValues, materialUniformValues, bufferedUniformValues };
+    return { attributeValues, defineValues, textureValues, uniformValues, materialUniformValues };
 }
 
 export type Versions<T extends RenderableValues> = { [k in keyof T]: number }
@@ -70,9 +68,9 @@ export function AttributeSpec<K extends AttributeKind>(kind: K, itemSize: Attrib
     return { type: 'attribute', kind, itemSize, divisor };
 }
 
-export type UniformSpec<K extends UniformKind> = { type: 'uniform', kind: K, variant?: 'material' | 'buffered' }
-export function UniformSpec<K extends UniformKind>(kind: K, variant?: 'material' | 'buffered'): UniformSpec<K> {
-    return { type: 'uniform', kind, variant };
+export type UniformSpec<K extends UniformKind> = { type: 'uniform', kind: K, isMaterial: boolean }
+export function UniformSpec<K extends UniformKind>(kind: K, isMaterial = false): UniformSpec<K> {
+    return { type: 'uniform', kind, isMaterial };
 }
 
 export type TextureSpec<K extends TextureKind> = { type: 'texture', kind: K, format: TextureFormat, dataType: TextureType, filter: TextureFilter }
@@ -182,7 +180,7 @@ export type InternalValues = Values<InternalSchema>
 
 export const ColorSchema = {
     // aColor: AttributeSpec('float32', 3, 0), // TODO
-    uColor: UniformSpec('v3', 'material'),
+    uColor: UniformSpec('v3', true),
     uColorTexDim: UniformSpec('v2'),
     tColor: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
     dColorType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'group', 'groupInstance', 'vertex', 'vertexInstance']),
@@ -192,7 +190,7 @@ export type ColorValues = Values<ColorSchema>
 
 export const SizeSchema = {
     // aSize: AttributeSpec('float32', 1, 0), // TODO
-    uSize: UniformSpec('f', 'material'),
+    uSize: UniformSpec('f', true),
     uSizeTexDim: UniformSpec('v2'),
     tSize: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
     dSizeType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'group', 'groupInstance']),
@@ -253,7 +251,7 @@ export const BaseSchema = {
     /**
      * final alpha, calculated as `values.alpha * state.alpha`
      */
-    uAlpha: UniformSpec('f', 'material'),
+    uAlpha: UniformSpec('f', true),
     uVertexCount: UniformSpec('i'),
     uInstanceCount: UniformSpec('i'),
     uGroupCount: UniformSpec('i'),

src/mol-gl/renderable/texture-mesh.ts

@@ -13,7 +13,7 @@ import { ValueCell } from '../../mol-util';
 
 export const TextureMeshSchema = {
     ...BaseSchema,
-    uGeoTexDim: UniformSpec('v2', 'buffered'),
+    uGeoTexDim: UniformSpec('v2'),
     tPosition: TextureSpec('texture', 'rgb', 'float', 'nearest'),
     tGroup: TextureSpec('texture', 'alpha', 'float', 'nearest'),
     tNormal: TextureSpec('texture', 'rgb', 'float', 'nearest'),

src/mol-gl/renderer.ts

@@ -6,7 +6,7 @@
 
 import { Viewport } from '../mol-canvas3d/camera/util';
 import { ICamera } from '../mol-canvas3d/camera';
-import { Scene } from './scene';
+import Scene from './scene';
 import { WebGLContext } from './webgl/context';
 import { Mat4, Vec3, Vec4, Vec2, Quat } from '../mol-math/linear-algebra';
 import { GraphicsRenderable } from './renderable';
@@ -678,4 +678,4 @@ namespace Renderer {
     }
 }
 
-export { Renderer };
+export default Renderer;