3.31.0

add consoleStats, improve timer

.eslintrc.json

@@ -18,7 +18,7 @@
         ],
         "brace-style": "off",
         "comma-spacing": "off",
-        "space-infix-ops": "error",
+        "space-infix-ops": "off",
         "comma-dangle": "off",
         "eqeqeq": [
             "error",
@@ -107,6 +107,7 @@
                     "1tbs", { "allowSingleLine": true }
                 ],
                 "@typescript-eslint/comma-spacing": "error",
+                "@typescript-eslint/space-infix-ops": "error",
                 "@typescript-eslint/space-before-function-paren": ["error", {
                     "anonymous": "always",
                     "named": "never",

.github/workflows/node.yml

@@ -1,3 +1,5 @@
+name: Build
+
 on:
   push:
   pull_request:
@@ -15,6 +17,6 @@ jobs:
     - name: Lint
       run: npm run lint
     - name: Test
-      run: npm install --no-save "gl@^5.0.0" && xvfb-run --auto-servernum npm run jest
+      run: npm install --no-save "gl@^6.0.2" && xvfb-run --auto-servernum npm run jest
     - name: Build
       run: npm run build

.travis.yml

@@ -1,18 +0,0 @@
-language: node_js
-os: linux
-sudo: required
-dist: trusty
-before_install:
-  - sudo apt-get install -y mesa-utils
-  - sudo apt-get install -y xvfb
-  - sudo apt-get install -y libgl1-mesa-dri
-  - sudo apt-get install -y libglapi-mesa
-  - sudo apt-get install -y libosmesa6
-  - sudo apt-get install -y gcc-4.9
-  - sudo apt-get install -y libstdc++6
-  - sudo apt-get install -y libxi-dev
-node_js:
-  - "12"
-  - "10"
-before_script:
-  - export DISPLAY=:99.0; sh -e /etc/init.d/xvfb start

CHANGELOG.md

@@ -6,18 +6,122 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+- Improve Component camera focus based on the PCA of the structure and the following rules:
+    - The first residue should be in first quadrant if there is only one chain
+    - The average position of the residues of the first chain should be in the first quadrant if there is more than one chain
+- Add `HeadlessPluginContext` and `HeadlessScreenshotHelper` to be used in Node.js
+- Add example `image-renderer`
+- Fix wrong offset when rendering text with orthographic projectio
+n
+- Update camera/handle helper when `devicePixelRatio` changes
+- Add various options to customize the axes camera-helper
+- Fix issue with texture-mesh color smoothing when changing themes
+- Add fast boundary helper and corresponding unit trait
+- Add Observable for Canvas3D commits
+
+## [v3.30.0] - 2023-01-29
+
+- Improve `Dnatco` extension
+    - Factor out common code in `Dnatco` extension
+    - Add `NtC tube` visual. Applicable for structures with NtC annotation
+    - [Breaking] Rename `DnatcoConfalPyramids` to `DnatcoNtCs`
+- Improve boundary calculation performance
+- Add option to create & include images in state snapshots
+- Fix SSAO artefacts with high bias values
+- Fix SSAO resolution scale parameter handling
+- Improve outlines, visually more stable at different view distances
+
+## [v3.29.0] - 2023-01-15
+
+- `meshes` extension: Fixed a bug in mesh visualization (show backfaces when opacity < 1)
+- Add color quick select control to Volume controls
+- Fix `dropFiles` bug
+- Fix some cyclic imports and reduce the use of const enums. This should make it easier to use the library with the `isolatedModules: true` TS config.
+- Fix `dropFiles` bug (#679)
+- Add `input type='color'` picker to `CombinedColorControl`
+- Set `ParameterMappingControl` disabled when state is updating
+- Performance tweaks
+    - Update clip `defines` only when changed
+    - Check for identity in structure/unit areEqual methods
+    - Avoid cloning of structure representation parameters
+    - Make SymmetryOperator.createMapping monomorphic
+    - Improve bonding-sphere calculation
+    - Defer Scene properties calculation (markerAverage, opacityAverage, hasOpaque)
+    - Improve checks in in UnitsRepresentation setVisualState
+- Add StructureElement.Loci.forEachLocation
+- Add RepresentationRegistry.clear and ThemeRegistry.clear
+- Add generic Loci support for overpaint, substance, clipping themes
+- Add `.getCenter` and `.center` to `Camera`
+- Add support to dim unmarked groups
+- Add support for marker edge strength
+
+## [v3.28.0] - 2022-12-20
+
+- Show histogram in direct volume control point settings
+- Add `solidInterior` parameter to sphere/cylinder impostors
+- [Breaking] Tweak `ignoreHydrogens` non-polar handling (introduced in 3.27.0)
+- Add `meshes` and `volumes-and-segmentations` extensions
+    - See https://molstarvolseg.ncbr.muni.cz/ for more info
+- Fix missing support for info in `ParamDefinition.Converted`
+- Add support for multi-visual volume representations
+- Improve volume isosurface bounding-sphere
+- Add basic volume segmentation support to core
+    - Add `Volume.Segment` model
+    - Add `Segmentation` custom volume property
+    - Add `SegmentRepresentation` representation
+    - Add `volume-segment` color theme
+- Fix GPU marching cubes failing for large meshes with webgl2 (due to use of float16)
+
+## [v3.27.0] - 2022-12-15
+
+- Add an `includeTransparent` parameter to hide/show outlines of components that are transparent
+- Fix 'once' for animations of systems with many frames
+- Better guard against issue (black fringes) with bumpiness in impostors
+- Improve impostor shaders
+    - Fix sphere near-clipping with orthographic projection
+    - Fix cylinder near-clipping
+    - Add interior cylinder caps
+    - Add per-pixel object clipping
+- Fix `QualityAssessment` assignment bug for structures with different auth vs label sequence numbering
+- Refresh `ApplyActionControl`'s param definition when toggling expanded state
+- Fix `struct_conn` bond assignment for ions
+- Ability to show only polar hydrogens
+
+## [v3.26.0] - 2022-12-04
+
+- Support for ``powerPreference`` webgl attribute. Add ``PluginConfig.General.PowerPreference`` and ``power-preference`` Viewer GET param.
+- Excluded common protein caps `NME` and `ACE` from the ligand selection query
+- Add screen-space shadow post-processing effect
+- Add "Structure Molecular Surface" visual
+- Add `external-volume` theme (coloring of arbitrary geometries by user-selected volume)
+
+## [v3.25.1] - 2022-11-20
+
+- Fix edge-case in `Structure.eachUnitPair` with single-element units
+- Fix 'auto' structure-quality for coarse models
+
+## [v3.25.0] - 2022-11-16
+
+- Fix handling of gzipped assets (reverts #615)
+
+## [v3.24.0] - 2022-11-13
+
 - Make `PluginContext.initContainer` checkered canvas background optional
+- Store URL of downloaded assets to detect zip/gzip based on extension (#615)
+- Add optional `operator.key`; can be referenced in `IndexPairBonds`
+- Add overpaint/transparency/substance theme strength to representations
+- Fix viewport color for transparent background
 
 ## [v3.23.0] - 2022-10-19
 
 - Add `PluginContext.initContainer/mount/unmount` methods; these should make it easier to reuse a plugin context with both custom and built-in UI
 - Add `PluginContext.canvas3dInitialized`
 - `createPluginUI` now resolves after the 3d canvas has been initialized
-- Change EM Volume Streaming default from `Whote Structure` to `Auto`
+- Change EM Volume Streaming default from `Whole Structure` to `Auto`
 
 ## [v3.22.0] - 2022-10-17
 
-- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality` 
+- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
 
 ## [v3.21.0] - 2022-10-17
 

README.md

@@ -1,6 +1,6 @@
 [![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)
 [![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)
-[![Build Status](https://travis-ci.org/molstar/molstar.svg?branch=master)](https://travis-ci.org/molstar/molstar)
+[![Build](https://github.com/molstar/molstar/actions/workflows/node.yml/badge.svg)](https://github.com/molstar/molstar/actions/workflows/node.yml)
 [![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)
 
 # Mol*

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.23.0",
+  "version": "3.31.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -13,7 +13,7 @@
   "scripts": {
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
-    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
+    "test": "npm install --no-save \"gl@^6.0.2\" && npm run lint && jest",
     "jest": "jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "clean": "node ./scripts/clean.js",
@@ -92,57 +92,62 @@
     "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>",
     "Adam Midlik <midlik@gmail.com>",
     "Koya Sakuma <koya.sakuma.work@gmail.com>",
-    "Gianluca Tomasello <giagitom@gmail.com>"
+    "Gianluca Tomasello <giagitom@gmail.com>",
+    "Ke Ma <mark.ma@rcsb.org>",
+    "Jason Pattle <jpattle@exscientia.co.uk>",
+    "David Williams <dwilliams@nobiastx.com>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.2.1",
-    "@graphql-codegen/cli": "^2.13.7",
-    "@graphql-codegen/time": "^3.2.1",
-    "@graphql-codegen/typescript": "^2.7.4",
+    "@graphql-codegen/add": "^4.0.0",
+    "@graphql-codegen/cli": "^3.0.0",
+    "@graphql-codegen/time": "^4.0.0",
+    "@graphql-codegen/typescript": "^3.0.0",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.5.6",
-    "@graphql-codegen/typescript-operations": "^2.5.4",
-    "@types/cors": "^2.8.12",
-    "@types/gl": "^4.1.1",
-    "@types/jest": "^29.1.2",
-    "@types/react": "^18.0.21",
-    "@types/react-dom": "^18.0.6",
-    "@typescript-eslint/eslint-plugin": "^5.40.0",
-    "@typescript-eslint/parser": "^5.40.0",
+    "@graphql-codegen/typescript-graphql-request": "^4.5.8",
+    "@graphql-codegen/typescript-operations": "^3.0.0",
+    "@types/cors": "^2.8.13",
+    "@types/gl": "^6.0.2",
+    "@types/jpeg-js": "^0.3.7",
+    "@types/pngjs": "^6.0.1",
+    "@types/jest": "^29.4.0",
+    "@types/react": "^18.0.27",
+    "@types/react-dom": "^18.0.10",
+    "@typescript-eslint/eslint-plugin": "^5.50.0",
+    "@typescript-eslint/parser": "^5.50.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^7.4.0",
+    "concurrently": "^7.6.0",
     "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.7.1",
-    "eslint": "^8.25.0",
+    "css-loader": "^6.7.3",
+    "eslint": "^8.33.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
-    "fs-extra": "^10.1.0",
+    "fs-extra": "^11.1.0",
     "graphql": "^16.6.0",
     "http-server": "^14.1.1",
-    "jest": "^29.2.0",
-    "mini-css-extract-plugin": "^2.6.1",
+    "jest": "^29.4.1",
+    "mini-css-extract-plugin": "^2.7.2",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "sass": "^1.55.0",
-    "sass-loader": "^13.1.0",
-    "simple-git": "^3.14.1",
+    "sass": "^1.58.0",
+    "sass-loader": "^13.2.0",
+    "simple-git": "^3.16.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.8.4",
-    "webpack": "^5.74.0",
-    "webpack-cli": "^4.10.0"
+    "ts-jest": "^29.0.5",
+    "typescript": "^4.9.5",
+    "webpack": "^5.75.0",
+    "webpack-cli": "^5.0.1"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.2",
     "@types/compression": "1.7.2",
-    "@types/express": "^4.17.14",
-    "@types/node": "^16.11.66",
+    "@types/express": "^4.17.17",
+    "@types/node": "^16.18.12",
     "@types/node-fetch": "^2.6.2",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
@@ -151,17 +156,22 @@
     "cors": "^2.8.5",
     "express": "^4.18.2",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.15",
-    "immutable": "^4.1.0",
-    "node-fetch": "^2.6.7",
-    "rxjs": "^7.5.7",
-    "swagger-ui-dist": "^4.14.3",
-    "tslib": "^2.4.0",
+    "immer": "^9.0.19",
+    "immutable": "^4.2.3",
+    "node-fetch": "^2.6.9",
+    "rxjs": "^7.8.0",
+    "swagger-ui-dist": "^4.15.5",
+    "tslib": "^2.5.0",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"
   },
   "peerDependencies": {
     "react": "^18.1.0 || ^17.0.2 || ^16.14.0",
     "react-dom": "^18.1.0 || ^17.0.2 || ^16.14.0"
+  },
+  "optionalDependencies": {
+    "gl": "^6.0.2",
+    "jpeg-js": "^0.4.4",
+    "pngjs": "^6.0.0"
   }
 }

src/apps/docking-viewer/viewport.tsx

@@ -31,7 +31,8 @@ function shinyStyle(plugin: PluginContext) {
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'off', params: {} },
-            outline: { name: 'off', params: {} }
+            shadow: { name: 'off', params: {} },
+            outline: { name: 'off', params: {} },
         }
     } });
 }
@@ -48,13 +49,15 @@ function occlusionStyle(plugin: PluginContext) {
                 blurKernelSize: 15,
                 radius: 5,
                 samples: 32,
-                resolutionScale: 1
+                resolutionScale: 1,
             } },
             outline: { name: 'on', params: {
                 scale: 1.0,
                 threshold: 0.33,
                 color: Color(0x0000),
-            } }
+                includeTransparent: true,
+            } },
+            shadow: { name: 'off', params: {} },
         }
     } });
 }

src/apps/viewer/app.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -7,8 +7,9 @@
 
 import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { CellPack } from '../../extensions/cellpack';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+import { DnatcoNtCs } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
 import { GeometryExport } from '../../extensions/geo-export';
 import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
@@ -49,16 +50,17 @@ import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/car
 import { Backgrounds } from '../../extensions/backgrounds';
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode, setTimingMode, consoleStats } from '../../mol-util/debug';
 
 const CustomFormats = [
     ['g3d', G3dProvider] as const
 ];
 
 const Extensions = {
+    'volseg': PluginSpec.Behavior(Volseg),
     'backgrounds': PluginSpec.Behavior(Backgrounds),
     'cellpack': PluginSpec.Behavior(CellPack),
-    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
+    'dnatco-ntcs': PluginSpec.Behavior(DnatcoNtCs),
     'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
     'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
@@ -91,6 +93,7 @@ const DefaultViewerOptions = {
     enableDpoit: PluginConfig.General.EnableDpoit.defaultValue,
     preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
     allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
+    powerPreference: PluginConfig.General.PowerPreference.defaultValue,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -104,6 +107,7 @@ const DefaultViewerOptions = {
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default' as SaccharideCompIdMapType,
+    volumesAndSegmentationsDefaultServer: VolsegVolumeServerConfig.DefaultServer.defaultValue,
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 
@@ -163,6 +167,7 @@ export class Viewer {
                 [PluginConfig.General.EnableDpoit, o.enableDpoit],
                 [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
                 [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
+                [PluginConfig.General.PowerPreference, o.powerPreference],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
@@ -177,6 +182,7 @@ export class Viewer {
                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                 [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
                 [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+                [VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
             ]
         };
 

src/apps/viewer/index.html

@@ -63,6 +63,7 @@
             var enableDpoit = getParam('enable-dpoit', '[^&]+').trim() === '1';
             var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
             var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
+            var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
 
             molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
@@ -80,6 +81,7 @@
                 enableDpoit: enableDpoit ? true : void 0,
                 preferWebgl1: preferWebgl1,
                 allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
+                powerPreference: powerPreference || 'high-performance',
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();
                 if (snapshotId) viewer.setRemoteSnapshot(snapshotId);

src/cli/cifschema/util/cif-dic.ts

@@ -152,7 +152,7 @@ function getImportFrames(d: Data.CifFrame, imports: Imports) {
 }
 
 /** get field from given or linked category */
-function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField|undefined {
+function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField | undefined {
     const { categories, links } = ctx;
     const cat = d.categories[category];
     if (cat) {

src/cli/structure-info/helpers.ts

@@ -25,7 +25,7 @@ async function readFile(path: string) {
     }
 }
 
-async function parseCif(data: string|Uint8Array) {
+async function parseCif(data: string | Uint8Array) {
     const comp = CIF.parse(data);
     const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
     if (parsed.isError) throw parsed;

src/cli/structure-info/volume.ts

@@ -38,7 +38,7 @@ function print(volume: Volume) {
 }
 
 async function doMesh(volume: Volume, filename: string) {
-    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) })).run();
+    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, -1, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) })).run();
     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
 
     // Export the mesh in OBJ format.

src/examples/alpha-orbitals/index.ts

@@ -25,7 +25,7 @@ import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
 
-import { setDebugMode, setTimingMode } from '../../mol-util/debug';
+import { setDebugMode, setTimingMode, consoleStats } from '../../mol-util/debug';
 
 interface DemoInput {
     moleculeSdf: string,
@@ -222,4 +222,5 @@ export class AlphaOrbitalsExample {
 
 (window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();
 (window as any).AlphaOrbitalsExample.setDebugMode = setDebugMode;
-(window as any).AlphaOrbitalsExample.setTimingMode = setTimingMode;
+(window as any).AlphaOrbitalsExample.setTimingMode = setTimingMode;
+(window as any).AlphaOrbitalsExample.consoleStats = consoleStats;

src/examples/image-renderer/index.ts

@@ -0,0 +1,87 @@
+/**
+ * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ *
+ * Example command-line application generating images of PDB structures
+ * Build: npm install --no-save gl jpeg-js pngjs  // these packages are not listed in dependencies for performance reasons
+ *        npm run build
+ * Run:   node lib/commonjs/examples/image-renderer 1cbs ../outputs_1cbs/
+ */
+
+import { ArgumentParser } from 'argparse';
+import fs from 'fs';
+import path from 'path';
+
+import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
+import { ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif } from '../../mol-plugin-state/transforms/model';
+import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { HeadlessPluginContext } from '../../mol-plugin/headless-plugin-context';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { STYLIZED_POSTPROCESSING } from '../../mol-plugin/util/headless-screenshot';
+
+
+interface Args {
+    pdbId: string,
+    outDirectory: string
+}
+
+function parseArguments(): Args {
+    const parser = new ArgumentParser({ description: 'Example command-line application generating images of PDB structures' });
+    parser.add_argument('pdbId', { help: 'PDB identifier' });
+    parser.add_argument('outDirectory', { help: 'Directory for outputs' });
+    const args = parser.parse_args();
+    return { ...args };
+}
+
+async function main() {
+    const args = parseArguments();
+    const url = `https://www.ebi.ac.uk/pdbe/entry-files/download/${args.pdbId}.bcif`;
+    console.log('PDB ID:', args.pdbId);
+    console.log('Source URL:', url);
+    console.log('Outputs:', args.outDirectory);
+
+    // Create a headless plugin
+    const plugin = new HeadlessPluginContext(DefaultPluginSpec(), { width: 800, height: 800 });
+    await plugin.init();
+
+    // Download and visualize data in the plugin
+    const update = plugin.build();
+    const structure = update.toRoot()
+        .apply(Download, { url, isBinary: true })
+        .apply(ParseCif)
+        .apply(TrajectoryFromMmCif)
+        .apply(ModelFromTrajectory)
+        .apply(StructureFromModel);
+    const polymer = structure.apply(StructureComponent, { type: { name: 'static', params: 'polymer' } });
+    const ligand = structure.apply(StructureComponent, { type: { name: 'static', params: 'ligand' } });
+    polymer.apply(StructureRepresentation3D, {
+        type: { name: 'cartoon', params: { alpha: 1 } },
+        colorTheme: { name: 'sequence-id', params: {} },
+    });
+    ligand.apply(StructureRepresentation3D, {
+        type: { name: 'ball-and-stick', params: { sizeFactor: 1 } },
+        colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'element-symbol', params: {} } } },
+        sizeTheme: { name: 'physical', params: {} },
+    });
+    await update.commit();
+
+    // Export images
+    fs.mkdirSync(args.outDirectory, { recursive: true });
+    await plugin.saveImage(path.join(args.outDirectory, 'basic.png'));
+    await plugin.saveImage(path.join(args.outDirectory, 'basic.jpg'));
+    await plugin.saveImage(path.join(args.outDirectory, 'large.png'), { width: 1600, height: 1200 });
+    await plugin.saveImage(path.join(args.outDirectory, 'large.jpg'), { width: 1600, height: 1200 });
+    await plugin.saveImage(path.join(args.outDirectory, 'stylized.png'), undefined, STYLIZED_POSTPROCESSING);
+    await plugin.saveImage(path.join(args.outDirectory, 'stylized.jpg'), undefined, STYLIZED_POSTPROCESSING);
+    await plugin.saveImage(path.join(args.outDirectory, 'stylized-compressed-jpg.jpg'), undefined, STYLIZED_POSTPROCESSING, undefined, 10);
+
+    // Export state loadable in Mol* Viewer
+    await plugin.saveStateSnapshot(path.join(args.outDirectory, 'molstar-state.molj'));
+
+    // Cleanup
+    await plugin.clear();
+    plugin.dispose();
+}
+
+main();

src/examples/lighting/index.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,7 +25,8 @@ const Canvas3DPresets = {
         canvas3d: <Preset>{
             postprocessing: {
                 occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
-                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000) } }
+                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000), includeTransparent: true, } },
+                shadow: { name: 'off', params: {} },
             },
             renderer: {
                 ambientIntensity: 1.0,
@@ -37,7 +38,8 @@ const Canvas3DPresets = {
         canvas3d: <Preset>{
             postprocessing: {
                 occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
-                outline: { name: 'off', params: {} }
+                outline: { name: 'off', params: {} },
+                shadow: { name: 'off', params: {} },
             },
             renderer: {
                 ambientIntensity: 0.4,
@@ -50,7 +52,8 @@ const Canvas3DPresets = {
         canvas3d: <Preset>{
             postprocessing: {
                 occlusion: { name: 'off', params: {} },
-                outline: { name: 'off', params: {} }
+                outline: { name: 'off', params: {} },
+                shadow: { name: 'off', params: {} },
             },
             renderer: {
                 ambientIntensity: 0.4,

src/extensions/cellpack/data.ts

@@ -52,7 +52,7 @@ export interface Compartment {
 }
 
 // Primitives discribing a compartment
-export const enum CompartmentPrimitiveType {
+export enum CompartmentPrimitiveType {
     MetaBall = 0,
     Sphere = 1,
     Cube = 2,

src/extensions/cellpack/model.ts

@@ -236,7 +236,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
         structure = await getCurve(name, getCurveTransforms(ingredient), model);
     } else {
         if ((!results || results.length === 0)) return;
-        let bu: string|undefined = source.bu ? source.bu : undefined;
+        let bu: string | undefined = source.bu ? source.bu : undefined;
         if (bu) {
             if (bu === 'AU') {
                 bu = undefined;
@@ -585,7 +585,7 @@ export const LoadCellPackModel = StateAction.build({
             ... ctx.managers.structure.component.state.options,
             visualQuality: 'custom',
             ignoreLight: true,
-            showHydrogens: false,
+            hydrogens: 'hide-all',
         });
         ctx.canvas3d?.setProps({
             multiSample: { mode: 'off' },
@@ -606,12 +606,22 @@ export const LoadCellPackModel = StateAction.build({
                         resolutionScale: 1,
                     }
                 },
+                shadow: {
+                    name: 'on',
+                    params: {
+                        bias: 0.6,
+                        maxDistance: 80,
+                        steps: 3,
+                        tolerance: 1.0,
+                    }
+                },
                 outline: {
                     name: 'on',
                     params: {
                         scale: 1,
                         threshold: 0.33,
                         color: ColorNames.black,
+                        includeTransparent: true,
                     }
                 }
             }

src/extensions/dnatco/behavior.ts

@@ -0,0 +1,59 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { ConfalPyramidsPreset } from './confal-pyramids/behavior';
+import { ConfalPyramidsColorThemeProvider } from './confal-pyramids/color';
+import { ConfalPyramidsProvider } from './confal-pyramids/property';
+import { ConfalPyramidsRepresentationProvider } from './confal-pyramids/representation';
+import { NtCTubePreset } from './ntc-tube/behavior';
+import { NtCTubeColorThemeProvider } from './ntc-tube/color';
+import { NtCTubeProvider } from './ntc-tube/property';
+import { NtCTubeRepresentationProvider } from './ntc-tube/representation';
+
+
+export const DnatcoNtCs = PluginBehavior.create<{ autoAttach: boolean, showToolTip: boolean }>({
+    name: 'dnatco-ntcs',
+    category: 'custom-props',
+    display: {
+        name: 'DNATCO NtC Annotations',
+        description: 'DNATCO NtC Annotations',
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showToolTip: boolean }> {
+        register(): void {
+            this.ctx.customModelProperties.register(ConfalPyramidsProvider, this.params.autoAttach);
+            this.ctx.customModelProperties.register(NtCTubeProvider, this.params.autoAttach);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
+            this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(NtCTubeColorThemeProvider);
+            this.ctx.representation.structure.registry.add(NtCTubeRepresentationProvider);
+
+            this.ctx.builders.structure.representation.registerPreset(ConfalPyramidsPreset);
+            this.ctx.builders.structure.representation.registerPreset(NtCTubePreset);
+        }
+
+        unregister() {
+            this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
+            this.ctx.customModelProperties.unregister(NtCTubeProvider.descriptor.name);
+
+            this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
+            this.ctx.representation.structure.registry.remove(NtCTubeRepresentationProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(NtCTubeColorThemeProvider);
+
+            this.ctx.builders.structure.representation.unregisterPreset(ConfalPyramidsPreset);
+            this.ctx.builders.structure.representation.unregisterPreset(NtCTubePreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(true),
+        showToolTip: PD.Boolean(true)
+    })
+});
+

src/extensions/dnatco/color.ts

@@ -0,0 +1,219 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { Color, ColorMap } from '../../mol-util/color';
+
+export const DefaultNtCClassColors = {
+    A: 0xFFC1C1,
+    B: 0xC8CFFF,
+    BII: 0x0059DA,
+    miB: 0x3BE8FB,
+    Z: 0x01F60E,
+    IC: 0xFA5CFB,
+    OPN: 0xE90000,
+    SYN: 0xFFFF01,
+    N: 0xF2F2F2,
+};
+export const ErrorColor = Color(0xFFA10A);
+
+export const NtCColors = ColorMap({
+    NANT_Upr: DefaultNtCClassColors.N,
+    NANT_Lwr: DefaultNtCClassColors.N,
+    AA00_Upr: DefaultNtCClassColors.A,
+    AA00_Lwr: DefaultNtCClassColors.A,
+    AA02_Upr: DefaultNtCClassColors.A,
+    AA02_Lwr: DefaultNtCClassColors.A,
+    AA03_Upr: DefaultNtCClassColors.A,
+    AA03_Lwr: DefaultNtCClassColors.A,
+    AA04_Upr: DefaultNtCClassColors.A,
+    AA04_Lwr: DefaultNtCClassColors.A,
+    AA08_Upr: DefaultNtCClassColors.A,
+    AA08_Lwr: DefaultNtCClassColors.A,
+    AA09_Upr: DefaultNtCClassColors.A,
+    AA09_Lwr: DefaultNtCClassColors.A,
+    AA01_Upr: DefaultNtCClassColors.A,
+    AA01_Lwr: DefaultNtCClassColors.A,
+    AA05_Upr: DefaultNtCClassColors.A,
+    AA05_Lwr: DefaultNtCClassColors.A,
+    AA06_Upr: DefaultNtCClassColors.A,
+    AA06_Lwr: DefaultNtCClassColors.A,
+    AA10_Upr: DefaultNtCClassColors.A,
+    AA10_Lwr: DefaultNtCClassColors.A,
+    AA11_Upr: DefaultNtCClassColors.A,
+    AA11_Lwr: DefaultNtCClassColors.A,
+    AA07_Upr: DefaultNtCClassColors.A,
+    AA07_Lwr: DefaultNtCClassColors.A,
+    AA12_Upr: DefaultNtCClassColors.A,
+    AA12_Lwr: DefaultNtCClassColors.A,
+    AA13_Upr: DefaultNtCClassColors.A,
+    AA13_Lwr: DefaultNtCClassColors.A,
+    AB01_Upr: DefaultNtCClassColors.A,
+    AB01_Lwr: DefaultNtCClassColors.B,
+    AB02_Upr: DefaultNtCClassColors.A,
+    AB02_Lwr: DefaultNtCClassColors.B,
+    AB03_Upr: DefaultNtCClassColors.A,
+    AB03_Lwr: DefaultNtCClassColors.B,
+    AB04_Upr: DefaultNtCClassColors.A,
+    AB04_Lwr: DefaultNtCClassColors.B,
+    AB05_Upr: DefaultNtCClassColors.A,
+    AB05_Lwr: DefaultNtCClassColors.B,
+    BA01_Upr: DefaultNtCClassColors.B,
+    BA01_Lwr: DefaultNtCClassColors.A,
+    BA05_Upr: DefaultNtCClassColors.B,
+    BA05_Lwr: DefaultNtCClassColors.A,
+    BA09_Upr: DefaultNtCClassColors.B,
+    BA09_Lwr: DefaultNtCClassColors.A,
+    BA08_Upr: DefaultNtCClassColors.BII,
+    BA08_Lwr: DefaultNtCClassColors.A,
+    BA10_Upr: DefaultNtCClassColors.B,
+    BA10_Lwr: DefaultNtCClassColors.A,
+    BA13_Upr: DefaultNtCClassColors.BII,
+    BA13_Lwr: DefaultNtCClassColors.A,
+    BA16_Upr: DefaultNtCClassColors.BII,
+    BA16_Lwr: DefaultNtCClassColors.A,
+    BA17_Upr: DefaultNtCClassColors.BII,
+    BA17_Lwr: DefaultNtCClassColors.A,
+    BB00_Upr: DefaultNtCClassColors.B,
+    BB00_Lwr: DefaultNtCClassColors.B,
+    BB01_Upr: DefaultNtCClassColors.B,
+    BB01_Lwr: DefaultNtCClassColors.B,
+    BB17_Upr: DefaultNtCClassColors.B,
+    BB17_Lwr: DefaultNtCClassColors.B,
+    BB02_Upr: DefaultNtCClassColors.B,
+    BB02_Lwr: DefaultNtCClassColors.B,
+    BB03_Upr: DefaultNtCClassColors.B,
+    BB03_Lwr: DefaultNtCClassColors.B,
+    BB11_Upr: DefaultNtCClassColors.B,
+    BB11_Lwr: DefaultNtCClassColors.B,
+    BB16_Upr: DefaultNtCClassColors.B,
+    BB16_Lwr: DefaultNtCClassColors.B,
+    BB04_Upr: DefaultNtCClassColors.B,
+    BB04_Lwr: DefaultNtCClassColors.BII,
+    BB05_Upr: DefaultNtCClassColors.B,
+    BB05_Lwr: DefaultNtCClassColors.BII,
+    BB07_Upr: DefaultNtCClassColors.BII,
+    BB07_Lwr: DefaultNtCClassColors.BII,
+    BB08_Upr: DefaultNtCClassColors.BII,
+    BB08_Lwr: DefaultNtCClassColors.BII,
+    BB10_Upr: DefaultNtCClassColors.miB,
+    BB10_Lwr: DefaultNtCClassColors.miB,
+    BB12_Upr: DefaultNtCClassColors.miB,
+    BB12_Lwr: DefaultNtCClassColors.miB,
+    BB13_Upr: DefaultNtCClassColors.miB,
+    BB13_Lwr: DefaultNtCClassColors.miB,
+    BB14_Upr: DefaultNtCClassColors.miB,
+    BB14_Lwr: DefaultNtCClassColors.miB,
+    BB15_Upr: DefaultNtCClassColors.miB,
+    BB15_Lwr: DefaultNtCClassColors.miB,
+    BB20_Upr: DefaultNtCClassColors.miB,
+    BB20_Lwr: DefaultNtCClassColors.miB,
+    IC01_Upr: DefaultNtCClassColors.IC,
+    IC01_Lwr: DefaultNtCClassColors.IC,
+    IC02_Upr: DefaultNtCClassColors.IC,
+    IC02_Lwr: DefaultNtCClassColors.IC,
+    IC03_Upr: DefaultNtCClassColors.IC,
+    IC03_Lwr: DefaultNtCClassColors.IC,
+    IC04_Upr: DefaultNtCClassColors.IC,
+    IC04_Lwr: DefaultNtCClassColors.IC,
+    IC05_Upr: DefaultNtCClassColors.IC,
+    IC05_Lwr: DefaultNtCClassColors.IC,
+    IC06_Upr: DefaultNtCClassColors.IC,
+    IC06_Lwr: DefaultNtCClassColors.IC,
+    IC07_Upr: DefaultNtCClassColors.IC,
+    IC07_Lwr: DefaultNtCClassColors.IC,
+    OP01_Upr: DefaultNtCClassColors.OPN,
+    OP01_Lwr: DefaultNtCClassColors.OPN,
+    OP02_Upr: DefaultNtCClassColors.OPN,
+    OP02_Lwr: DefaultNtCClassColors.OPN,
+    OP03_Upr: DefaultNtCClassColors.OPN,
+    OP03_Lwr: DefaultNtCClassColors.OPN,
+    OP04_Upr: DefaultNtCClassColors.OPN,
+    OP04_Lwr: DefaultNtCClassColors.OPN,
+    OP05_Upr: DefaultNtCClassColors.OPN,
+    OP05_Lwr: DefaultNtCClassColors.OPN,
+    OP06_Upr: DefaultNtCClassColors.OPN,
+    OP06_Lwr: DefaultNtCClassColors.OPN,
+    OP07_Upr: DefaultNtCClassColors.OPN,
+    OP07_Lwr: DefaultNtCClassColors.OPN,
+    OP08_Upr: DefaultNtCClassColors.OPN,
+    OP08_Lwr: DefaultNtCClassColors.OPN,
+    OP09_Upr: DefaultNtCClassColors.OPN,
+    OP09_Lwr: DefaultNtCClassColors.OPN,
+    OP10_Upr: DefaultNtCClassColors.OPN,
+    OP10_Lwr: DefaultNtCClassColors.OPN,
+    OP11_Upr: DefaultNtCClassColors.OPN,
+    OP11_Lwr: DefaultNtCClassColors.OPN,
+    OP12_Upr: DefaultNtCClassColors.OPN,
+    OP12_Lwr: DefaultNtCClassColors.OPN,
+    OP13_Upr: DefaultNtCClassColors.OPN,
+    OP13_Lwr: DefaultNtCClassColors.OPN,
+    OP14_Upr: DefaultNtCClassColors.OPN,
+    OP14_Lwr: DefaultNtCClassColors.OPN,
+    OP15_Upr: DefaultNtCClassColors.OPN,
+    OP15_Lwr: DefaultNtCClassColors.OPN,
+    OP16_Upr: DefaultNtCClassColors.OPN,
+    OP16_Lwr: DefaultNtCClassColors.OPN,
+    OP17_Upr: DefaultNtCClassColors.OPN,
+    OP17_Lwr: DefaultNtCClassColors.OPN,
+    OP18_Upr: DefaultNtCClassColors.OPN,
+    OP18_Lwr: DefaultNtCClassColors.OPN,
+    OP19_Upr: DefaultNtCClassColors.OPN,
+    OP19_Lwr: DefaultNtCClassColors.OPN,
+    OP20_Upr: DefaultNtCClassColors.OPN,
+    OP20_Lwr: DefaultNtCClassColors.OPN,
+    OP21_Upr: DefaultNtCClassColors.OPN,
+    OP21_Lwr: DefaultNtCClassColors.OPN,
+    OP22_Upr: DefaultNtCClassColors.OPN,
+    OP22_Lwr: DefaultNtCClassColors.OPN,
+    OP23_Upr: DefaultNtCClassColors.OPN,
+    OP23_Lwr: DefaultNtCClassColors.OPN,
+    OP24_Upr: DefaultNtCClassColors.OPN,
+    OP24_Lwr: DefaultNtCClassColors.OPN,
+    OP25_Upr: DefaultNtCClassColors.OPN,
+    OP25_Lwr: DefaultNtCClassColors.OPN,
+    OP26_Upr: DefaultNtCClassColors.OPN,
+    OP26_Lwr: DefaultNtCClassColors.OPN,
+    OP27_Upr: DefaultNtCClassColors.OPN,
+    OP27_Lwr: DefaultNtCClassColors.OPN,
+    OP28_Upr: DefaultNtCClassColors.OPN,
+    OP28_Lwr: DefaultNtCClassColors.OPN,
+    OP29_Upr: DefaultNtCClassColors.OPN,
+    OP29_Lwr: DefaultNtCClassColors.OPN,
+    OP30_Upr: DefaultNtCClassColors.OPN,
+    OP30_Lwr: DefaultNtCClassColors.OPN,
+    OP31_Upr: DefaultNtCClassColors.OPN,
+    OP31_Lwr: DefaultNtCClassColors.OPN,
+    OPS1_Upr: DefaultNtCClassColors.OPN,
+    OPS1_Lwr: DefaultNtCClassColors.OPN,
+    OP1S_Upr: DefaultNtCClassColors.OPN,
+    OP1S_Lwr: DefaultNtCClassColors.SYN,
+    AAS1_Upr: DefaultNtCClassColors.SYN,
+    AAS1_Lwr: DefaultNtCClassColors.A,
+    AB1S_Upr: DefaultNtCClassColors.A,
+    AB1S_Lwr: DefaultNtCClassColors.SYN,
+    AB2S_Upr: DefaultNtCClassColors.A,
+    AB2S_Lwr: DefaultNtCClassColors.SYN,
+    BB1S_Upr: DefaultNtCClassColors.B,
+    BB1S_Lwr: DefaultNtCClassColors.SYN,
+    BB2S_Upr: DefaultNtCClassColors.B,
+    BB2S_Lwr: DefaultNtCClassColors.SYN,
+    BBS1_Upr: DefaultNtCClassColors.SYN,
+    BBS1_Lwr: DefaultNtCClassColors.B,
+    ZZ01_Upr: DefaultNtCClassColors.Z,
+    ZZ01_Lwr: DefaultNtCClassColors.Z,
+    ZZ02_Upr: DefaultNtCClassColors.Z,
+    ZZ02_Lwr: DefaultNtCClassColors.Z,
+    ZZ1S_Upr: DefaultNtCClassColors.Z,
+    ZZ1S_Lwr: DefaultNtCClassColors.SYN,
+    ZZ2S_Upr: DefaultNtCClassColors.Z,
+    ZZ2S_Lwr: DefaultNtCClassColors.SYN,
+    ZZS1_Upr: DefaultNtCClassColors.SYN,
+    ZZS1_Lwr: DefaultNtCClassColors.Z,
+    ZZS2_Upr: DefaultNtCClassColors.SYN,
+    ZZS2_Lwr: DefaultNtCClassColors.Z,
+});
+

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

@@ -6,23 +6,22 @@
  */
 
 import { ConfalPyramidsColorThemeProvider } from './color';
-import { ConfalPyramids, ConfalPyramidsProvider } from './property';
+import { ConfalPyramidsProvider } from './property';
 import { ConfalPyramidsRepresentationProvider } from './representation';
-import { ConfalPyramidsTypes } from './types';
-import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { Dnatco } from '../property';
+import { DnatcoTypes } from '../types';
 import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
 import { StateObjectRef } from '../../../mol-state';
 import { Task } from '../../../mol-task';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 
-export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider({
+export const ConfalPyramidsPreset = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-confal-pyramids',
     display: {
         name: 'Confal Pyramids', group: 'Annotation',
         description: 'Schematic depiction of conformer class and confal value.',
     },
     isApplicable(a) {
-        return a.data.models.length >= 1 && a.data.models.some(m => ConfalPyramids.isApplicable(m));
+        return a.data.models.length >= 1 && a.data.models.some(m => Dnatco.isApplicable(m));
     },
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {
@@ -48,50 +47,7 @@ export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider(
     }
 });
 
-export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean, showToolTip: boolean }>({
-    name: 'dnatco-confal-pyramids-prop',
-    category: 'custom-props',
-    display: {
-        name: 'Confal Pyramids',
-        description: 'Schematic depiction of conformer class and confal value.',
-    },
-    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showToolTip: boolean }> {
-        private provider = ConfalPyramidsProvider;
-
-        register(): void {
-            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
-            this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
-
-            this.ctx.builders.structure.representation.registerPreset(DnatcoConfalPyramidsPreset);
-        }
-
-        update(p: { autoAttach: boolean, showToolTip: boolean }) {
-            const updated = this.params.autoAttach !== p.autoAttach;
-            this.params.autoAttach = p.autoAttach;
-            this.params.showToolTip = p.showToolTip;
-            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
-            return updated;
-        }
-
-        unregister() {
-            this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
-
-            this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
-
-            this.ctx.builders.structure.representation.unregisterPreset(DnatcoConfalPyramidsPreset);
-        }
-    },
-    params: () => ({
-        autoAttach: PD.Boolean(true),
-        showToolTip: PD.Boolean(true)
-    })
-});
-
-export function confalPyramidLabel(halfPyramid: ConfalPyramidsTypes.HalfPyramid) {
-    const { step } = halfPyramid;
+export function confalPyramidLabel(step: DnatcoTypes.Step) {
     return `
         <b>${step.auth_asym_id_1}</b> |
         <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}

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

@@ -5,8 +5,10 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
-import { ConfalPyramids, ConfalPyramidsProvider } from './property';
+import { ErrorColor, NtCColors } from '../color';
+import { ConfalPyramidsProvider } from './property';
 import { ConfalPyramidsTypes as CPT } from './types';
+import { Dnatco } from '../property';
 import { Location } from '../../../mol-model/location';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
 import { ColorTheme } from '../../../mol-theme/color';
@@ -19,215 +21,7 @@ import { ObjectKeys } from '../../../mol-util/type-helpers';
 
 const Description = 'Assigns colors to confal pyramids';
 
-const DefaultClassColors = {
-    A: 0xFFC1C1,
-    B: 0xC8CFFF,
-    BII: 0x0059DA,
-    miB: 0x3BE8FB,
-    Z: 0x01F60E,
-    IC: 0xFA5CFB,
-    OPN: 0xE90000,
-    SYN: 0xFFFF01,
-    N: 0xF2F2F2,
-};
-const ErrorColor = Color(0xFFA10A);
-
-const PyramidsColors = ColorMap({
-    NANT_Upr: DefaultClassColors.N,
-    NANT_Lwr: DefaultClassColors.N,
-    AA00_Upr: DefaultClassColors.A,
-    AA00_Lwr: DefaultClassColors.A,
-    AA02_Upr: DefaultClassColors.A,
-    AA02_Lwr: DefaultClassColors.A,
-    AA03_Upr: DefaultClassColors.A,
-    AA03_Lwr: DefaultClassColors.A,
-    AA04_Upr: DefaultClassColors.A,
-    AA04_Lwr: DefaultClassColors.A,
-    AA08_Upr: DefaultClassColors.A,
-    AA08_Lwr: DefaultClassColors.A,
-    AA09_Upr: DefaultClassColors.A,
-    AA09_Lwr: DefaultClassColors.A,
-    AA01_Upr: DefaultClassColors.A,
-    AA01_Lwr: DefaultClassColors.A,
-    AA05_Upr: DefaultClassColors.A,
-    AA05_Lwr: DefaultClassColors.A,
-    AA06_Upr: DefaultClassColors.A,
-    AA06_Lwr: DefaultClassColors.A,
-    AA10_Upr: DefaultClassColors.A,
-    AA10_Lwr: DefaultClassColors.A,
-    AA11_Upr: DefaultClassColors.A,
-    AA11_Lwr: DefaultClassColors.A,
-    AA07_Upr: DefaultClassColors.A,
-    AA07_Lwr: DefaultClassColors.A,
-    AA12_Upr: DefaultClassColors.A,
-    AA12_Lwr: DefaultClassColors.A,
-    AA13_Upr: DefaultClassColors.A,
-    AA13_Lwr: DefaultClassColors.A,
-    AB01_Upr: DefaultClassColors.A,
-    AB01_Lwr: DefaultClassColors.B,
-    AB02_Upr: DefaultClassColors.A,
-    AB02_Lwr: DefaultClassColors.B,
-    AB03_Upr: DefaultClassColors.A,
-    AB03_Lwr: DefaultClassColors.B,
-    AB04_Upr: DefaultClassColors.A,
-    AB04_Lwr: DefaultClassColors.B,
-    AB05_Upr: DefaultClassColors.A,
-    AB05_Lwr: DefaultClassColors.B,
-    BA01_Upr: DefaultClassColors.B,
-    BA01_Lwr: DefaultClassColors.A,
-    BA05_Upr: DefaultClassColors.B,
-    BA05_Lwr: DefaultClassColors.A,
-    BA09_Upr: DefaultClassColors.B,
-    BA09_Lwr: DefaultClassColors.A,
-    BA08_Upr: DefaultClassColors.BII,
-    BA08_Lwr: DefaultClassColors.A,
-    BA10_Upr: DefaultClassColors.B,
-    BA10_Lwr: DefaultClassColors.A,
-    BA13_Upr: DefaultClassColors.BII,
-    BA13_Lwr: DefaultClassColors.A,
-    BA16_Upr: DefaultClassColors.BII,
-    BA16_Lwr: DefaultClassColors.A,
-    BA17_Upr: DefaultClassColors.BII,
-    BA17_Lwr: DefaultClassColors.A,
-    BB00_Upr: DefaultClassColors.B,
-    BB00_Lwr: DefaultClassColors.B,
-    BB01_Upr: DefaultClassColors.B,
-    BB01_Lwr: DefaultClassColors.B,
-    BB17_Upr: DefaultClassColors.B,
-    BB17_Lwr: DefaultClassColors.B,
-    BB02_Upr: DefaultClassColors.B,
-    BB02_Lwr: DefaultClassColors.B,
-    BB03_Upr: DefaultClassColors.B,
-    BB03_Lwr: DefaultClassColors.B,
-    BB11_Upr: DefaultClassColors.B,
-    BB11_Lwr: DefaultClassColors.B,
-    BB16_Upr: DefaultClassColors.B,
-    BB16_Lwr: DefaultClassColors.B,
-    BB04_Upr: DefaultClassColors.B,
-    BB04_Lwr: DefaultClassColors.BII,
-    BB05_Upr: DefaultClassColors.B,
-    BB05_Lwr: DefaultClassColors.BII,
-    BB07_Upr: DefaultClassColors.BII,
-    BB07_Lwr: DefaultClassColors.BII,
-    BB08_Upr: DefaultClassColors.BII,
-    BB08_Lwr: DefaultClassColors.BII,
-    BB10_Upr: DefaultClassColors.miB,
-    BB10_Lwr: DefaultClassColors.miB,
-    BB12_Upr: DefaultClassColors.miB,
-    BB12_Lwr: DefaultClassColors.miB,
-    BB13_Upr: DefaultClassColors.miB,
-    BB13_Lwr: DefaultClassColors.miB,
-    BB14_Upr: DefaultClassColors.miB,
-    BB14_Lwr: DefaultClassColors.miB,
-    BB15_Upr: DefaultClassColors.miB,
-    BB15_Lwr: DefaultClassColors.miB,
-    BB20_Upr: DefaultClassColors.miB,
-    BB20_Lwr: DefaultClassColors.miB,
-    IC01_Upr: DefaultClassColors.IC,
-    IC01_Lwr: DefaultClassColors.IC,
-    IC02_Upr: DefaultClassColors.IC,
-    IC02_Lwr: DefaultClassColors.IC,
-    IC03_Upr: DefaultClassColors.IC,
-    IC03_Lwr: DefaultClassColors.IC,
-    IC04_Upr: DefaultClassColors.IC,
-    IC04_Lwr: DefaultClassColors.IC,
-    IC05_Upr: DefaultClassColors.IC,
-    IC05_Lwr: DefaultClassColors.IC,
-    IC06_Upr: DefaultClassColors.IC,
-    IC06_Lwr: DefaultClassColors.IC,
-    IC07_Upr: DefaultClassColors.IC,
-    IC07_Lwr: DefaultClassColors.IC,
-    OP01_Upr: DefaultClassColors.OPN,
-    OP01_Lwr: DefaultClassColors.OPN,
-    OP02_Upr: DefaultClassColors.OPN,
-    OP02_Lwr: DefaultClassColors.OPN,
-    OP03_Upr: DefaultClassColors.OPN,
-    OP03_Lwr: DefaultClassColors.OPN,
-    OP04_Upr: DefaultClassColors.OPN,
-    OP04_Lwr: DefaultClassColors.OPN,
-    OP05_Upr: DefaultClassColors.OPN,
-    OP05_Lwr: DefaultClassColors.OPN,
-    OP06_Upr: DefaultClassColors.OPN,
-    OP06_Lwr: DefaultClassColors.OPN,
-    OP07_Upr: DefaultClassColors.OPN,
-    OP07_Lwr: DefaultClassColors.OPN,
-    OP08_Upr: DefaultClassColors.OPN,
-    OP08_Lwr: DefaultClassColors.OPN,
-    OP09_Upr: DefaultClassColors.OPN,
-    OP09_Lwr: DefaultClassColors.OPN,
-    OP10_Upr: DefaultClassColors.OPN,
-    OP10_Lwr: DefaultClassColors.OPN,
-    OP11_Upr: DefaultClassColors.OPN,
-    OP11_Lwr: DefaultClassColors.OPN,
-    OP12_Upr: DefaultClassColors.OPN,
-    OP12_Lwr: DefaultClassColors.OPN,
-    OP13_Upr: DefaultClassColors.OPN,
-    OP13_Lwr: DefaultClassColors.OPN,
-    OP14_Upr: DefaultClassColors.OPN,
-    OP14_Lwr: DefaultClassColors.OPN,
-    OP15_Upr: DefaultClassColors.OPN,
-    OP15_Lwr: DefaultClassColors.OPN,
-    OP16_Upr: DefaultClassColors.OPN,
-    OP16_Lwr: DefaultClassColors.OPN,
-    OP17_Upr: DefaultClassColors.OPN,
-    OP17_Lwr: DefaultClassColors.OPN,
-    OP18_Upr: DefaultClassColors.OPN,
-    OP18_Lwr: DefaultClassColors.OPN,
-    OP19_Upr: DefaultClassColors.OPN,
-    OP19_Lwr: DefaultClassColors.OPN,
-    OP20_Upr: DefaultClassColors.OPN,
-    OP20_Lwr: DefaultClassColors.OPN,
-    OP21_Upr: DefaultClassColors.OPN,
-    OP21_Lwr: DefaultClassColors.OPN,
-    OP22_Upr: DefaultClassColors.OPN,
-    OP22_Lwr: DefaultClassColors.OPN,
-    OP23_Upr: DefaultClassColors.OPN,
-    OP23_Lwr: DefaultClassColors.OPN,
-    OP24_Upr: DefaultClassColors.OPN,
-    OP24_Lwr: DefaultClassColors.OPN,
-    OP25_Upr: DefaultClassColors.OPN,
-    OP25_Lwr: DefaultClassColors.OPN,
-    OP26_Upr: DefaultClassColors.OPN,
-    OP26_Lwr: DefaultClassColors.OPN,
-    OP27_Upr: DefaultClassColors.OPN,
-    OP27_Lwr: DefaultClassColors.OPN,
-    OP28_Upr: DefaultClassColors.OPN,
-    OP28_Lwr: DefaultClassColors.OPN,
-    OP29_Upr: DefaultClassColors.OPN,
-    OP29_Lwr: DefaultClassColors.OPN,
-    OP30_Upr: DefaultClassColors.OPN,
-    OP30_Lwr: DefaultClassColors.OPN,
-    OP31_Upr: DefaultClassColors.OPN,
-    OP31_Lwr: DefaultClassColors.OPN,
-    OPS1_Upr: DefaultClassColors.OPN,
-    OPS1_Lwr: DefaultClassColors.OPN,
-    OP1S_Upr: DefaultClassColors.OPN,
-    OP1S_Lwr: DefaultClassColors.SYN,
-    AAS1_Upr: DefaultClassColors.SYN,
-    AAS1_Lwr: DefaultClassColors.A,
-    AB1S_Upr: DefaultClassColors.A,
-    AB1S_Lwr: DefaultClassColors.SYN,
-    AB2S_Upr: DefaultClassColors.A,
-    AB2S_Lwr: DefaultClassColors.SYN,
-    BB1S_Upr: DefaultClassColors.B,
-    BB1S_Lwr: DefaultClassColors.SYN,
-    BB2S_Upr: DefaultClassColors.B,
-    BB2S_Lwr: DefaultClassColors.SYN,
-    BBS1_Upr: DefaultClassColors.SYN,
-    BBS1_Lwr: DefaultClassColors.B,
-    ZZ01_Upr: DefaultClassColors.Z,
-    ZZ01_Lwr: DefaultClassColors.Z,
-    ZZ02_Upr: DefaultClassColors.Z,
-    ZZ02_Lwr: DefaultClassColors.Z,
-    ZZ1S_Upr: DefaultClassColors.Z,
-    ZZ1S_Lwr: DefaultClassColors.SYN,
-    ZZ2S_Upr: DefaultClassColors.Z,
-    ZZ2S_Lwr: DefaultClassColors.SYN,
-    ZZS1_Upr: DefaultClassColors.SYN,
-    ZZS1_Lwr: DefaultClassColors.Z,
-    ZZS2_Upr: DefaultClassColors.SYN,
-    ZZS2_Lwr: DefaultClassColors.Z,
-});
+const PyramidsColors = ColorMap({ ...NtCColors });
 type PyramidsColors = typeof PyramidsColors;
 
 export const ConfalPyramidsColorThemeParams = {
@@ -272,7 +66,7 @@ export const ConfalPyramidsColorThemeProvider: ColorTheme.Provider<ConfalPyramid
     factory: ConfalPyramidsColorTheme,
     getParams: getConfalPyramidsColorThemeParams,
     defaultValues: PD.getDefaultValues(ConfalPyramidsColorThemeParams),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => ConfalPyramids.isApplicable(m)),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => Dnatco.isApplicable(m)),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ConfalPyramidsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
         detach: (data) => data.structure && ConfalPyramidsProvider.ref(data.structure.models[0], false)

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

@@ -5,90 +5,18 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
-import { ConfalPyramidsTypes as CPT } from './types';
-import { Column, Table } from '../../../mol-data/db';
-import { toTable } from '../../../mol-io/reader/cif/schema';
+import { Dnatco, DnatcoParams, DnatcoSteps } from '../property';
 import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { Model } from '../../../mol-model/structure';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
-import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 
-export type ConfalPyramids = PropertyWrapper<CPT.Steps | undefined>;
-
-export namespace ConfalPyramids {
-    export const Schema = {
-        ndb_struct_ntc_step: {
-            id: Column.Schema.int,
-            name: Column.Schema.str,
-            PDB_model_number: Column.Schema.int,
-            label_entity_id_1: Column.Schema.int,
-            label_asym_id_1: Column.Schema.str,
-            label_seq_id_1: Column.Schema.int,
-            label_comp_id_1: Column.Schema.str,
-            label_alt_id_1: Column.Schema.str,
-            label_entity_id_2: Column.Schema.int,
-            label_asym_id_2: Column.Schema.str,
-            label_seq_id_2: Column.Schema.int,
-            label_comp_id_2: Column.Schema.str,
-            label_alt_id_2: Column.Schema.str,
-            auth_asym_id_1: Column.Schema.str,
-            auth_seq_id_1: Column.Schema.int,
-            auth_asym_id_2: Column.Schema.str,
-            auth_seq_id_2: Column.Schema.int,
-            PDB_ins_code_1: Column.Schema.str,
-            PDB_ins_code_2: Column.Schema.str,
-        },
-        ndb_struct_ntc_step_summary: {
-            step_id: Column.Schema.int,
-            assigned_CANA: Column.Schema.str,
-            assigned_NtC: Column.Schema.str,
-            confal_score: Column.Schema.int,
-            euclidean_distance_NtC_ideal: Column.Schema.float,
-            cartesian_rmsd_closest_NtC_representative: Column.Schema.float,
-            closest_CANA: Column.Schema.str,
-            closest_NtC: Column.Schema.str,
-            closest_step_golden: Column.Schema.str
-        }
-    };
-    export type Schema = typeof Schema;
-
-    export async function fromCif(ctx: CustomProperty.Context, model: Model, props: ConfalPyramidsProps): Promise<CustomProperty.Data<ConfalPyramids>> {
-        const info = PropertyWrapper.createInfo();
-        const data = getCifData(model);
-        if (data === undefined) return { value: { info, data: undefined } };
-
-        const fromCif = createPyramidsFromCif(model, data.steps, data.stepsSummary);
-        return { value: { info, data: fromCif } };
-    }
-
-    function getCifData(model: Model) {
-        if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF');
-        if (!hasNdbStructNtcCategories(model)) return undefined;
-        return {
-            steps: toTable(Schema.ndb_struct_ntc_step, model.sourceData.data.frame.categories.ndb_struct_ntc_step),
-            stepsSummary: toTable(Schema.ndb_struct_ntc_step_summary, model.sourceData.data.frame.categories.ndb_struct_ntc_step_summary)
-        };
-    }
-
-    function hasNdbStructNtcCategories(model: Model): boolean {
-        if (!MmcifFormat.is(model.sourceData)) return false;
-        const names = (model.sourceData).data.frame.categoryNames;
-        return names.includes('ndb_struct_ntc_step') && names.includes('ndb_struct_ntc_step_summary');
-    }
-
-    export function isApplicable(model?: Model): boolean {
-        return !!model && hasNdbStructNtcCategories(model);
-    }
-}
-
-export const ConfalPyramidsParams = {};
+export const ConfalPyramidsParams = { ...DnatcoParams };
 export type ConfalPyramidsParams = typeof ConfalPyramidsParams;
 export type ConfalPyramidsProps = PD.Values<ConfalPyramidsParams>;
 
-export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramidsParams, ConfalPyramids> = CustomModelProperty.createProvider({
+export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramidsParams, DnatcoSteps> = CustomModelProperty.createProvider({
     label: 'Confal Pyramids',
     descriptor: CustomPropertyDescriptor({
         name: 'confal_pyramids',
@@ -96,94 +24,9 @@ export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramids
     type: 'static',
     defaultParams: ConfalPyramidsParams,
     getParams: (data: Model) => ConfalPyramidsParams,
-    isApplicable: (data: Model) => ConfalPyramids.isApplicable(data),
+    isApplicable: (data: Model) => Dnatco.isApplicable(data),
     obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<ConfalPyramidsProps>) => {
         const p = { ...PD.getDefaultValues(ConfalPyramidsParams), ...props };
-        return ConfalPyramids.fromCif(ctx, data, p);
+        return Dnatco.fromCif(ctx, data, p);
     }
 });
-
-type StepsSummaryTable = Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step_summary>;
-
-function createPyramidsFromCif(
-    model: Model,
-    cifSteps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
-    stepsSummary: StepsSummaryTable
-): CPT.Steps {
-    const steps = new Array<CPT.Step>();
-    const mapping = new Array<CPT.MappedChains>();
-
-    const {
-        id, PDB_model_number, name,
-        auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
-        auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
-        _rowCount
-    } = cifSteps;
-
-    if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
-
-    for (let i = 0; i < _rowCount; i++) {
-        const {
-            NtC,
-            confal_score,
-            rmsd
-        } = getSummaryData(id.value(i), i, stepsSummary);
-        const modelNum = PDB_model_number.value(i);
-        const chainId = auth_asym_id_1.value(i);
-        const seqId = auth_seq_id_1.value(i);
-        const modelIdx = modelNum - 1;
-
-        if (mapping.length <= modelIdx || !mapping[modelIdx])
-            mapping[modelIdx] = new Map<string, CPT.MappedResidues>();
-
-        const step = {
-            PDB_model_number: modelNum,
-            name: name.value(i),
-            auth_asym_id_1: chainId,
-            auth_seq_id_1: seqId,
-            label_comp_id_1: label_comp_id_1.value(i),
-            label_alt_id_1: label_alt_id_1.value(i),
-            PDB_ins_code_1: PDB_ins_code_1.value(i),
-            auth_asym_id_2: auth_asym_id_2.value(i),
-            auth_seq_id_2: auth_seq_id_2.value(i),
-            label_comp_id_2: label_comp_id_2.value(i),
-            label_alt_id_2: label_alt_id_2.value(i),
-            PDB_ins_code_2: PDB_ins_code_2.value(i),
-            confal_score,
-            NtC,
-            rmsd,
-        };
-
-        steps.push(step);
-
-        const mappedChains = mapping[modelIdx];
-        const residuesOnChain = mappedChains.get(chainId) ?? new Map<number, number[]>();
-        const stepsForResidue = residuesOnChain.get(seqId) ?? [];
-        stepsForResidue.push(steps.length - 1);
-
-        residuesOnChain.set(seqId, stepsForResidue);
-        mappedChains.set(chainId, residuesOnChain);
-        mapping[modelIdx] = mappedChains;
-    }
-
-    return { steps, mapping };
-}
-
-function getSummaryData(id: number, i: number, stepsSummary: StepsSummaryTable) {
-    const {
-        step_id,
-        confal_score,
-        assigned_NtC,
-        cartesian_rmsd_closest_NtC_representative,
-    } = stepsSummary;
-
-    // Assume that step_ids in ntc_step_summary are in the same order as steps in ntc_step
-    for (let j = i; j < stepsSummary._rowCount; j++) {
-        if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
-    }
-    // Safety net for cases where the previous assumption is not met
-    for (let j = 0; j < i; j++) {
-        if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
-    }
-    throw new Error('Inconsistent mmCIF data');
-}

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

@@ -5,9 +5,10 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
-import { ConfalPyramids, ConfalPyramidsProvider } from './property';
+import { ConfalPyramidsProvider } from './property';
 import { ConfalPyramidsIterator } from './util';
 import { ConfalPyramidsTypes as CPT } from './types';
+import { Dnatco } from '../property';
 import { Interval } from '../../../mol-data/int';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
@@ -87,6 +88,8 @@ function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Str
     const it = new ConfalPyramidsIterator(structure, unit);
     while (it.hasNext) {
         const allPoints = it.move();
+        if (!allPoints)
+            continue;
 
         for (const points of allPoints) {
             const { O3, P, OP1, OP2, O5, confalScore } = points;
@@ -150,9 +153,7 @@ function getConfalPyramidLoci(pickingId: PickingId, structureGroup: StructureGro
     if (halfPyramidsCount <= groupId) return EmptyLoci;
 
     const idx = Math.floor(groupId / 2); // Map groupIndex to a step, see createConfalPyramidsMesh() for full explanation
-    const step = data.steps[idx];
-
-    return CPT.Loci({ step, isLower: groupId % 2 === 1 }, [{}]);
+    return CPT.Loci(data.steps, [idx]);
 }
 
 function eachConfalPyramid(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
@@ -197,7 +198,7 @@ export const ConfalPyramidsRepresentationProvider = StructureRepresentationProvi
     defaultValues: PD.getDefaultValues(ConfalPyramidsParams),
     defaultColorTheme: { name: 'confal-pyramids' },
     defaultSizeTheme: { name: 'uniform' },
-    isApplicable: (structure: Structure) => structure.models.some(m => ConfalPyramids.isApplicable(m)),
+    isApplicable: (structure: Structure) => structure.models.some(m => Dnatco.isApplicable(m)),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, structure: Structure) => ConfalPyramidsProvider.attach(ctx, structure.model, void 0, true),
         detach: (data) => ConfalPyramidsProvider.ref(data.model, false),

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

@@ -5,61 +5,29 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
+import { DnatcoTypes } from '../types';
 import { DataLocation } from '../../../mol-model/location';
 import { DataLoci } from '../../../mol-model/loci';
 import { confalPyramidLabel } from './behavior';
 
 export namespace ConfalPyramidsTypes {
-    export const DataTag = 'dnatco-confal-half-pyramid';
+    export interface Location extends DataLocation<DnatcoTypes.HalfStep, {}> {}
 
-    export type Step = {
-        PDB_model_number: number,
-        name: string,
-        auth_asym_id_1: string,
-        auth_seq_id_1: number,
-        label_comp_id_1: string,
-        label_alt_id_1: string,
-        PDB_ins_code_1: string,
-        auth_asym_id_2: string,
-        auth_seq_id_2: number,
-        label_comp_id_2: string,
-        label_alt_id_2: string,
-        PDB_ins_code_2: string,
-        confal_score: number,
-        NtC: string,
-        rmsd: number,
-    }
-
-    export type MappedChains = Map<string, MappedResidues>;
-    export type MappedResidues = Map<number, number[]>;
-
-    export interface Steps {
-        steps: Array<Step>,
-        mapping: MappedChains[],
-    }
-
-    export interface HalfPyramid {
-        step: Step,
-        isLower: boolean,
-    }
-
-    export interface Location extends DataLocation<HalfPyramid, {}> {}
-
-    export function Location(step: Step, isLower: boolean) {
-        return DataLocation(DataTag, { step, isLower }, {});
+    export function Location(step: DnatcoTypes.Step, isLower: boolean) {
+        return DataLocation(DnatcoTypes.DataTag, { step, isLower }, {});
     }
 
     export function isLocation(x: any): x is Location {
-        return !!x && x.kind === 'data-location' && x.tag === DataTag;
+        return !!x && x.kind === 'data-location' && x.tag === DnatcoTypes.DataTag;
     }
 
-    export interface Loci extends DataLoci<HalfPyramid, {}> {}
+    export interface Loci extends DataLoci<DnatcoTypes.Step[], number> {}
 
-    export function Loci(data: HalfPyramid, elements: ReadonlyArray<{}>): Loci {
-        return DataLoci(DataTag, data, elements, undefined, () => confalPyramidLabel(data));
+    export function Loci(data: DnatcoTypes.Step[], elements: ReadonlyArray<number>): Loci {
+        return DataLoci(DnatcoTypes.DataTag, data, elements, undefined, () => elements[0] !== undefined ? confalPyramidLabel(data[elements[0]]) : '');
     }
 
     export function isLoci(x: any): x is Loci {
-        return !!x && x.kind === 'data-loci' && x.tag === DataTag;
+        return !!x && x.kind === 'data-loci' && x.tag === DnatcoTypes.DataTag;
     }
 }

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

@@ -1,16 +1,15 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Michal Malý <michal.maly@ibt.cas.cz>
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
 import { ConfalPyramidsProvider } from './property';
-import { ConfalPyramidsTypes as CPT } from './types';
+import { DnatcoTypes } from '../types';
+import { DnatcoUtil } from '../util';
 import { Segmentation } from '../../../mol-data/int';
-import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../../mol-model/structure';
-
-type Residue = Segmentation.Segment<ResidueIndex>;
+import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
 
 export type Pyramid = {
     O3: ElementIndex,
@@ -22,31 +21,17 @@ export type Pyramid = {
     stepIdx: number,
 };
 
-const EmptyStepIndices = new Array<number>();
-
-function copyResidue(r?: Residue) {
-    return r ? { index: r.index, start: r.start, end: r.end } : void 0;
-}
-
-function getAtomIndex(loc: StructureElement.Location, residue: Residue, names: string[], altId: string): ElementIndex {
-    for (let eI = residue.start; eI < residue.end; eI++) {
-        loc.element = loc.unit.elements[eI];
-        const elName = StructureProperties.atom.label_atom_id(loc);
-        const elAltId = StructureProperties.atom.label_alt_id(loc);
-
-        if (names.includes(elName) && (elAltId === altId || elAltId.length === 0))
-            return loc.element;
-    }
-
-    return -1 as ElementIndex;
-}
-
-function getPyramid(loc: StructureElement.Location, one: Residue, two: Residue, altIdOne: string, altIdTwo: string, confalScore: number, stepIdx: number): Pyramid {
-    const O3 = getAtomIndex(loc, one, ['O3\'', 'O3*'], altIdOne);
-    const P = getAtomIndex(loc, two, ['P'], altIdTwo);
-    const OP1 = getAtomIndex(loc, two, ['OP1'], altIdTwo);
-    const OP2 = getAtomIndex(loc, two, ['OP2'], altIdTwo);
-    const O5 = getAtomIndex(loc, two, ['O5\'', 'O5*'], altIdTwo);
+function getPyramid(
+    loc: StructureElement.Location,
+    one: DnatcoUtil.Residue, two: DnatcoUtil.Residue,
+    altIdOne: string, altIdTwo: string,
+    insCodeOne: string, insCodeTwo: string,
+    confalScore: number, stepIdx: number): Pyramid {
+    const O3 = DnatcoUtil.getAtomIndex(loc, one, ['O3\'', 'O3*'], altIdOne, insCodeOne);
+    const P = DnatcoUtil.getAtomIndex(loc, two, ['P'], altIdTwo, insCodeTwo);
+    const OP1 = DnatcoUtil.getAtomIndex(loc, two, ['OP1'], altIdTwo, insCodeTwo);
+    const OP2 = DnatcoUtil.getAtomIndex(loc, two, ['OP2'], altIdTwo, insCodeTwo);
+    const O5 = DnatcoUtil.getAtomIndex(loc, two, ['O5\'', 'O5*'], altIdTwo, insCodeTwo);
 
     return { O3, P, OP1, OP2, O5, confalScore, stepIdx };
 }
@@ -54,39 +39,29 @@ function getPyramid(loc: StructureElement.Location, one: Residue, two: Residue,
 export class ConfalPyramidsIterator {
     private chainIt: Segmentation.SegmentIterator<ChainIndex>;
     private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
-    private residueOne?: Residue;
-    private residueTwo: Residue;
-    private data?: CPT.Steps;
+    private residueOne?: DnatcoUtil.Residue;
+    private residueTwo: DnatcoUtil.Residue;
+    private data?: DnatcoTypes.Steps;
     private loc: StructureElement.Location;
 
-    private getStepIndices(r: Residue) {
-        this.loc.element = this.loc.unit.elements[r.start];
-
-        const modelIdx = StructureProperties.unit.model_num(this.loc) - 1;
-        const chainId = StructureProperties.chain.auth_asym_id(this.loc);
-        const seqId = StructureProperties.residue.auth_seq_id(this.loc);
-
-        const chains = this.data!.mapping[modelIdx];
-        if (!chains) return EmptyStepIndices;
-        const residues = chains.get(chainId);
-        if (!residues) return EmptyStepIndices;
-        return residues.get(seqId) ?? EmptyStepIndices;
-    }
-
     private moveStep() {
-        this.residueOne = copyResidue(this.residueTwo);
-        this.residueTwo = copyResidue(this.residueIt.move())!;
+        this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
+        this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+
+        // Check for discontinuity
+        if (this.residueTwo.index !== (this.residueOne!.index + 1))
+            return void 0;
 
         return this.toPyramids(this.residueOne!, this.residueTwo);
     }
 
-    private toPyramids(one: Residue, two: Residue) {
-        const indices = this.getStepIndices(one);
+    private toPyramids(one: DnatcoUtil.Residue, two: DnatcoUtil.Residue) {
+        const indices = DnatcoUtil.getStepIndices(this.data!, this.loc, one);
 
         const points = [];
         for (const idx of indices) {
             const step = this.data!.steps[idx];
-            points.push(getPyramid(this.loc, one, two, step.label_alt_id_1, step.label_alt_id_2, step.confal_score, idx));
+            points.push(getPyramid(this.loc, one, two, step.label_alt_id_1, step.label_alt_id_2, step.PDB_ins_code_1, step.PDB_ins_code_2, step.confal_score, idx));
         }
 
         return points;
@@ -121,6 +96,8 @@ export class ConfalPyramidsIterator {
             return this.moveStep();
         } else {
             this.residueIt.setSegment(this.chainIt.move());
+            if (this.residueIt.hasNext)
+                this.residueTwo = this.residueIt.move();
             return this.moveStep();
         }
     }

src/extensions/dnatco/index.ts

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Michal Malý <michal.maly@ibt.cas.cz>
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
-export { DnatcoConfalPyramids } from './confal-pyramids/behavior';
+export { DnatcoNtCs } from './behavior';

src/extensions/dnatco/ntc-tube/behavior.ts

@@ -0,0 +1,57 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { NtCTubeColorThemeProvider } from './color';
+import { NtCTubeProvider } from './property';
+import { NtCTubeRepresentationProvider } from './representation';
+import { DnatcoTypes } from '../types';
+import { Dnatco } from '../property';
+import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
+import { StateObjectRef } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+
+export const NtCTubePreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-ntc-tube',
+    display: {
+        name: 'NtC Tube', group: 'Annotation',
+        description: 'NtC Tube',
+    },
+    isApplicable(a) {
+        return a.data.models.length >= 1 && a.data.models.some(m => Dnatco.isApplicable(m));
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const model = structureCell?.obj?.data.model;
+        if (!structureCell || !model) return {};
+
+        await plugin.runTask(Task.create('NtC tube', async runtime => {
+            await NtCTubeProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+        }));
+
+        const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);
+
+        const tube = await plugin.builders.structure.tryCreateComponentStatic(structureCell, 'nucleic', { label: 'NtC Tube' });
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+
+        let tubeRepr;
+        if (representations)
+            tubeRepr = builder.buildRepresentation(update, tube, { type: NtCTubeRepresentationProvider, typeParams, color: NtCTubeColorThemeProvider }, { tag: 'ntc-tube' });
+
+        await update.commit({ revertOnError: true });
+        return { components: { ...components, tube }, representations: { ...representations, tubeRepr } };
+    }
+});
+
+export function NtCTubeSegmentLabel(step: DnatcoTypes.Step) {
+    return `
+        <b>${step.auth_asym_id_1}</b> |
+        <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
+           ${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
+        <i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
+    `;
+}

src/extensions/dnatco/ntc-tube/color.ts

@@ -0,0 +1,90 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { ErrorColor, NtCColors } from '../color';
+import { NtCTubeProvider } from './property';
+import { NtCTubeTypes as NTT } from './types';
+import { Dnatco } from '../property';
+import { Location } from '../../../mol-model/location';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { ColorTheme } from '../../../mol-theme/color';
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { Color, ColorMap } from '../../../mol-util/color';
+import { getColorMapParams } from '../../../mol-util/color/params';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { TableLegend } from '../../../mol-util/legend';
+import { ObjectKeys } from '../../../mol-util/type-helpers';
+
+const Description = 'Assigns colors to NtC Tube segments';
+
+const NtCTubeColors = ColorMap({
+    ...NtCColors,
+    residueMarker: Color(0x222222),
+    stepBoundaryMarker: Color(0x656565),
+});
+type NtCTubeColors = typeof NtCTubeColors;
+
+export const NtCTubeColorThemeParams = {
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(NtCTubeColors))
+    }),
+    markResidueBoundaries: PD.Boolean(true),
+    markSegmentBoundaries: PD.Boolean(true),
+};
+export type NtCTubeColorThemeParams = typeof NtCTubeColorThemeParams;
+
+export function getNtCTubeColorThemeParams(ctx: ThemeDataContext) {
+    return PD.clone(NtCTubeColorThemeParams);
+}
+
+export function NtCTubeColorTheme(ctx: ThemeDataContext, props: PD.Values<NtCTubeColorThemeParams>): ColorTheme<NtCTubeColorThemeParams> {
+    const colorMap = props.colors.name === 'default' ? NtCTubeColors : props.colors.params;
+
+    function color(location: Location, isSecondary: boolean): Color {
+        if (NTT.isLocation(location)) {
+            const { data } = location;
+            const { step, kind } = data;
+            let key;
+            if (kind === 'upper')
+                key = step.NtC + '_Upr' as keyof NtCTubeColors;
+            else if (kind === 'lower')
+                key = step.NtC + '_Lwr' as keyof NtCTubeColors;
+            else if (kind === 'residue-boundary')
+                key = (!props.markResidueBoundaries ? step.NtC + '_Lwr' : 'residueMarker') as keyof NtCTubeColors;
+            else /* segment-boundary */
+                key = (!props.markSegmentBoundaries ? step.NtC + '_Lwr' : 'stepBoundaryMarker') as keyof NtCTubeColors;
+
+            return colorMap[key] ?? ErrorColor;
+        }
+
+        return ErrorColor;
+    }
+
+    return {
+        factory: NtCTubeColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        description: Description,
+        legend: TableLegend(ObjectKeys(colorMap).map(k => [k.replace('_', ' '), colorMap[k]] as [string, Color]).concat([['Error', ErrorColor]])),
+    };
+}
+
+export const NtCTubeColorThemeProvider: ColorTheme.Provider<NtCTubeColorThemeParams, 'ntc-tube'> = {
+    name: 'ntc-tube',
+    label: 'NtC Tube',
+    category: ColorTheme.Category.Residue,
+    factory: NtCTubeColorTheme,
+    getParams: getNtCTubeColorThemeParams,
+    defaultValues: PD.getDefaultValues(NtCTubeColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => Dnatco.isApplicable(m)),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? NtCTubeProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && NtCTubeProvider.ref(data.structure.models[0], false)
+    }
+};

src/extensions/dnatco/ntc-tube/property.ts

@@ -0,0 +1,44 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { NtCTubeTypes as NTT } from './types';
+import { Dnatco, DnatcoParams } from '../property';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+import { Model } from '../../../mol-model/structure';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+export const NtCTubeParams = { ...DnatcoParams };
+export type NtCTubeParams = typeof NtCTubeParams;
+export type NtCTubeProps = PD.Values<NtCTubeParams>;
+export type NtCTubeData = PropertyWrapper<NTT.Data | undefined>;
+
+async function fromCif(ctx: CustomProperty.Context, model: Model, props: NtCTubeProps): Promise<CustomProperty.Data<NtCTubeData>> {
+    const info = PropertyWrapper.createInfo();
+    const data = Dnatco.getCifData(model);
+    if (data === undefined) return { value: { info, data: undefined } };
+
+    const steps = Dnatco.getStepsFromCif(model, data.steps, data.stepsSummary);
+    return { value: { info, data: { data: steps } } };
+}
+
+export const NtCTubeProvider: CustomModelProperty.Provider<NtCTubeParams, NtCTubeData> = CustomModelProperty.createProvider({
+    label: 'NtC Tube',
+    descriptor: CustomPropertyDescriptor({
+        name: 'ntc-tube',
+    }),
+    type: 'static',
+    defaultParams: NtCTubeParams,
+    getParams: (data: Model) => NtCTubeParams,
+    isApplicable: (data: Model) => Dnatco.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<NtCTubeProps>) => {
+        const p = { ...PD.getDefaultValues(NtCTubeParams), ...props };
+        return fromCif(ctx, data, p);
+    }
+});

src/extensions/dnatco/ntc-tube/representation.ts

@@ -0,0 +1,454 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { NtCTubeProvider } from './property';
+import { NtCTubeSegmentsIterator } from './util';
+import { NtCTubeTypes as NTT } from './types';
+import { Dnatco } from '../property';
+import { DnatcoTypes } from '../types';
+import { DnatcoUtil } from '../util';
+import { Interval } from '../../../mol-data/int';
+import { BaseGeometry, VisualQuality } from '../../../mol-geo/geometry/base';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { addFixedCountDashedCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
+import { PickingId } from '../../../mol-geo/geometry/picking';
+import { CylinderProps } from '../../../mol-geo/primitive/cylinder';
+import { LocationIterator } from '../../../mol-geo/util/location-iterator';
+import { Sphere3D } from '../../../mol-math/geometry/primitives/sphere3d';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { smoothstep } from '../../../mol-math/interpolate';
+import { NullLocation } from '../../../mol-model/location';
+import { EmptyLoci, Loci } from '../../../mol-model/loci';
+import { Structure, StructureElement, Unit } from '../../../mol-model/structure';
+import { structureUnion } from '../../../mol-model/structure/query/utils/structure-set';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
+import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder, UnitsRepresentation } from '../../../mol-repr/structure/representation';
+import { UnitsMeshParams, UnitsMeshVisual, UnitsVisual } from '../../../mol-repr/structure/units-visual';
+import { createCurveSegmentState, CurveSegmentState } from '../../../mol-repr/structure/visual/util/polymer';
+import { getStructureQuality, VisualUpdateState } from '../../../mol-repr/util';
+import { VisualContext } from '../../../mol-repr/visual';
+import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
+import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+const v3add = Vec3.add;
+const v3copy = Vec3.copy;
+const v3cross = Vec3.cross;
+const v3fromArray = Vec3.fromArray;
+const v3matchDirection = Vec3.matchDirection;
+const v3normalize = Vec3.normalize;
+const v3orthogonalize = Vec3.orthogonalize;
+const v3scale = Vec3.scale;
+const v3slerp = Vec3.slerp;
+const v3spline = Vec3.spline;
+const v3sub = Vec3.sub;
+const v3toArray = Vec3.toArray;
+
+const NtCTubeMeshParams = {
+    ...UnitsMeshParams,
+    linearSegments: PD.Numeric(4, { min: 2, max: 8, step: 1 }, BaseGeometry.CustomQualityParamInfo),
+    radialSegments: PD.Numeric(22, { min: 4, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
+    residueMarkerWidth: PD.Numeric(0.05, { min: 0.01, max: 0.25, step: 0.01 }),
+    segmentBoundaryWidth: PD.Numeric(0.05, { min: 0.01, max: 0.25, step: 0.01 }),
+};
+type NtCTubeMeshParams = typeof NtCTubeMeshParams;
+
+type QualityOptions = Exclude<VisualQuality, 'auto' | 'custom'>;
+const LinearSegmentCount: Record<QualityOptions, number> = {
+    highest: 6,
+    higher: 6,
+    high: 4,
+    medium: 4,
+    low: 3,
+    lower: 3,
+    lowest: 2,
+};
+const RadialSegmentCount: Record<QualityOptions, number> = {
+    highest: 32,
+    higher: 26,
+    high: 22,
+    medium: 18,
+    low: 14,
+    lower: 10,
+    lowest: 6,
+};
+
+const _curvePoint = Vec3();
+const _tanA = Vec3();
+const _tanB = Vec3();
+const _firstTangentVec = Vec3();
+const _lastTangentVec = Vec3();
+const _firstNormalVec = Vec3();
+const _lastNormalVec = Vec3();
+
+const _tmpNormal = Vec3();
+const _tangentVec = Vec3();
+const _normalVec = Vec3();
+const _binormalVec = Vec3();
+const _prevNormal = Vec3();
+const _nextNormal = Vec3();
+
+function interpolatePointsAndTangents(state: CurveSegmentState, p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, tRange: number[]) {
+    const { curvePoints, tangentVectors, linearSegments } = state;
+    const tension = 0.5;
+    const r = tRange[1] - tRange[0];
+
+    for (let j = 0; j <= linearSegments; ++j) {
+        const t = j * r / linearSegments + tRange[0];
+
+        v3spline(_curvePoint, p0, p1, p2, p3, t, tension);
+        v3spline(_tanA, p0, p1, p2, p3, t - 0.01, tension);
+        v3spline(_tanB, p0, p1, p2, p3, t + 0.01, tension);
+
+        v3toArray(_curvePoint, curvePoints, j * 3);
+        v3normalize(_tangentVec, v3sub(_tangentVec, _tanA, _tanB));
+        v3toArray(_tangentVec, tangentVectors, j * 3);
+    }
+}
+
+function interpolateNormals(state: CurveSegmentState, firstDirection: Vec3, lastDirection: Vec3) {
+    const { curvePoints, tangentVectors, normalVectors, binormalVectors } = state;
+
+    const n = curvePoints.length / 3;
+
+    v3fromArray(_firstTangentVec, tangentVectors, 0);
+    v3fromArray(_lastTangentVec, tangentVectors, (n - 1) * 3);
+
+    v3orthogonalize(_firstNormalVec, _firstTangentVec, firstDirection);
+    v3orthogonalize(_lastNormalVec, _lastTangentVec, lastDirection);
+    v3matchDirection(_lastNormalVec, _lastNormalVec, _firstNormalVec);
+
+    v3copy(_prevNormal, _firstNormalVec);
+
+    const n1 = n - 1;
+    for (let i = 0; i < n; ++i) {
+        const j = smoothstep(0, n1, i) * n1;
+        const t = i === 0 ? 0 : 1 / (n - j);
+
+        v3fromArray(_tangentVec, tangentVectors, i * 3);
+
+        v3orthogonalize(_normalVec, _tangentVec, v3slerp(_tmpNormal, _prevNormal, _lastNormalVec, t));
+        v3toArray(_normalVec, normalVectors, i * 3);
+
+        v3copy(_prevNormal, _normalVec);
+
+        v3normalize(_binormalVec, v3cross(_binormalVec, _tangentVec, _normalVec));
+        v3toArray(_binormalVec, binormalVectors, i * 3);
+    }
+
+    for (let i = 1; i < n1; ++i) {
+        v3fromArray(_prevNormal, normalVectors, (i - 1) * 3);
+        v3fromArray(_normalVec, normalVectors, i * 3);
+        v3fromArray(_nextNormal, normalVectors, (i + 1) * 3);
+
+        v3scale(_normalVec, v3add(_normalVec, _prevNormal, v3add(_normalVec, _nextNormal, _normalVec)), 1 / 3);
+        v3toArray(_normalVec, normalVectors, i * 3);
+
+        v3fromArray(_tangentVec, tangentVectors, i * 3);
+        v3normalize(_binormalVec, v3cross(_binormalVec, _tangentVec, _normalVec));
+        v3toArray(_binormalVec, binormalVectors, i * 3);
+    }
+}
+
+function interpolate(state: CurveSegmentState, p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, firstDir: Vec3, lastDir: Vec3, tRange = [0, 1]) {
+    interpolatePointsAndTangents(state, p0, p1, p2, p3, tRange);
+    interpolateNormals(state, firstDir, lastDir);
+}
+
+function createNtCTubeSegmentsIterator(structureGroup: StructureGroup): LocationIterator {
+    const { structure, group } = structureGroup;
+    const instanceCount = group.units.length;
+
+    const data = NtCTubeProvider.get(structure.model)?.value?.data;
+    if (!data) return LocationIterator(0, 1, 1, () => NullLocation);
+
+    const numBlocks = data.data.steps.length * 4;
+
+    const getLocation = (groupId: number, instanceId: number) => {
+        if (groupId > numBlocks) return NullLocation;
+        const stepIdx = Math.floor(groupId / 4);
+        const step = data.data.steps[stepIdx];
+        const r = groupId % 4;
+        const kind =
+            r === 0 ? 'upper' :
+                r === 1 ? 'lower' :
+                    r === 2 ? 'residue-boundary' : 'segment-boundary';
+
+        return NTT.Location({ step, kind });
+    };
+    return LocationIterator(totalMeshGroupsCount(data.data.steps) + 1, instanceCount, 1, getLocation);
+}
+
+function segmentCount(structure: Structure, props: PD.Values<NtCTubeMeshParams>): { linear: number, radial: number } {
+    const quality = props.quality;
+
+    if (quality === 'custom')
+        return { linear: props.linearSegments, radial: props.radialSegments };
+    else if (quality === 'auto') {
+        const autoQuality = getStructureQuality(structure) as QualityOptions;
+        return { linear: LinearSegmentCount[autoQuality], radial: RadialSegmentCount[autoQuality] };
+    } else
+        return { linear: LinearSegmentCount[quality], radial: RadialSegmentCount[quality] };
+}
+
+function stepBoundingSphere(step: DnatcoTypes.Step, struLoci: StructureElement.Loci): Sphere3D | undefined {
+    const one = DnatcoUtil.residueToLoci(step.auth_asym_id_1, step.auth_seq_id_1, step.label_alt_id_1, step.PDB_ins_code_1, struLoci, 'auth');
+    const two = DnatcoUtil.residueToLoci(step.auth_asym_id_2, step.auth_seq_id_2, step.label_alt_id_2, step.PDB_ins_code_2, struLoci, 'auth');
+
+    if (StructureElement.Loci.is(one) && StructureElement.Loci.is(two)) {
+        const union = structureUnion(struLoci.structure, [StructureElement.Loci.toStructure(one), StructureElement.Loci.toStructure(two)]);
+        return union.boundary.sphere;
+    }
+    return void 0;
+}
+
+function totalMeshGroupsCount(steps: DnatcoTypes.Step[]) {
+    // Each segment has two blocks, Residue Boundary marker and a Segment Boundary marker
+    return steps.length * 4 - 1; // Subtract one because the last Segment Boundary marker is not drawn
+}
+
+function createNtCTubeMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<NtCTubeMeshParams>, mesh?: Mesh) {
+    if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
+
+    const prop = NtCTubeProvider.get(structure.model).value;
+    if (prop === undefined || prop.data === undefined) return Mesh.createEmpty(mesh);
+
+    const { data } = prop.data;
+    if (data.steps.length === 0) return Mesh.createEmpty(mesh);
+
+    const MarkerLinearSegmentCount = 2;
+    const segCount = segmentCount(structure, props);
+    const vertexCount = Math.floor((segCount.linear * 4 * data.steps.length / structure.model.atomicHierarchy.chains._rowCount) * segCount.radial);
+    const chunkSize = Math.floor(vertexCount / 3);
+    const diameter = 1.0 * theme.size.props.value;
+
+    const mb = MeshBuilder.createState(vertexCount, chunkSize, mesh);
+
+    const state = createCurveSegmentState(segCount.linear);
+    const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state;
+    for (let idx = 0; idx <= segCount.linear; idx++) {
+        widthValues[idx] = diameter;
+        heightValues[idx] = diameter;
+    }
+    const [normals, binormals] = [binormalVectors, normalVectors]; // Needed so that the tube is not drawn from inside out
+
+    const markerState = createCurveSegmentState(MarkerLinearSegmentCount);
+    const { curvePoints: mCurvePoints, normalVectors: mNormalVectors, binormalVectors: mBinormalVectors, widthValues: mWidthValues, heightValues: mHeightValues } = markerState;
+    for (let idx = 0; idx <= MarkerLinearSegmentCount; idx++) {
+        mWidthValues[idx] = diameter;
+        mHeightValues[idx] = diameter;
+    }
+    const [mNormals, mBinormals] = [mBinormalVectors, mNormalVectors];
+
+    const firstDir = Vec3();
+    const lastDir = Vec3();
+    const markerDir = Vec3();
+
+    const residueMarkerWidth = props.residueMarkerWidth / 2;
+    const it = new NtCTubeSegmentsIterator(structure, unit);
+    while (it.hasNext) {
+        const segment = it.move();
+        if (!segment)
+            continue;
+
+        const { p_1, p0, p1, p2, p3, p4, pP } = segment;
+        const FirstBlockId = segment.stepIdx * 4;
+        const SecondBlockId = FirstBlockId + 1;
+        const ResidueMarkerId = FirstBlockId + 2;
+        const SegmentBoundaryMarkerId = FirstBlockId + 3;
+
+        const { rmShift, rmPos } = calcResidueMarkerShift(p2, p3, pP);
+
+        if (segment.firstInChain) {
+            v3normalize(firstDir, v3sub(firstDir, p2, p1));
+            v3normalize(lastDir, v3sub(lastDir, rmPos, p2));
+        } else {
+            v3copy(firstDir, lastDir);
+            v3normalize(lastDir, v3sub(lastDir, rmPos, p2));
+        }
+
+        // C5' -> O3' block
+        interpolate(state, p0, p1, p2, p3, firstDir, lastDir);
+        mb.currentGroup = FirstBlockId;
+        addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, segment.firstInChain || segment.followsGap, false, 'rounded');
+
+        // O3' -> C5' block
+        v3copy(firstDir, lastDir);
+        v3normalize(markerDir, v3sub(markerDir, p3, rmPos));
+        v3normalize(lastDir, v3sub(lastDir, p4, p3));
+
+        // From O3' to the residue marker
+        interpolate(state, p1, p2, p3, p4, firstDir, markerDir, [0, rmShift - residueMarkerWidth]);
+        mb.currentGroup = SecondBlockId;
+        addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, false, false, 'rounded');
+
+        // Residue marker
+        interpolate(markerState, p1, p2, p3, p4, markerDir, markerDir, [rmShift - residueMarkerWidth, rmShift + residueMarkerWidth]);
+        mb.currentGroup = ResidueMarkerId;
+        addTube(mb, mCurvePoints, mNormals, mBinormals, MarkerLinearSegmentCount, segCount.radial, mWidthValues, mHeightValues, false, false, 'rounded');
+
+        if (segment.capEnd) {
+            // From the residue marker to C5' of the end
+            interpolate(state, p1, p2, p3, p4, markerDir, lastDir, [rmShift + residueMarkerWidth, 1]);
+            mb.currentGroup = SecondBlockId;
+            addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, false, true, 'rounded');
+        } else {
+            // From the residue marker to C5' of the step boundary marker
+            interpolate(state, p1, p2, p3, p4, markerDir, lastDir, [rmShift + residueMarkerWidth, 1 - props.segmentBoundaryWidth]);
+            mb.currentGroup = SecondBlockId;
+            addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, false, false, 'rounded');
+
+            // Step boundary marker
+            interpolate(markerState, p1, p2, p3, p4, lastDir, lastDir, [1 - props.segmentBoundaryWidth, 1]);
+            mb.currentGroup = SegmentBoundaryMarkerId;
+            addTube(mb, mCurvePoints, mNormals, mBinormals, MarkerLinearSegmentCount, segCount.radial, mWidthValues, mHeightValues, false, false, 'rounded');
+        }
+
+        if (segment.followsGap) {
+            const cylinderProps: CylinderProps = {
+                radiusTop: diameter / 2, radiusBottom: diameter / 2, topCap: true, bottomCap: true, radialSegments: segCount.radial,
+            };
+            mb.currentGroup = FirstBlockId;
+            addFixedCountDashedCylinder(mb, p_1, p1, 1, 2 * segCount.linear, cylinderProps);
+        }
+    }
+
+    const boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1.05);
+
+    const m = MeshBuilder.getMesh(mb);
+    m.setBoundingSphere(boundingSphere);
+    return m;
+}
+
+const _rmvCO = Vec3();
+const _rmvPO = Vec3();
+const _rmPos = Vec3();
+const _HalfPi = Math.PI / 2;
+function calcResidueMarkerShift(pO: Vec3, pC: Vec3, pP: Vec3): { rmShift: number, rmPos: Vec3 } {
+    v3sub(_rmvCO, pC, pO);
+    v3sub(_rmvPO, pP, pO);
+
+    // Project position of P atom on the O3' -> C5' vector
+    const beta = Vec3.angle(_rmvPO, _rmvCO);
+    const alpha = _HalfPi - Math.abs(beta);
+    const lengthMO = Math.cos(alpha) * Vec3.magnitude(_rmvPO);
+    const shift = lengthMO / Vec3.magnitude(_rmvCO);
+
+    v3scale(_rmvCO, _rmvCO, shift);
+    v3add(_rmPos, _rmvCO, pO);
+
+    return { rmShift: shift, rmPos: _rmPos };
+}
+
+function getNtCTubeSegmentLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number) {
+    const { groupId, objectId, instanceId } = pickingId;
+    if (objectId !== id) return EmptyLoci;
+
+    const { structure } = structureGroup;
+
+    const unit = structureGroup.group.units[instanceId];
+    if (!Unit.isAtomic(unit)) return EmptyLoci;
+
+    const data = NtCTubeProvider.get(structure.model)?.value?.data ?? undefined;
+    if (!data) return EmptyLoci;
+
+    const MeshGroupsCount = totalMeshGroupsCount(data.data.steps);
+    if (groupId > MeshGroupsCount) return EmptyLoci;
+
+    const stepIdx = Math.floor(groupId / 4);
+    const bs = stepBoundingSphere(data.data.steps[stepIdx], Structure.toStructureElementLoci(structure));
+
+    /*
+     * NOTE 1) Each step is drawn with 4 mesh groups. We need to divide/multiply by 4 to convert between steps and mesh groups.
+     * NOTE 2) Molstar will create a mesh only for the asymmetric unit. When the entire biological assembly
+     *         is displayed, Molstar just copies and transforms the mesh. This means that even though the mesh
+     *         might be displayed multiple times, groupIds of the individual blocks in the mesh will be the same.
+     *         If there are multiple copies of a mesh, Molstar needs to be able to tell which block belongs to which copy of the mesh.
+     *         To do that, Molstar adds an offset to groupIds of the copied meshes. Offset is calculated as follows:
+     *
+     *         offset = NumberOfBlocks * UnitIndex
+     *
+     *         "NumberOfBlocks" is the number of valid Location objects got from LocationIterator *or* the greatest groupId set by
+     *         the mesh generator - whichever is smaller.
+     *
+     *         UnitIndex is the index of the Unit the mesh belongs to, starting from 0. (See "unitMap" in the Structure object).
+     *         We can also get this index from the value "instanceId" of the "pickingId" object.
+     *
+     *         If this offset is not applied, picking a piece of one of the copied meshes would actually pick that piece in the original mesh.
+     *         This is particularly apparent with highlighting - hovering over items in a copied mesh incorrectly highlights those items in the source mesh.
+     *
+     *         Molstar can take advantage of the fact that ElementLoci has a reference to the Unit object attached to it. Since we cannot attach ElementLoci
+     *         to a step, we need to calculate the offseted groupId here and pass it as part of the DataLoci.
+     */
+    const offsetGroupId = stepIdx * 4 + (MeshGroupsCount + 1) * instanceId;
+    return NTT.Loci(data.data.steps, [stepIdx], [offsetGroupId], bs);
+}
+
+function eachNtCTubeSegment(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+    if (NTT.isLoci(loci)) {
+        const offsetGroupId = loci.elements[0];
+        return apply(Interval.ofBounds(offsetGroupId, offsetGroupId + 4));
+    }
+    return false;
+}
+
+function NtCTubeVisual(materialId: number): UnitsVisual<NtCTubeMeshParams> {
+    return UnitsMeshVisual<NtCTubeMeshParams>({
+        defaultProps: PD.getDefaultValues(NtCTubeMeshParams),
+        createGeometry: createNtCTubeMesh,
+        createLocationIterator: createNtCTubeSegmentsIterator,
+        getLoci: getNtCTubeSegmentLoci,
+        eachLocation: eachNtCTubeSegment,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<NtCTubeMeshParams>, currentProps: PD.Values<NtCTubeMeshParams>) => {
+            state.createGeometry = (
+                newProps.quality !== currentProps.quality ||
+                newProps.residueMarkerWidth !== currentProps.residueMarkerWidth ||
+                newProps.segmentBoundaryWidth !== currentProps.segmentBoundaryWidth ||
+                newProps.doubleSided !== currentProps.doubleSided ||
+                newProps.alpha !== currentProps.alpha ||
+                newProps.linearSegments !== currentProps.linearSegments ||
+                newProps.radialSegments !== currentProps.radialSegments
+            );
+        }
+    }, materialId);
+
+}
+const NtCTubeVisuals = {
+    'ntc-tube-symbol': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, NtCTubeMeshParams>) => UnitsRepresentation('NtC Tube Mesh', ctx, getParams, NtCTubeVisual),
+};
+
+export const NtCTubeParams = {
+    ...NtCTubeMeshParams
+};
+export type NtCTubeParams = typeof NtCTubeParams;
+export function getNtCTubeParams(ctx: ThemeRegistryContext, structure: Structure) {
+    return PD.clone(NtCTubeParams);
+}
+
+export type NtCTubeRepresentation = StructureRepresentation<NtCTubeParams>;
+export function NtCTubeRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, NtCTubeParams>): NtCTubeRepresentation {
+    return Representation.createMulti('NtC Tube', ctx, getParams, StructureRepresentationStateBuilder, NtCTubeVisuals as unknown as Representation.Def<Structure, NtCTubeParams>);
+}
+
+export const NtCTubeRepresentationProvider = StructureRepresentationProvider({
+    name: 'ntc-tube',
+    label: 'NtC Tube',
+    description: 'Displays schematic representation of NtC conformers',
+    factory: NtCTubeRepresentation,
+    getParams: getNtCTubeParams,
+    defaultValues: PD.getDefaultValues(NtCTubeParams),
+    defaultColorTheme: { name: 'ntc-tube' },
+    defaultSizeTheme: { name: 'uniform', props: { value: 2.0 } },
+    isApplicable: (structure: Structure) => structure.models.every(m => Dnatco.isApplicable(m)),
+    ensureCustomProperties: {
+        attach: async (ctx: CustomProperty.Context, structure: Structure) => structure.models.forEach(m => NtCTubeProvider.attach(ctx, m, void 0, true)),
+        detach: (data) => data.models.forEach(m => NtCTubeProvider.ref(m, false)),
+    },
+});

src/extensions/dnatco/ntc-tube/types.ts

@@ -0,0 +1,51 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { NtCTubeSegmentLabel } from './behavior';
+import { DnatcoTypes } from '../types';
+import { Sphere3D } from '../../../mol-math/geometry/primitives/sphere3d';
+import { DataLocation } from '../../../mol-model/location';
+import { DataLoci } from '../../../mol-model/loci';
+
+export namespace NtCTubeTypes {
+    const DataTag = 'dnatco-tube-segment-data';
+    const DummyTag = 'dnatco-tube-dummy';
+
+    export type Data = {
+        data: DnatcoTypes.Steps,
+    }
+
+    export type TubeBlock = {
+        step: DnatcoTypes.Step,
+        kind: 'upper' | 'lower' | 'residue-boundary' | 'segment-boundary';
+    }
+
+    export interface Location extends DataLocation<TubeBlock> {}
+
+    export function Location(payload: TubeBlock) {
+        return DataLocation(DataTag, payload, {});
+    }
+
+    export function isLocation(x: any): x is Location {
+        return !!x && x.kind === 'data-location' && x.tag === DataTag;
+    }
+
+    export interface Loci extends DataLoci<DnatcoTypes.Step[], number> {}
+    export interface DummyLoci extends DataLoci<{}, number> {}
+
+    export function Loci(data: DnatcoTypes.Step[], stepIndices: number[], elements: number[], boundingSphere?: Sphere3D): Loci {
+        return DataLoci(DataTag, data, elements, boundingSphere ? () => boundingSphere : undefined, () => stepIndices[0] !== undefined ? NtCTubeSegmentLabel(data[stepIndices[0]]) : '');
+    }
+
+    export function DummyLoci(): DummyLoci {
+        return DataLoci(DummyTag, {}, [], undefined, () => '');
+    }
+
+    export function isLoci(x: any): x is Loci {
+        return !!x && x.kind === 'data-loci' && x.tag === DataTag;
+    }
+}

src/extensions/dnatco/ntc-tube/util.ts

@@ -0,0 +1,191 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { NtCTubeTypes as NTT } from './types';
+import { NtCTubeProvider } from './property';
+import { DnatcoUtil } from '../util';
+import { Segmentation, SortedArray } from '../../../mol-data/int';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
+
+function getAtomPosition(vec: Vec3, loc: StructureElement.Location, residue: DnatcoUtil.Residue, names: string[], altId: string, insCode: string) {
+    const eI = DnatcoUtil.getAtomIndex(loc, residue, names, altId, insCode);
+    if (eI !== -1)
+        loc.unit.conformation.invariantPosition(eI, vec);
+    else {
+        vec[0] = 0; vec[1] = 0; vec[2] = 0;
+    }
+}
+
+const p_1 = Vec3();
+const p0 = Vec3();
+const p1 = Vec3();
+const p2 = Vec3();
+const p3 = Vec3();
+const p4 = Vec3();
+const pP = Vec3();
+
+function getPoints(
+    loc: StructureElement.Location,
+    r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue,
+    altId0: string, altId1: string, altId2: string,
+    insCode0: string, insCode1: string, insCode2: string,
+) {
+    if (r0) getAtomPosition(p_1, loc, r0, ['C5\'', 'C5*'], altId0, insCode0);
+    r0 ? getAtomPosition(p0, loc, r0, ['O3\'', 'O3*'], altId0, insCode0) : getAtomPosition(p0, loc, r1, ['O5\'', 'O5*'], altId1, insCode1);
+    getAtomPosition(p1, loc, r1, ['C5\'', 'C5*'], altId1, insCode1);
+    getAtomPosition(p2, loc, r1, ['O3\'', 'O3*'], altId1, insCode1);
+    getAtomPosition(p3, loc, r2, ['C5\'', 'C5*'], altId2, insCode2);
+    getAtomPosition(p4, loc, r2, ['O3\'', 'O3*'], altId2, insCode2);
+    getAtomPosition(pP, loc, r2, ['P'], altId2, insCode2);
+
+    return { p_1, p0, p1, p2, p3, p4, pP };
+}
+
+function hasGapElements(r: DnatcoUtil.Residue, unit: Unit) {
+    for (let xI = r.start; xI < r.end; xI++) {
+        const eI = unit.elements[xI];
+        if (SortedArray.has(unit.gapElements, eI)) {
+            return true;
+        }
+    }
+
+    return false;
+}
+
+export type NtCTubeSegment = {
+    p_1: Vec3,
+    p0: Vec3,
+    p1: Vec3,
+    p2: Vec3,
+    p3: Vec3,
+    p4: Vec3,
+    pP: Vec3,
+    stepIdx: number,
+    followsGap: boolean,
+    firstInChain: boolean,
+    capEnd: boolean,
+}
+
+export class NtCTubeSegmentsIterator {
+    private chainIt: Segmentation.SegmentIterator<ChainIndex>;
+    private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
+
+    /* Second residue of the previous step, may be undefined
+     * if we are at the beginning of a chain or right after a discontinuity */
+    private residuePrev?: DnatcoUtil.Residue;
+    /* First residue of the current step */
+    private residueOne?: DnatcoUtil.Residue;
+    /* Second residue of the current step */
+    private residueTwo: DnatcoUtil.Residue;
+    /* First residue of the next step, may be undefined
+     * if we are at the end of a chain.
+     * Undefined value indicates that the iterator has reached the end.*/
+    private residueNext?: DnatcoUtil.Residue;
+
+    private data?: NTT.Data;
+    private altIdOne = '';
+    private insCodeOne = '';
+    private loc: StructureElement.Location;
+
+    private moveStep() {
+        if (!this.residueNext)
+            return void 0;
+
+        /* Assume discontinuity of the ResidueIndex of the residue that would become residue one (= first residue of the corresponding step)
+         * does not equal to ResidueIndex of what would be residue two (= second residue of the corresponding step). */
+        if (this.residueTwo.index + 1 === this.residueNext.index) {
+            this.residuePrev = DnatcoUtil.copyResidue(this.residueOne);
+            this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
+            this.residueTwo = DnatcoUtil.copyResidue(this.residueNext)!;
+            this.residueNext = this.residueIt.hasNext ? DnatcoUtil.copyResidue(this.residueIt.move())! : void 0;
+        } else {
+            if (!this.residueIt.hasNext) {
+                this.residueNext = void 0;
+                return void 0;
+            }
+
+            // There is discontinuity, act as if we were at the beginning of a chain
+            this.residuePrev = void 0;
+            this.residueOne = DnatcoUtil.copyResidue(this.residueNext);
+            this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+            this.residueNext = this.residueIt.hasNext ? DnatcoUtil.copyResidue(this.residueIt.move())! : void 0;
+        }
+
+        return this.toSegment(this.residuePrev, this.residueOne!, this.residueTwo, this.residueNext);
+    }
+
+    private prime() {
+        if (this.residueIt.hasNext)
+            this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
+        if (this.residueIt.hasNext)
+            this.residueNext = this.residueIt.move();
+    }
+
+    private toSegment(r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue, r3: DnatcoUtil.Residue | undefined): NtCTubeSegment | undefined {
+        const indices = DnatcoUtil.getStepIndices(this.data!.data, this.loc, r1);
+        if (indices.length === 0)
+            return void 0;
+
+        const stepIdx = indices[0];
+        const step = this.data!.data.steps[stepIdx];
+
+        const altIdPrev = this.altIdOne;
+        const insCodePrev = this.insCodeOne;
+        this.altIdOne = step.label_alt_id_1;
+        this.insCodeOne = step.PDB_ins_code_1;
+        const altIdTwo = step.label_alt_id_2;
+        const insCodeTwo = step.PDB_ins_code_2;
+        const followsGap = !!r0 && hasGapElements(r0, this.loc.unit) && hasGapElements(r1, this.loc.unit);
+        const precedesDiscontinuity = r3 ? r3.index !== r2.index + 1 : false;
+
+        return {
+            ...getPoints(this.loc, r0, r1, r2, altIdPrev, this.altIdOne, altIdTwo, insCodePrev, this.insCodeOne, insCodeTwo),
+            stepIdx,
+            followsGap,
+            firstInChain: !r0,
+            capEnd: !this.residueNext || precedesDiscontinuity || hasGapElements(r2, this.loc.unit),
+        };
+    }
+
+    constructor(structure: Structure, unit: Unit.Atomic) {
+        this.chainIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
+        this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+
+        const prop = NtCTubeProvider.get(unit.model).value;
+        this.data = prop?.data;
+
+        if (this.chainIt.hasNext) {
+            this.residueIt.setSegment(this.chainIt.move());
+            this.prime();
+        }
+
+        this.loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
+    }
+
+    get hasNext() {
+        if (!this.data)
+            return false;
+        return !!this.residueNext
+            ? true
+            : this.chainIt.hasNext;
+    }
+
+    move() {
+        if (!!this.residueNext) {
+            return this.moveStep();
+        } else {
+            this.residuePrev = void 0; // Assume discontinuity when we switch chains
+            this.residueNext = void 0;
+
+            this.residueIt.setSegment(this.chainIt.move());
+            this.prime();
+
+            return this.moveStep();
+        }
+    }
+}

src/extensions/dnatco/property.ts

@@ -0,0 +1,172 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { DnatcoTypes } from './types';
+import { Column, Table } from '../../mol-data/db';
+import { toTable } from '../../mol-io/reader/cif/schema';
+import { Model } from '../../mol-model/structure';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
+import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+export type DnatcoSteps = PropertyWrapper<DnatcoTypes.Steps | undefined>;
+
+export const DnatcoParams = {};
+export type DnatcoParams = typeof DnatcoParams;
+export type DnatcoProps = PD.Values<DnatcoParams>;
+
+export namespace Dnatco {
+    export const Schema = {
+        ndb_struct_ntc_step: {
+            id: Column.Schema.int,
+            name: Column.Schema.str,
+            PDB_model_number: Column.Schema.int,
+            label_entity_id_1: Column.Schema.int,
+            label_asym_id_1: Column.Schema.str,
+            label_seq_id_1: Column.Schema.int,
+            label_comp_id_1: Column.Schema.str,
+            label_alt_id_1: Column.Schema.str,
+            label_entity_id_2: Column.Schema.int,
+            label_asym_id_2: Column.Schema.str,
+            label_seq_id_2: Column.Schema.int,
+            label_comp_id_2: Column.Schema.str,
+            label_alt_id_2: Column.Schema.str,
+            auth_asym_id_1: Column.Schema.str,
+            auth_seq_id_1: Column.Schema.int,
+            auth_asym_id_2: Column.Schema.str,
+            auth_seq_id_2: Column.Schema.int,
+            PDB_ins_code_1: Column.Schema.str,
+            PDB_ins_code_2: Column.Schema.str,
+        },
+        ndb_struct_ntc_step_summary: {
+            step_id: Column.Schema.int,
+            assigned_CANA: Column.Schema.str,
+            assigned_NtC: Column.Schema.str,
+            confal_score: Column.Schema.int,
+            euclidean_distance_NtC_ideal: Column.Schema.float,
+            cartesian_rmsd_closest_NtC_representative: Column.Schema.float,
+            closest_CANA: Column.Schema.str,
+            closest_NtC: Column.Schema.str,
+            closest_step_golden: Column.Schema.str
+        }
+    };
+    export type Schema = typeof Schema;
+
+    export function getStepsFromCif(
+        model: Model,
+        cifSteps: Table<typeof Dnatco.Schema.ndb_struct_ntc_step>,
+        stepsSummary: StepsSummaryTable
+    ): DnatcoTypes.Steps {
+        const steps = new Array<DnatcoTypes.Step>();
+        const mapping = new Array<DnatcoTypes.MappedChains>();
+
+        const {
+            id, PDB_model_number, name,
+            auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
+            auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
+            _rowCount
+        } = cifSteps;
+
+        if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
+
+        for (let i = 0; i < _rowCount; i++) {
+            const {
+                NtC,
+                confal_score,
+                rmsd
+            } = getSummaryData(id.value(i), i, stepsSummary);
+            const modelNum = PDB_model_number.value(i);
+            const chainId = auth_asym_id_1.value(i);
+            const seqId = auth_seq_id_1.value(i);
+            const modelIdx = modelNum - 1;
+
+            if (mapping.length <= modelIdx || !mapping[modelIdx])
+                mapping[modelIdx] = new Map<string, DnatcoTypes.MappedResidues>();
+
+            const step = {
+                PDB_model_number: modelNum,
+                name: name.value(i),
+                auth_asym_id_1: chainId,
+                auth_seq_id_1: seqId,
+                label_comp_id_1: label_comp_id_1.value(i),
+                label_alt_id_1: label_alt_id_1.value(i),
+                PDB_ins_code_1: PDB_ins_code_1.value(i),
+                auth_asym_id_2: auth_asym_id_2.value(i),
+                auth_seq_id_2: auth_seq_id_2.value(i),
+                label_comp_id_2: label_comp_id_2.value(i),
+                label_alt_id_2: label_alt_id_2.value(i),
+                PDB_ins_code_2: PDB_ins_code_2.value(i),
+                confal_score,
+                NtC,
+                rmsd,
+            };
+
+            steps.push(step);
+
+            const mappedChains = mapping[modelIdx];
+            const residuesOnChain = mappedChains.get(chainId) ?? new Map<number, number[]>();
+            const stepsForResidue = residuesOnChain.get(seqId) ?? [];
+            stepsForResidue.push(steps.length - 1);
+
+            residuesOnChain.set(seqId, stepsForResidue);
+            mappedChains.set(chainId, residuesOnChain);
+            mapping[modelIdx] = mappedChains;
+        }
+
+        return { steps, mapping };
+    }
+
+    export async function fromCif(ctx: CustomProperty.Context, model: Model, props: DnatcoProps): Promise<CustomProperty.Data<DnatcoSteps>> {
+        const info = PropertyWrapper.createInfo();
+        const data = getCifData(model);
+        if (data === undefined) return { value: { info, data: undefined } };
+
+        const fromCif = getStepsFromCif(model, data.steps, data.stepsSummary);
+        return { value: { info, data: fromCif } };
+    }
+
+    export function getCifData(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF');
+        if (!hasNdbStructNtcCategories(model)) return undefined;
+        return {
+            steps: toTable(Schema.ndb_struct_ntc_step, model.sourceData.data.frame.categories.ndb_struct_ntc_step),
+            stepsSummary: toTable(Schema.ndb_struct_ntc_step_summary, model.sourceData.data.frame.categories.ndb_struct_ntc_step_summary)
+        };
+    }
+
+    function hasNdbStructNtcCategories(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const names = (model.sourceData).data.frame.categoryNames;
+        return names.includes('ndb_struct_ntc_step') && names.includes('ndb_struct_ntc_step_summary');
+    }
+
+    export function isApplicable(model?: Model): boolean {
+        return !!model && hasNdbStructNtcCategories(model);
+    }
+}
+
+type StepsSummaryTable = Table<typeof Dnatco.Schema.ndb_struct_ntc_step_summary>;
+
+function getSummaryData(id: number, i: number, stepsSummary: StepsSummaryTable) {
+    const {
+        step_id,
+        confal_score,
+        assigned_NtC,
+        cartesian_rmsd_closest_NtC_representative,
+    } = stepsSummary;
+
+    // Assume that step_ids in ntc_step_summary are in the same order as steps in ntc_step
+    for (let j = i; j < stepsSummary._rowCount; j++) {
+        if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
+    }
+    // Safety net for cases where the previous assumption is not met
+    for (let j = 0; j < i; j++) {
+        if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
+    }
+    throw new Error('Inconsistent mmCIF data');
+}

src/extensions/dnatco/types.ts

@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+export namespace DnatcoTypes {
+    export const DataTag = 'dnatco-confal-half-step';
+
+    export type Step = {
+        PDB_model_number: number,
+        name: string,
+        auth_asym_id_1: string,
+        auth_seq_id_1: number,
+        label_comp_id_1: string,
+        label_alt_id_1: string,
+        PDB_ins_code_1: string,
+        auth_asym_id_2: string,
+        auth_seq_id_2: number,
+        label_comp_id_2: string,
+        label_alt_id_2: string,
+        PDB_ins_code_2: string,
+        confal_score: number,
+        NtC: string,
+        rmsd: number,
+    }
+
+    export type MappedChains = Map<string, MappedResidues>;
+    export type MappedResidues = Map<number, number[]>;
+
+    export interface Steps {
+        steps: Array<Step>,
+        mapping: MappedChains[],
+    }
+
+    export interface HalfStep {
+        step: Step,
+        isLower: boolean,
+    }
+}

src/extensions/dnatco/util.ts

@@ -0,0 +1,117 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { DnatcoTypes } from './types';
+import { OrderedSet, Segmentation } from '../../mol-data/int';
+import { EmptyLoci } from '../../mol-model/loci';
+import { ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
+
+const EmptyStepIndices = new Array<number>();
+
+export namespace DnatcoUtil {
+    export type Residue = Segmentation.Segment<ResidueIndex>;
+
+    export function copyResidue(r?: Residue) {
+        return r ? { index: r.index, start: r.start, end: r.end } : void 0;
+    }
+
+    export function getAtomIndex(loc: StructureElement.Location, residue: Residue, names: string[], altId: string, insCode: string): ElementIndex {
+        for (let eI = residue.start; eI < residue.end; eI++) {
+            loc.element = loc.unit.elements[eI];
+            const elName = StructureProperties.atom.label_atom_id(loc);
+            const elAltId = StructureProperties.atom.label_alt_id(loc);
+            const elInsCode = StructureProperties.residue.pdbx_PDB_ins_code(loc);
+
+            if (names.includes(elName) && (elAltId === altId || elAltId.length === 0) && (elInsCode === insCode))
+                return loc.element;
+        }
+
+        return -1 as ElementIndex;
+    }
+
+    export function getStepIndices(data: DnatcoTypes.Steps, loc: StructureElement.Location, r: DnatcoUtil.Residue) {
+        loc.element = loc.unit.elements[r.start];
+
+        const modelIdx = StructureProperties.unit.model_num(loc) - 1;
+        const chainId = StructureProperties.chain.auth_asym_id(loc);
+        const seqId = StructureProperties.residue.auth_seq_id(loc);
+        const insCode = StructureProperties.residue.pdbx_PDB_ins_code(loc);
+
+        const chains = data.mapping[modelIdx];
+        if (!chains) return EmptyStepIndices;
+        const residues = chains.get(chainId);
+        if (!residues) return EmptyStepIndices;
+        const indices = residues.get(seqId);
+        if (!indices) return EmptyStepIndices;
+
+        return insCode !== '' ? indices.filter(idx => data.steps[idx].PDB_ins_code_1 === insCode) : indices;
+    }
+
+    export function residueAltIds(structure: Structure, unit: Unit, residue: Residue) {
+        const altIds = new Array<string>();
+        const loc = StructureElement.Location.create(structure, unit);
+        for (let eI = residue.start; eI < residue.end; eI++) {
+            loc.element = OrderedSet.getAt(unit.elements, eI);
+            const altId = StructureProperties.atom.label_alt_id(loc);
+            if (altId !== '' && !altIds.includes(altId))
+                altIds.push(altId);
+        }
+
+        return altIds;
+    }
+
+    const _loc = StructureElement.Location.create();
+    export function residueToLoci(asymId: string, seqId: number, altId: string | undefined, insCode: string, loci: StructureElement.Loci, source: 'label' | 'auth') {
+        _loc.structure = loci.structure;
+        for (const e of loci.elements) {
+            _loc.unit = e.unit;
+
+            const getAsymId = source === 'label' ? StructureProperties.chain.label_asym_id : StructureProperties.chain.auth_asym_id;
+            const getSeqId = source === 'label' ? StructureProperties.residue.label_seq_id : StructureProperties.residue.auth_seq_id;
+
+            // Walk the entire unit and look for the requested residue
+            const chainIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.chainAtomSegments, e.unit.elements);
+            const residueIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.residueAtomSegments, e.unit.elements);
+
+            const elemIndex = (idx: number) => OrderedSet.getAt(e.unit.elements, idx);
+            while (chainIt.hasNext) {
+                const chain = chainIt.move();
+                _loc.element = elemIndex(chain.start);
+                const _asymId = getAsymId(_loc);
+                if (_asymId !== asymId)
+                    continue; // Wrong chain, skip it
+
+                residueIt.setSegment(chain);
+                while (residueIt.hasNext) {
+                    const residue = residueIt.move();
+                    _loc.element = elemIndex(residue.start);
+
+                    const _seqId = getSeqId(_loc);
+                    if (_seqId === seqId) {
+                        const _insCode = StructureProperties.residue.pdbx_PDB_ins_code(_loc);
+                        if (_insCode !== insCode)
+                            continue;
+                        if (altId) {
+                            const _altIds = residueAltIds(loci.structure, e.unit, residue);
+                            if (!_altIds.includes(altId))
+                                continue;
+                        }
+
+                        const start = residue.start as StructureElement.UnitIndex;
+                        const end = residue.end as StructureElement.UnitIndex;
+                        return StructureElement.Loci(
+                            loci.structure,
+                            [{ unit: e.unit, indices: OrderedSet.ofBounds(start, end) }]
+                        );
+                    }
+                }
+            }
+        }
+
+        return EmptyLoci;
+    }
+}

src/extensions/meshes/examples.ts

@@ -0,0 +1,187 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+/** Testing examples for using mesh-extension.ts. */
+
+import { CIF } from '../../mol-io/reader/cif';
+import { Volume } from '../../mol-model/volume';
+import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
+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 { PluginContext } from '../../mol-plugin/context';
+import { StateObjectSelector } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import { ParamDefinition } from '../../mol-util/param-definition';
+
+import { createMeshFromUrl } from './mesh-extension';
+import { MeshServerInfo } from './mesh-streaming/server-info';
+import { InitMeshStreaming } from './mesh-streaming/transformers';
+import * as MeshUtils from './mesh-utils';
+
+
+export const DB_URL = '/db'; // local
+
+
+export async function runMeshExtensionExamples(plugin: PluginContext, db_url: string = DB_URL) {
+    console.time('TIME MESH EXAMPLES');
+    // await runIsosurfaceExample(plugin, db_url);
+    // await runMolsurfaceExample(plugin);
+
+    // Focused Ion Beam-Scanning Electron Microscopy of mitochondrial reticulum in murine skeletal muscle: https://www.ebi.ac.uk/empiar/EMPIAR-10070/
+    // await runMeshExample(plugin, 'all', db_url);
+    // await runMeshExample(plugin, 'fg', db_url);
+    // await runMultimeshExample(plugin, 'fg', 'worst', db_url);
+    // await runCifMeshExample(plugin);
+    // await runMeshExample2(plugin, 'fg');
+    await runMeshStreamingExample(plugin);
+
+    console.timeEnd('TIME MESH EXAMPLES');
+}
+
+/** Example for downloading multiple separate segments, each containing 1 mesh. */
+export async function runMeshExample(plugin: PluginContext, segments: 'fg' | 'all', db_url: string = DB_URL) {
+    const detail = 2;
+    const segmentIds = (segments === 'all') ?
+        [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17] // segment-16 has no detail-2
+        : [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17]; // segment-13 and segment-15 are quasi background
+
+    for (const segmentId of segmentIds) {
+        await createMeshFromUrl(plugin, `${db_url}/empiar-10070-mesh-rounded/segment-${segmentId}/detail-${detail}`, segmentId, detail, true, undefined);
+    }
+}
+
+/** Example for downloading multiple separate segments, each containing 1 mesh. */
+export async function runMeshExample2(plugin: PluginContext, segments: 'one' | 'few' | 'fg' | 'all') {
+    const detail = 1;
+    const segmentIds = (segments === 'one') ? [15]
+        : (segments === 'few') ? [1, 4, 7, 10, 16]
+            : (segments === 'all') ? [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17] // segment-16 has no detail-2
+                : [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17]; // segment-13 and segment-15 are quasi background
+
+    for (const segmentId of segmentIds) {
+        await createMeshFromUrl(plugin, `http://localhost:9000/v2/empiar/empiar-10070/mesh_bcif/${segmentId}/${detail}`, segmentId, detail, false, undefined);
+    }
+}
+
+/** Example for downloading a single segment containing multiple meshes. */
+export async function runMultimeshExample(plugin: PluginContext, segments: 'fg' | 'all', detailChoice: 'best' | 'worst', db_url: string = DB_URL) {
+    const urlDetail = (detailChoice === 'best') ? '2' : 'worst';
+    const numDetail = (detailChoice === 'best') ? 2 : 1000;
+    await createMeshFromUrl(plugin, `${db_url}/empiar-10070-multimesh-rounded/segments-${segments}/detail-${urlDetail}`, 0, numDetail, false, undefined);
+}
+
+export async function runMeshStreamingExample(plugin: PluginContext, source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070', serverUrl?: string, parent?: StateObjectSelector) {
+    const params = ParamDefinition.getDefaultValues(MeshServerInfo.Params);
+    if (serverUrl) params.serverUrl = serverUrl;
+    params.source = source;
+    params.entryId = entryId;
+    await plugin.runTask(plugin.state.data.applyAction(InitMeshStreaming, params, parent?.ref), { useOverlay: false });
+}
+
+/** Example for downloading a protein structure and visualizing molecular surface. */
+export async function runMolsurfaceExample(plugin: PluginContext) {
+    const entryId = 'pdb-7etq';
+
+    // Node "https://www.ebi.ac.uk/pdbe/entry-files/download/7etq.bcif" ("transformer": "ms-plugin.download") -> var data
+    const data = await plugin.builders.data.download({ url: 'https://www.ebi.ac.uk/pdbe/entry-files/download/7etq.bcif', isBinary: true }, { state: { isGhost: false } });
+    console.log('formats:', plugin.dataFormats.list);
+
+    // Node "CIF File" ("transformer": "ms-plugin.parse-cif")
+    // Node "7ETQ 1 model" ("transformer": "ms-plugin.trajectory-from-mmcif") -> var trajectory
+    const parsed = await plugin.dataFormats.get('mmcif')!.parse(plugin, data, { entryId });
+    const trajectory: StateObjectSelector<PluginStateObject.Molecule.Trajectory> = parsed.trajectory;
+    console.log('parsed', parsed);
+    console.log('trajectory', trajectory);
+
+    // Node "Model 1" ("transformer": "ms-plugin.model-from-trajectory") -> var model
+    const model = await plugin.build().to(trajectory).apply(StateTransforms.Model.ModelFromTrajectory).commit();
+    console.log('model:', model);
+
+    // Node "Model 91 elements" ("transformer": "ms-plugin.structure-from-model") -> var structure
+    const structure = await plugin.build().to(model).apply(StateTransforms.Model.StructureFromModel,).commit();
+    console.log('structure:', structure);
+
+    // Node "Molecular Surface" ("transformer": "ms-plugin.structure-representation-3d") -> var repr
+    const reprParams = createStructureRepresentationParams(plugin, undefined, { type: 'molecular-surface' });
+    const repr = await plugin.build().to(structure).apply(StateTransforms.Representation.StructureRepresentation3D, reprParams).commit();
+    console.log('repr:', repr);
+}
+
+/** Example for downloading an EMDB density data and visualizing isosurface. */
+export async function runIsosurfaceExample(plugin: PluginContext, db_url: string = DB_URL) {
+    const entryId = 'emd-1832';
+    const isoLevel = 2.73;
+
+    let root = await plugin.build();
+    const data = await plugin.builders.data.download({ url: `${db_url}/emd-1832-box`, isBinary: true }, { state: { isGhost: false } });
+    const parsed = await plugin.dataFormats.get('dscif')!.parse(plugin, data, { entryId });
+
+    const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[0] ?? parsed.volume;
+    const volumeData = volume.cell!.obj!.data;
+    console.log('data:', data);
+    console.log('parsed:', parsed);
+    console.log('volume:', volume);
+    console.log('volumeData:', volumeData);
+
+    root = await plugin.build();
+    console.log('root:', root);
+    console.log('to:', root.to(volume));
+    console.log('toRoot:', root.toRoot());
+
+    let volumeParams;
+    volumeParams = createVolumeRepresentationParams(plugin, volumeData, {
+        type: 'isosurface',
+        typeParams: {
+            alpha: 0.5,
+            isoValue: Volume.adjustedIsoValue(volumeData, isoLevel, 'relative'),
+            visuals: ['solid'],
+            sizeFactor: 1,
+        },
+        color: 'uniform',
+        colorParams: { value: Color(0x00aaaa) },
+
+    });
+    root.to(volume).apply(StateTransforms.Representation.VolumeRepresentation3D, volumeParams);
+
+    volumeParams = createVolumeRepresentationParams(plugin, volumeData, {
+        type: 'isosurface',
+        typeParams: {
+            alpha: 1.0,
+            isoValue: Volume.adjustedIsoValue(volumeData, isoLevel, 'relative'),
+            visuals: ['wireframe'],
+            sizeFactor: 1,
+        },
+        color: 'uniform',
+        colorParams: { value: Color(0x8800aa) },
+
+    });
+    root.to(volume).apply(StateTransforms.Representation.VolumeRepresentation3D, volumeParams);
+    await root.commit();
+}
+
+
+export async function runCifMeshExample(plugin: PluginContext, api: string = 'http://localhost:9000/v2',
+    source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070',
+    segmentId: number = 1, detail: number = 10,
+) {
+    const url = `${api}/${source}/${entryId}/mesh_bcif/${segmentId}/${detail}`;
+    getMeshFromBcif(plugin, url);
+}
+
+async function getMeshFromBcif(plugin: PluginContext, url: string) {
+    const urlAsset = Asset.getUrlAsset(plugin.managers.asset, url);
+    const asset = await plugin.runTask(plugin.managers.asset.resolve(urlAsset, 'binary'));
+    const parsed = await plugin.runTask(CIF.parseBinary(asset.data));
+    if (parsed.isError) {
+        plugin.log.error('VolumeStreaming, parsing CIF: ' + parsed.toString());
+        return;
+    }
+    console.log('blocks:', parsed.result.blocks);
+    const mesh = await MeshUtils.meshFromCif(parsed.result);
+    console.log(mesh);
+}

src/extensions/meshes/mesh-cif-schema.ts

@@ -0,0 +1,40 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Column, Database } from '../../mol-data/db';
+import { CifFrame } from '../../mol-io/reader/cif';
+import { toDatabase } from '../../mol-io/reader/cif/schema';
+
+
+const int = Column.Schema.int;
+const float = Column.Schema.float;
+
+
+// TODO in future, move to molstar/src/mol-io/reader/cif/schema/mesh.ts
+export const Mesh_Data_Schema = {
+    mesh: {
+        id: int,
+    },
+    mesh_vertex: {
+        mesh_id: int,
+        vertex_id: int,
+        x: float,
+        y: float,
+        z: float,
+    },
+    /** Table of triangles, 3 rows per triangle */
+    mesh_triangle: {
+        mesh_id: int,
+        /** Indices of vertices within mesh */
+        vertex_id: int,
+    }
+};
+export type Mesh_Data_Schema = typeof Mesh_Data_Schema;
+export interface Mesh_Data_Database extends Database<Mesh_Data_Schema> {}
+
+
+// TODO in future, move to molstar/src/mol-io/reader/cif.ts: CIF.schema.mesh
+export const CIF_schema_mesh = (frame: CifFrame) => toDatabase<Mesh_Data_Schema, Mesh_Data_Database>(Mesh_Data_Schema, frame);

src/extensions/meshes/mesh-extension.ts

@@ -0,0 +1,223 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+/** Defines new types of State tree transformers for dealing with mesh data. */
+
+
+import { BaseGeometry, VisualQuality, VisualQualityOptions } from '../../mol-geo/geometry/base';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { CifFile } from '../../mol-io/reader/cif';
+import { Box3D } from '../../mol-math/geometry';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { Shape } from '../../mol-model/shape';
+import { ShapeProvider } from '../../mol-model/shape/provider';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { Download } from '../../mol-plugin-state/transforms/data';
+import { ShapeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectRef, StateObjectSelector, StateTransformer } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { Color } from '../../mol-util/color';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import * as MeshUtils from './mesh-utils';
+
+
+export const BACKGROUND_OPACITY = 0.2;
+export const FOREROUND_OPACITY = 1;
+
+export const VolsegTransform: StateTransformer.Builder.Root = StateTransformer.builderFactory('volseg');
+
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+// Parsed data
+
+/** Data type for `MeshlistStateObject` - list of meshes */
+export interface MeshlistData {
+    segmentId: number,
+    segmentName: string,
+    detail: number,
+    meshIds: number[],
+    mesh: Mesh,
+    /** Reference to the object which created this meshlist (e.g. `MeshStreaming.Behavior`) */
+    ownerId?: string,
+}
+
+export namespace MeshlistData {
+    export function empty(): MeshlistData {
+        return {
+            segmentId: 0,
+            segmentName: 'Empty',
+            detail: 0,
+            meshIds: [],
+            mesh: Mesh.createEmpty(),
+        };
+    };
+    export async function fromCIF(data: CifFile, segmentId: number, segmentName: string, detail: number): Promise<MeshlistData> {
+        const { mesh, meshIds } = await MeshUtils.meshFromCif(data);
+        return {
+            segmentId,
+            segmentName,
+            detail,
+            meshIds,
+            mesh,
+        };
+    }
+    export function stats(meshListData: MeshlistData): string {
+        return `Meshlist "${meshListData.segmentName}" (detail ${meshListData.detail}): ${meshListData.meshIds.length} meshes, ${meshListData.mesh.vertexCount} vertices, ${meshListData.mesh.triangleCount} triangles`;
+    }
+    export function getShape(data: MeshlistData, color: Color): Shape<Mesh> {
+        const mesh = data.mesh;
+        const meshShape: Shape<Mesh> = Shape.create(data.segmentName, data, mesh,
+            () => color,
+            () => 1,
+            // group => `${data.segmentName} | Segment ${data.segmentId} | Detail ${data.detail} | Mesh ${group}`,
+            group => data.segmentName,
+        );
+        return meshShape;
+    }
+
+    export function combineBBoxes(boxes: (Box3D | null)[]): Box3D | null {
+        let result = null;
+        for (const box of boxes) {
+            if (!box) continue;
+            if (result) {
+                Vec3.min(result.min, result.min, box.min);
+                Vec3.max(result.max, result.max, box.max);
+            } else {
+                result = Box3D.zero();
+                Box3D.copy(result, box);
+            }
+        }
+        return result;
+    }
+    export function bbox(data: MeshlistData): Box3D | null {
+        return MeshUtils.bbox(data.mesh);
+    }
+
+    export function allVerticesUsed(data: MeshlistData): boolean {
+        const unusedVertices = new Set();
+        for (let i = 0; i < data.mesh.vertexCount; i++) {
+            unusedVertices.add(i);
+        }
+        for (let i = 0; i < 3 * data.mesh.triangleCount; i++) {
+            const v = data.mesh.vertexBuffer.ref.value[i];
+            unusedVertices.delete(v);
+        }
+        return unusedVertices.size === 0;
+    }
+}
+
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+// Raw Data -> Parsed data
+
+export class MeshlistStateObject extends PluginStateObject.Create<MeshlistData>({ name: 'Parsed Meshlist', typeClass: 'Object' }) { }
+
+export const ParseMeshlistTransformer = VolsegTransform({
+    name: 'meshlist-from-string',
+    from: PluginStateObject.Format.Cif,
+    to: MeshlistStateObject,
+    params: {
+        label: PD.Text(MeshlistStateObject.type.name, { isHidden: true }),
+        segmentId: PD.Numeric(1, {}, { isHidden: true }),
+        segmentName: PD.Text('Segment'),
+        detail: PD.Numeric(1, {}, { isHidden: true }),
+        /** Reference to the object which manages this meshlist (e.g. `MeshStreaming.Behavior`) */
+        ownerId: PD.Text('', { isHidden: true }),
+    }
+})({
+    apply({ a, params }, globalCtx) { // `a` is the parent node, params are 2nd argument to To.apply(), `globalCtx` is the plugin
+        return Task.create('Create Parsed Meshlist', async ctx => {
+            const meshlistData = await MeshlistData.fromCIF(a.data, params.segmentId, params.segmentName, params.detail);
+            meshlistData.ownerId = params.ownerId;
+            const es = meshlistData.meshIds.length === 1 ? '' : 'es';
+            return new MeshlistStateObject(meshlistData, { label: params.label, description: `${meshlistData.segmentName} (${meshlistData.meshIds.length} mesh${es})` });
+        });
+    }
+});
+
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+// Parsed data -> Shape
+
+/** Data type for PluginStateObject.Shape.Provider */
+type MeshShapeProvider = ShapeProvider<MeshlistData, Mesh, Mesh.Params>;
+namespace MeshShapeProvider {
+    export function fromMeshlistData(meshlist: MeshlistData, color?: Color): MeshShapeProvider {
+        const theColor = color ?? MeshUtils.ColorGenerator.next().value;
+        return {
+            label: 'Mesh',
+            data: meshlist,
+            params: meshShapeProviderParams,
+            geometryUtils: Mesh.Utils,
+            getShape: (ctx, data: MeshlistData) => MeshlistData.getShape(data, theColor),
+        };
+    }
+}
+
+const meshShapeProviderParams: Mesh.Params = {
+    ...Mesh.Params,
+    quality: PD.Select<VisualQuality>('custom', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }), // use 'custom' when wanting to apply doubleSided
+    doubleSided: PD.Boolean(true, BaseGeometry.CustomQualityParamInfo),
+    // set `flatShaded`: true to see the real mesh vertices and triangles
+    transparentBackfaces: PD.Select('on', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory), // 'on' means: show backfaces with correct opacity, even when opacity < 1 (requires doubleSided) ¯\_(ツ)_/¯
+};
+
+
+export const MeshShapeTransformer = VolsegTransform({
+    name: 'shape-from-meshlist',
+    display: { name: 'Shape from Meshlist', description: 'Create Shape from Meshlist data' },
+    from: MeshlistStateObject,
+    to: PluginStateObject.Shape.Provider,
+    params: {
+        color: PD.Value<Color | undefined>(undefined), // undefined means random color
+    },
+})({
+    apply({ a, params }) {
+        const shapeProvider = MeshShapeProvider.fromMeshlistData(a.data, params.color);
+        return new PluginStateObject.Shape.Provider(shapeProvider, { label: PluginStateObject.Shape.Provider.type.name, description: a.description });
+    }
+});
+
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+
+
+/** Download data and create state tree hierarchy down to visual representation. */
+export async function createMeshFromUrl(plugin: PluginContext, meshDataUrl: string, segmentId: number, detail: number,
+    collapseTree: boolean, color?: Color, parent?: StateObjectSelector | StateObjectRef, transparentIfBboxAbove?: number,
+    name?: string, ownerId?: string) {
+
+    const update = parent ? plugin.build().to(parent) : plugin.build().toRoot();
+    const rawDataNodeRef = update.apply(Download,
+        { url: meshDataUrl, isBinary: true, label: `Downloaded Data ${segmentId}` },
+        { state: { isCollapsed: collapseTree } }
+    ).ref;
+    const parsedDataNode = await update.to(rawDataNodeRef)
+        .apply(StateTransforms.Data.ParseCif)
+        .apply(ParseMeshlistTransformer,
+            { label: undefined, segmentId: segmentId, segmentName: name ?? `Segment ${segmentId}`, detail: detail, ownerId: ownerId },
+            {}
+        )
+        .commit();
+
+    let transparent = false;
+    if (transparentIfBboxAbove !== undefined && parsedDataNode.data) {
+        const bbox = MeshlistData.bbox(parsedDataNode.data) || Box3D.zero();
+        transparent = Box3D.volume(bbox) > transparentIfBboxAbove;
+    }
+
+    await plugin.build().to(parsedDataNode)
+        .apply(MeshShapeTransformer, { color: color },)
+        .apply(ShapeRepresentation3D,
+            { alpha: transparent ? BACKGROUND_OPACITY : FOREROUND_OPACITY },
+            { tags: ['mesh-segment-visual', `segment-${segmentId}`] }
+        )
+        .commit();
+
+    return rawDataNodeRef;
+}

src/extensions/meshes/mesh-streaming/behavior.ts

@@ -0,0 +1,332 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { distinctUntilChanged, map } from 'rxjs';
+
+import { CIF } from '../../../mol-io/reader/cif';
+import { Box3D } from '../../../mol-math/geometry';
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { PluginBehavior } from '../../../mol-plugin/behavior';
+import { PluginCommand } from '../../../mol-plugin/command';
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { PluginContext } from '../../../mol-plugin/context';
+import { UUID } from '../../../mol-util';
+import { Asset } from '../../../mol-util/assets';
+import { Color } from '../../../mol-util/color';
+import { ColorNames } from '../../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+import { Choice } from '../../volumes-and-segmentations/helpers';
+import { MetadataWrapper } from '../../volumes-and-segmentations/volseg-api/utils';
+
+import { MeshlistData } from '../mesh-extension';
+import { MeshServerInfo } from './server-info';
+
+
+const DEFAULT_SEGMENT_NAME = 'Untitled segment';
+const DEFAULT_SEGMENT_COLOR = ColorNames.lightgray;
+export const NO_SEGMENT = -1;
+/** Maximum (worst) detail level available in GUI (TODO set actual maximum possible value) */
+const MAX_DETAIL = 10;
+const DEFAULT_DETAIL = 7; // TODO decide a reasonable default
+/** Segments whose bounding box volume is above this value (relative to the overall bounding box) are considered as background segments */
+export const BACKGROUND_SEGMENT_VOLUME_THRESHOLD = 0.5;
+
+
+export class MeshStreaming extends PluginStateObject.CreateBehavior<MeshStreaming.Behavior>({ name: 'Mesh Streaming' }) { }
+
+export namespace MeshStreaming {
+
+    export namespace Params {
+        export const ViewTypeChoice = new Choice({ off: 'Off', select: 'Select', all: 'All' }, 'select'); // TODO add camera target?
+        export type ViewType = Choice.Values<typeof ViewTypeChoice>;
+
+        export function create(options: MeshServerInfo.Data) {
+            return {
+                view: PD.MappedStatic('select', {
+                    'off': PD.Group({}),
+                    'select': PD.Group({
+                        baseDetail: PD.Numeric(DEFAULT_DETAIL, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for the non-selected segments (lower number = better)' }),
+                        focusDetail: PD.Numeric(1, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for the selected segment (lower number = better)' }),
+                        selectedSegment: PD.Numeric(NO_SEGMENT, {}, { isHidden: true }),
+                    }, { isFlat: true }),
+                    'all': PD.Group({
+                        detail: PD.Numeric(DEFAULT_DETAIL, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for all segments (lower number = better)' })
+                    }, { isFlat: true }),
+                }, { description: '"Off" hides all segments. \n"Select" shows all segments in lower detail, clicked segment in better detail. "All" shows all segment in the same level.' }),
+            };
+        }
+
+        export type Definition = ReturnType<typeof create>
+        export type Values = PD.Values<Definition>
+
+        export function copyValues(params: Values): Values {
+            return {
+                view: {
+                    name: params.view.name,
+                    params: { ...params.view.params } as any,
+                }
+            };
+        }
+        export function valuesEqual(p: Values, q: Values): boolean {
+            if (p.view.name !== q.view.name) return false;
+            for (const key in p.view.params) {
+                if ((p.view.params as any)[key] !== (q.view.params as any)[key]) return false;
+            }
+            return true;
+        }
+        export function detailsEqual(p: Values, q: Values): boolean {
+            switch (p.view.name) {
+                case 'off':
+                    return q.view.name === 'off';
+                case 'select':
+                    return q.view.name === 'select' && p.view.params.baseDetail === q.view.params.baseDetail && p.view.params.focusDetail === q.view.params.focusDetail;
+                case 'all':
+                    return q.view.name === 'all' && p.view.params.detail === q.view.params.detail;
+                default:
+                    throw new Error('Not implemented');
+            }
+        }
+    }
+
+    export interface VisualInfo {
+        tag: string, // e.g. high-2, low-1 // ? remove if can be omitted
+        segmentId: number, // ? remove if unused
+        segmentName: string, // ? remove if unused
+        detailType: VisualInfo.DetailType, // ? remove if unused
+        detail: number, // ? remove if unused
+        color: Color, // move to MeshlistData?
+        visible: boolean,
+        data?: MeshlistData,
+    }
+    export namespace VisualInfo {
+        export type DetailType = 'low' | 'high';
+        export const DetailTypes: DetailType[] = ['low', 'high'];
+        export function tagFor(segmentId: number, detail: DetailType) {
+            return `${detail}-${segmentId}`;
+        }
+    }
+
+
+    export class Behavior extends PluginBehavior.WithSubscribers<Params.Values> {
+        private id: string;
+        private ref: string = '';
+        public parentData: MeshServerInfo.Data;
+        private metadata?: MetadataWrapper;
+        public visuals?: { [tag: string]: VisualInfo };
+        public backgroundSegments: { [segmentId: number]: boolean } = {};
+        private focusObservable = this.plugin.behaviors.interaction.click.pipe( // QUESTION is this OK way to get focused segment?
+            map(evt => evt.current.loci),
+            map(loci => (loci.kind === 'group-loci') ? loci.shape.sourceData as MeshlistData : null),
+            map(data => (data?.ownerId === this.id) ? data : null), // do not process shapes created by others
+            distinctUntilChanged((old, current) => old?.segmentId === current?.segmentId),
+        );
+        private focusSubscription?: PluginCommand.Subscription = undefined;
+        private backgroundSegmentsInitialized = false;
+
+        constructor(plugin: PluginContext, data: MeshServerInfo.Data, params: Params.Values) {
+            super(plugin, params);
+            this.id = UUID.create22();
+            this.parentData = data;
+        }
+
+        register(ref: string): void {
+            this.ref = ref;
+        }
+
+        unregister(): void {
+            if (this.focusSubscription) {
+                this.focusSubscription.unsubscribe();
+                this.focusSubscription = undefined;
+            }
+            // TODO empty cache here (if used)
+        }
+
+        selectSegment(segmentId: number) {
+            if (this.params.view.name === 'select') {
+                if (this.params.view.params.selectedSegment === segmentId) return;
+                const newParams = Params.copyValues(this.params);
+                if (newParams.view.name === 'select') {
+                    newParams.view.params.selectedSegment = segmentId;
+                }
+                const state = this.plugin.state.data;
+                const update = state.build().to(this.ref).update(newParams);
+                PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotUpdateCurrent: true } });
+            }
+        }
+
+        async update(params: Params.Values) {
+            const oldParams = this.params;
+            this.params = params;
+
+            if (!this.metadata) {
+                const response = await fetch(this.getMetadataUrl());
+                const rawMetadata = await response.json();
+                this.metadata = new MetadataWrapper(rawMetadata);
+            }
+
+            if (!this.visuals) {
+                this.initVisualInfos();
+            } else if (!Params.detailsEqual(this.params, oldParams)) {
+                this.updateVisualInfoDetails();
+            }
+
+            switch (params.view.name) {
+                case 'off':
+                    await this.disableVisuals();
+                    break;
+                case 'select':
+                    await this.enableVisuals(params.view.params.selectedSegment);
+                    break;
+                case 'all':
+                    await this.enableVisuals();
+                    break;
+                default:
+                    throw new Error('Not implemented');
+            }
+            if (params.view.name !== 'off' && !this.backgroundSegmentsInitialized) {
+                this.guessBackgroundSegments();
+                this.backgroundSegmentsInitialized = true;
+            }
+            if (params.view.name === 'select' && !this.focusSubscription) {
+                this.focusSubscription = this.subscribeObservable(this.focusObservable, data => { this.selectSegment(data?.segmentId ?? NO_SEGMENT); });
+            } else if (params.view.name !== 'select' && this.focusSubscription) {
+                this.focusSubscription.unsubscribe();
+                this.focusSubscription = undefined;
+            }
+            return true;
+        }
+
+        private getMetadataUrl() {
+            return `${this.parentData.serverUrl}/${this.parentData.source}/${this.parentData.entryId}/metadata`;
+        }
+
+        private getMeshUrl(segment: number, detail: number) {
+            return `${this.parentData.serverUrl}/${this.parentData.source}/${this.parentData.entryId}/mesh_bcif/${segment}/${detail}`;
+        }
+
+        private initVisualInfos() {
+            const visuals: { [tag: string]: VisualInfo } = {};
+            for (const segid of this.metadata!.meshSegmentIds) {
+                const name = this.metadata?.getSegment(segid)?.biological_annotation.name ?? DEFAULT_SEGMENT_NAME;
+                const color = this.metadata?.getSegmentColor(segid) ?? DEFAULT_SEGMENT_COLOR;
+                for (const detailType of VisualInfo.DetailTypes) {
+                    const visual: VisualInfo = {
+                        tag: VisualInfo.tagFor(segid, detailType),
+                        segmentId: segid,
+                        segmentName: name,
+                        detailType: detailType,
+                        detail: -1, // to be set at the end
+                        color: color,
+                        visible: false,
+                        data: undefined,
+                    };
+                    visuals[visual.tag] = visual;
+                }
+            }
+            this.visuals = visuals;
+            this.updateVisualInfoDetails();
+        }
+        private updateVisualInfoDetails() {
+            let highDetail: number | undefined;
+            let lowDetail: number | undefined;
+            switch (this.params.view.name) {
+                case 'off':
+                    lowDetail = undefined;
+                    highDetail = undefined;
+                    break;
+                case 'select':
+                    lowDetail = this.params.view.params.baseDetail;
+                    highDetail = this.params.view.params.focusDetail;
+                    break;
+                case 'all':
+                    lowDetail = this.params.view.params.detail;
+                    highDetail = undefined;
+                    break;
+            }
+            for (const tag in this.visuals) {
+                const visual = this.visuals[tag];
+                const preferredDetail = (visual.detailType === 'high') ? highDetail : lowDetail;
+                if (preferredDetail !== undefined) {
+                    visual.detail = this.metadata!.getSufficientMeshDetail(visual.segmentId, preferredDetail);
+                }
+            }
+        }
+
+        private async enableVisuals(highDetailSegment?: number) {
+            for (const tag in this.visuals) {
+                const visual = this.visuals[tag];
+                const requiredDetailType = visual.segmentId === highDetailSegment ? 'high' : 'low';
+                if (visual.detailType === requiredDetailType) {
+                    visual.data = await this.getMeshData(visual);
+                    visual.visible = true;
+                } else {
+                    visual.visible = false;
+                }
+            }
+        }
+
+        private async disableVisuals() {
+            for (const tag in this.visuals) {
+                const visual = this.visuals[tag];
+                visual.visible = false;
+            }
+        }
+
+        /** Fetch data in current `visual.detail`, or return already fetched data (if available in the correct detail). */
+        private async getMeshData(visual: VisualInfo): Promise<MeshlistData> {
+            if (visual.data && visual.data.detail === visual.detail) {
+                // Do not recreate
+                return visual.data;
+            }
+            // TODO cache
+            const url = this.getMeshUrl(visual.segmentId, visual.detail);
+            const urlAsset = Asset.getUrlAsset(this.plugin.managers.asset, url);
+            const asset = await this.plugin.runTask(this.plugin.managers.asset.resolve(urlAsset, 'binary'));
+            const parsed = await this.plugin.runTask(CIF.parseBinary(asset.data));
+            if (parsed.isError) {
+                throw new Error(`Failed parsing CIF file from ${url}`);
+            }
+            const meshlistData = await MeshlistData.fromCIF(parsed.result, visual.segmentId, visual.segmentName, visual.detail);
+            meshlistData.ownerId = this.id;
+            // const bbox = MeshlistData.bbox(meshlistData);
+            // const bboxVolume = bbox ? MS.Box3D.volume(bbox) : 0.0;
+            // console.log(`BBox ${visual.segmentId}: ${Math.round(bboxVolume! / 1e6)} M`, bbox); // DEBUG
+            return meshlistData;
+        }
+
+        private async guessBackgroundSegments() {
+            const bboxes: { [segid: number]: Box3D } = {};
+            for (const tag in this.visuals) {
+                const visual = this.visuals[tag];
+                if (visual.detailType === 'low' && visual.data) {
+                    const bbox = MeshlistData.bbox(visual.data);
+                    if (bbox) {
+                        bboxes[visual.segmentId] = bbox;
+                    }
+                }
+            }
+            const totalBbox = MeshlistData.combineBBoxes(Object.values(bboxes));
+            const totalVolume = totalBbox ? Box3D.volume(totalBbox) : 0.0;
+            // console.log(`BBox total: ${Math.round(totalVolume! / 1e6)} M`, totalBbox); // DEBUG
+
+            const isBgSegment: { [segid: number]: boolean } = {};
+            for (const segid in bboxes) {
+                const bbox = bboxes[segid];
+                const bboxVolume = Box3D.volume(bbox);
+                isBgSegment[segid] = (bboxVolume > totalVolume * BACKGROUND_SEGMENT_VOLUME_THRESHOLD);
+                // console.log(`BBox ${segid}: ${Math.round(bboxVolume! / 1e6)} M, ${bboxVolume / totalVolume}`, bbox); // DEBUG
+            }
+            this.backgroundSegments = isBgSegment;
+        }
+
+        getDescription() {
+            return Params.ViewTypeChoice.prettyName(this.params.view.name);
+        }
+
+    }
+}
+

src/extensions/meshes/mesh-streaming/server-info.ts

@@ -0,0 +1,28 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+import { Choice } from '../../volumes-and-segmentations/helpers';
+
+
+export const DEFAULT_MESH_SERVER = 'http://localhost:9000/v2';
+
+
+export class MeshServerInfo extends PluginStateObject.Create<MeshServerInfo.Data>({ name: 'Volume Server', typeClass: 'Object' }) { }
+
+export namespace MeshServerInfo {
+    export const MeshSourceChoice = new Choice({ empiar: 'EMPIAR', emdb: 'EMDB' }, 'empiar');
+    export type MeshSource = Choice.Values<typeof MeshSourceChoice>;
+
+    export const Params = {
+        serverUrl: PD.Text(DEFAULT_MESH_SERVER),
+        source: MeshSourceChoice.PDSelect(),
+        entryId: PD.Text(''),
+    };
+    export type Data = PD.Values<typeof Params>;
+}

src/extensions/meshes/mesh-streaming/transformers.ts

@@ -0,0 +1,214 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { PluginContext } from '../../../mol-plugin/context';
+import { ShapeRepresentation } from '../../../mol-repr/shape/representation';
+import { StateAction, StateTransformer } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { shallowEqualObjects } from '../../../mol-util';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+import { BACKGROUND_OPACITY, FOREROUND_OPACITY, MeshlistData, VolsegTransform } from '../mesh-extension';
+import { MeshStreaming, NO_SEGMENT } from './behavior';
+import { MeshServerInfo } from './server-info';
+
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+
+export const MeshServerTransformer = VolsegTransform({
+    name: 'mesh-server-info',
+    from: PluginStateObject.Root,
+    to: MeshServerInfo,
+    params: MeshServerInfo.Params,
+})({
+    apply({ a, params }, plugin: PluginContext) { // `a` is the parent node, `params` are 2nd argument to To.apply()
+        params.serverUrl = params.serverUrl.replace(/\/*$/, ''); // trim trailing slash
+        const description: string = params.entryId;
+        return new MeshServerInfo({ ...params }, { label: 'Mesh Server', description: description });
+    }
+});
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+
+export const MeshStreamingTransformer = VolsegTransform({
+    name: 'mesh-streaming-from-server-info',
+    display: { name: 'Mesh Streaming' },
+    from: MeshServerInfo,
+    to: MeshStreaming,
+    params: a => MeshStreaming.Params.create(a!.data),
+})({
+    canAutoUpdate() { return true; },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Mesh Streaming', async ctx => {
+            const behavior = new MeshStreaming.Behavior(plugin, a.data, params);
+            await behavior.update(params);
+            return new MeshStreaming(behavior, { label: 'Mesh Streaming', description: behavior.getDescription() });
+        });
+    },
+    update({ a, b, oldParams, newParams }) {
+        return Task.create('Update Mesh Streaming', async ctx => {
+            if (a.data.source !== b.data.parentData.source || a.data.entryId !== b.data.parentData.entryId) {
+                return StateTransformer.UpdateResult.Recreate;
+            }
+            b.data.parentData = a.data;
+            await b.data.update(newParams);
+            b.description = b.data.getDescription();
+            return StateTransformer.UpdateResult.Updated;
+        });
+    }
+});
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+
+interface MeshVisualGroupData {
+    opacity: number,
+}
+
+// export type MeshVisualGroupTransformer = typeof MeshVisualGroupTransformer;
+export const MeshVisualGroupTransformer = VolsegTransform({
+    name: 'mesh-visual-group-from-streaming',
+    display: { name: 'Mesh Visuals for a Segment' },
+    from: MeshStreaming,
+    to: PluginStateObject.Group,
+    params: {
+        /** Shown on the node in GUI */
+        label: PD.Text('', { isHidden: true }),
+        /** Shown on the node in GUI (gray letters) */
+        description: PD.Text(''),
+        segmentId: PD.Numeric(NO_SEGMENT, {}, { isHidden: true }),
+        opacity: PD.Numeric(-1, { min: 0, max: 1, step: 0.01 }),
+    }
+})({
+    apply({ a, params }, plugin) {
+        trySetAutoOpacity(params, a);
+        return new PluginStateObject.Group({ opacity: params.opacity }, params);
+    },
+    update({ a, b, oldParams, newParams }, plugin) {
+        if (shallowEqualObjects(oldParams, newParams)) {
+            return StateTransformer.UpdateResult.Unchanged;
+        }
+        newParams.label ||= oldParams.label; // Protect against resetting params to invalid defaults
+        if (newParams.segmentId === NO_SEGMENT) newParams.segmentId = oldParams.segmentId; // Protect against resetting params to invalid defaults
+        trySetAutoOpacity(newParams, a);
+        b.label = newParams.label;
+        b.description = newParams.description;
+        (b.data as MeshVisualGroupData).opacity = newParams.opacity;
+        return StateTransformer.UpdateResult.Updated;
+    },
+    canAutoUpdate({ oldParams, newParams }, plugin) {
+        return newParams.description === oldParams.description;
+    },
+});
+
+function trySetAutoOpacity(params: StateTransformer.Params<typeof MeshVisualGroupTransformer>, parent: MeshStreaming) {
+    if (params.opacity === -1) {
+        const isBgSegment = parent.data.backgroundSegments[params.segmentId];
+        if (isBgSegment !== undefined) {
+            params.opacity = isBgSegment ? BACKGROUND_OPACITY : FOREROUND_OPACITY;
+        }
+    }
+}
+
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+
+export const MeshVisualTransformer = VolsegTransform({
+    name: 'mesh-visual-from-streaming',
+    display: { name: 'Mesh Visual from Streaming' },
+    from: MeshStreaming,
+    to: PluginStateObject.Shape.Representation3D,
+    params: {
+        /** Must be set to PluginStateObject reference to self */
+        ref: PD.Text('', { isHidden: true, isEssential: true }), // QUESTION what is isEssential
+        /** Identification of the mesh visual, e.g. 'low-2' */
+        tag: PD.Text('', { isHidden: true, isEssential: true }),
+        /** Opacity of the visual (not to be set directly, but controlled by the opacity of the parent Group, and by VisualInfo.visible) */
+        opacity: PD.Numeric(-1, { min: 0, max: 1, step: 0.01 }, { isHidden: true }),
+    }
+})({
+    apply({ a, params, spine }, plugin: PluginContext) {
+        return Task.create('Mesh Visual', async ctx => {
+            const visualInfo: MeshStreaming.VisualInfo = a.data.visuals![params.tag];
+            if (!visualInfo) throw new Error(`VisualInfo with tag '${params.tag}' is missing.`);
+            const groupData = spine.getAncestorOfType(PluginStateObject.Group)?.data as MeshVisualGroupData | undefined;
+            params.opacity = visualInfo.visible ? (groupData?.opacity ?? FOREROUND_OPACITY) : 0.0;
+            const props = PD.getDefaultValues(Mesh.Params);
+            props.flatShaded = true; // `flatShaded: true` is to see the real mesh vertices and triangles (default: false)
+            props.alpha = params.opacity;
+            const repr = ShapeRepresentation((ctx, meshlist: MeshlistData) => MeshlistData.getShape(meshlist, visualInfo.color), Mesh.Utils);
+            await repr.createOrUpdate(props, visualInfo.data ?? MeshlistData.empty()).runInContext(ctx);
+            return new PluginStateObject.Shape.Representation3D({ repr, sourceData: visualInfo.data }, { label: 'Mesh Visual', description: params.tag });
+        });
+    },
+    update({ a, b, oldParams, newParams, spine }, plugin: PluginContext) {
+        return Task.create('Update Mesh Visual', async ctx => {
+            newParams.ref ||= oldParams.ref; // Protect against resetting params to invalid defaults
+            newParams.tag ||= oldParams.tag; // Protect against resetting params to invalid defaults
+            const visualInfo: MeshStreaming.VisualInfo = a.data.visuals![newParams.tag];
+            if (!visualInfo) throw new Error(`VisualInfo with tag '${newParams.tag}' is missing.`);
+            const oldData = b.data.sourceData as MeshlistData | undefined;
+            if (visualInfo.data?.detail !== oldData?.detail) {
+                return StateTransformer.UpdateResult.Recreate;
+            }
+            const groupData = spine.getAncestorOfType(PluginStateObject.Group)?.data as MeshVisualGroupData | undefined;
+            const newOpacity = visualInfo.visible ? (groupData?.opacity ?? FOREROUND_OPACITY) : 0.0; // do not store to newParams directly, because oldParams and newParams might point to the same object!
+            if (newOpacity !== oldParams.opacity) {
+                newParams.opacity = newOpacity;
+                await b.data.repr.createOrUpdate({ alpha: newParams.opacity }).runInContext(ctx);
+                return StateTransformer.UpdateResult.Updated;
+            } else {
+                return StateTransformer.UpdateResult.Unchanged;
+            }
+        });
+    },
+    canAutoUpdate(params, globalCtx) {
+        return true;
+    },
+    dispose({ b, params }, plugin) {
+        b?.data.repr.destroy(); // QUESTION is this correct?
+    },
+});
+
+// // // // // // // // // // // // // // // // // // // // // // // //
+
+export const InitMeshStreaming = StateAction.build({
+    display: { name: 'Mesh Streaming' },
+    from: PluginStateObject.Root,
+    params: MeshServerInfo.Params,
+    isApplicable: (a, _, plugin: PluginContext) => true
+})(function (p, plugin: PluginContext) {
+    return Task.create('Mesh Streaming', async ctx => {
+        const { params } = p;
+        // p.ref
+        const serverNode = await plugin.build().to(p.ref).apply(MeshServerTransformer, params).commit();
+        // const serverNode = await plugin.build().toRoot().apply(MeshServerTransformer, params).commit();
+        const streamingNode = await plugin.build().to(serverNode).apply(MeshStreamingTransformer, {}).commit();
+        const visuals = streamingNode.data?.visuals ?? {};
+        const bgSegments = streamingNode.data?.backgroundSegments ?? {};
+
+        const segmentGroups: { [segid: number]: string } = {};
+        for (const tag in visuals) {
+            const segid = visuals[tag].segmentId;
+            if (!segmentGroups[segid]) {
+                let description = visuals[tag].segmentName;
+                if (bgSegments[segid]) description += ' (background)';
+                const group = await plugin.build().to(streamingNode).apply(MeshVisualGroupTransformer, { label: `Segment ${segid}`, description: description, segmentId: segid }, { state: { isCollapsed: true } }).commit();
+                segmentGroups[segid] = group.ref;
+            }
+        }
+        const visualsUpdate = plugin.build();
+        for (const tag in visuals) {
+            const ref = `${streamingNode.ref}-${tag}`;
+            const segid = visuals[tag].segmentId;
+            visualsUpdate.to(segmentGroups[segid]).apply(MeshVisualTransformer, { ref: ref, tag: tag }, { ref: ref }); // ref - hack to allow the node make itself invisible
+        }
+        await plugin.state.data.updateTree(visualsUpdate).runInContext(ctx); // QUESTION what is really the difference between this and `visualsUpdate.commit()`?
+    });
+});
+
+// TODO make available in GUI, in left panel or in right panel like Volume Streaming in src/mol-plugin-ui/structure/volume.tsx?

src/extensions/meshes/mesh-utils.ts

@@ -0,0 +1,340 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+/** Helper functions for manipulation with mesh data. */
+
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { CIF, CifFile } from '../../mol-io/reader/cif';
+import { Box3D } from '../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
+import { Grid } from '../../mol-model/volume';
+import { ColorNames } from '../../mol-util/color/names';
+import { TypedArray } from '../../mol-util/type-helpers';
+
+import { CIF_schema_mesh } from './mesh-cif-schema';
+
+
+type MeshModificationParams = {
+    scale?: [number, number, number],
+    shift?: [number, number, number],
+    matrix?: Mat4,
+    group?: number,
+    invertSides?: boolean
+};
+
+/** Modify mesh in-place */
+export function modify(m: Mesh, params: MeshModificationParams) {
+    if (params.scale !== undefined) {
+        const [qx, qy, qz] = params.scale;
+        const vertices = m.vertexBuffer.ref.value;
+        for (let i = 0; i < vertices.length; i += 3) {
+            vertices[i] *= qx;
+            vertices[i + 1] *= qy;
+            vertices[i + 2] *= qz;
+        }
+    }
+    if (params.shift !== undefined) {
+        const [dx, dy, dz] = params.shift;
+        const vertices = m.vertexBuffer.ref.value;
+        for (let i = 0; i < vertices.length; i += 3) {
+            vertices[i] += dx;
+            vertices[i + 1] += dy;
+            vertices[i + 2] += dz;
+        }
+    }
+    if (params.matrix !== undefined) {
+        const r = m.vertexBuffer.ref.value;
+        const matrix = params.matrix;
+        const size = 3 * m.vertexCount;
+        for (let i = 0; i < size; i += 3) {
+            Vec3.transformMat4Offset(r, r, matrix, i, i, 0);
+        }
+    }
+    if (params.group !== undefined) {
+        const groups = m.groupBuffer.ref.value;
+        for (let i = 0; i < groups.length; i++) {
+            groups[i] = params.group;
+        }
+    }
+    if (params.invertSides) {
+        const indices = m.indexBuffer.ref.value;
+        let tmp;
+        for (let i = 0; i < indices.length; i += 3) {
+            tmp = indices[i];
+            indices[i] = indices[i + 1];
+            indices[i + 1] = tmp;
+        }
+        const normals = m.normalBuffer.ref.value;
+        for (let i = 0; i < normals.length; i++) {
+            normals[i] *= -1;
+        }
+    }
+}
+
+/** Create a copy a mesh, possibly modified */
+export function copy(m: Mesh, modification?: MeshModificationParams): Mesh {
+    const nVertices = m.vertexCount;
+    const nTriangles = m.triangleCount;
+    const vertices = new Float32Array(m.vertexBuffer.ref.value);
+    const indices = new Uint32Array(m.indexBuffer.ref.value);
+    const normals = new Float32Array(m.normalBuffer.ref.value);
+    const groups = new Float32Array(m.groupBuffer.ref.value);
+    const result = Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
+    if (modification) {
+        modify(result, modification);
+    }
+    return result;
+}
+
+/** Join more meshes into one */
+export function concat(...meshes: Mesh[]): Mesh {
+    const nVertices = sum(meshes.map(m => m.vertexCount));
+    const nTriangles = sum(meshes.map(m => m.triangleCount));
+    const vertices = concatArrays(Float32Array, meshes.map(m => m.vertexBuffer.ref.value));
+    const normals = concatArrays(Float32Array, meshes.map(m => m.normalBuffer.ref.value));
+    const groups = concatArrays(Float32Array, meshes.map(m => m.groupBuffer.ref.value));
+    const newIndices = [];
+    let offset = 0;
+    for (const m of meshes) {
+        newIndices.push(m.indexBuffer.ref.value.map(i => i + offset));
+        offset += m.vertexCount;
+    }
+    const indices = concatArrays(Uint32Array, newIndices);
+    return Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
+}
+
+/** Return Mesh from CIF data and mesh IDs (group IDs).
+ * Assume the CIF contains coords in grid space,
+ * transform the output mesh to `space` */
+export async function meshFromCif(data: CifFile, invertSides: boolean | undefined = undefined, outSpace: 'grid' | 'fractional' | 'cartesian' = 'cartesian'): Promise<{ mesh: Mesh, meshIds: number[] }> {
+    const volumeInfoBlock = data.blocks.find(b => b.header === 'VOLUME_INFO');
+    const meshesBlock = data.blocks.find(b => b.header === 'MESHES');
+    if (!volumeInfoBlock || !meshesBlock) throw new Error('Missing VOLUME_INFO or MESHES block in mesh CIF file');
+    const volumeInfoCif = CIF.schema.densityServer(volumeInfoBlock);
+    const meshCif = CIF_schema_mesh(meshesBlock);
+
+    const nVertices = meshCif.mesh_vertex._rowCount;
+    const nTriangles = Math.floor(meshCif.mesh_triangle._rowCount / 3);
+
+    const mesh_id = meshCif.mesh.id.toArray();
+    const vertex_meshId = meshCif.mesh_vertex.mesh_id.toArray();
+    const x = meshCif.mesh_vertex.x.toArray();
+    const y = meshCif.mesh_vertex.y.toArray();
+    const z = meshCif.mesh_vertex.z.toArray();
+    const triangle_meshId = meshCif.mesh_triangle.mesh_id.toArray();
+    const triangle_vertexId = meshCif.mesh_triangle.vertex_id.toArray();
+
+    // Shift indices from within-mesh indices to overall indices
+    const indices = new Uint32Array(3 * nTriangles);
+    const offsets = offsetMap(vertex_meshId);
+    for (let i = 0; i < 3 * nTriangles; i++) {
+        const offset = offsets.get(triangle_meshId[i])!;
+        indices[i] = offset + triangle_vertexId[i];
+    }
+    const vertices = flattenCoords(x, y, z);
+    const normals = new Float32Array(3 * nVertices);
+    const groups = new Float32Array(vertex_meshId);
+    const mesh = Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
+
+    invertSides ??= isInverted(mesh);
+    if (invertSides) {
+        modify(mesh, { invertSides: true }); // Vertex orientation convention is opposite in Volseg API and in MolStar
+    }
+
+    if (outSpace === 'cartesian') {
+        const volume = await volumeFromDensityServerData(volumeInfoCif).run();
+        const gridToCartesian = Grid.getGridToCartesianTransform(volume.grid);
+        modify(mesh, { matrix: gridToCartesian });
+    } else if (outSpace === 'fractional') {
+        const gridSize = volumeInfoCif.volume_data_3d_info.sample_count.value(0);
+        const originFract = volumeInfoCif.volume_data_3d_info.origin.value(0);
+        const dimensionFract = volumeInfoCif.volume_data_3d_info.dimensions.value(0);
+        if (dimensionFract[0] !== 1 || dimensionFract[1] !== 1 || dimensionFract[2] !== 1) throw new Error(`Asserted the fractional dimensions are [1,1,1], but are actually [${dimensionFract}]`);
+        const scale: [number, number, number] = [1 / gridSize[0], 1 / gridSize[1], 1 / gridSize[2]];
+        modify(mesh, { scale: scale, shift: Array.from(originFract) as any });
+    }
+
+    Mesh.computeNormals(mesh); // normals only necessary if flatShaded==false
+
+    // const boxMesh = makeMeshFromBox([[0,0,0], [1,1,1]], 1);
+    // const gridSize = volumeInfoCif.volume_data_3d_info.sample_count.value(0); const boxMesh = makeMeshFromBox([[0,0,0], Array.from(gridSize)] as any, 1);
+    // const cellSize = volumeInfoCif.volume_data_3d_info.spacegroup_cell_size.value(0); const boxMesh = makeMeshFromBox([[0, 0, 0], Array.from(cellSize)] as any, 1);
+    // mesh = concat(mesh, boxMesh);  // debug
+    return { mesh: mesh, meshIds: Array.from(mesh_id) };
+}
+
+function isInverted(mesh: Mesh): boolean {
+    const vertices = mesh.vertexBuffer.ref.value;
+    const indices = mesh.indexBuffer.ref.value;
+    const center = meshCenter(mesh);
+    const center3 = Vec3.create(3 * center[0], 3 * center[1], 3 * center[2]);
+
+    let dirMetric = 0.0;
+    const [a, b, c, u, v, normal, radius] = [Vec3(), Vec3(), Vec3(), Vec3(), Vec3(), Vec3(), Vec3()];
+    for (let i = 0; i < indices.length; i += 3) {
+        Vec3.fromArray(a, vertices, 3 * indices[i]);
+        Vec3.fromArray(b, vertices, 3 * indices[i + 1]);
+        Vec3.fromArray(c, vertices, 3 * indices[i + 2]);
+        Vec3.sub(u, b, a);
+        Vec3.sub(v, c, b);
+        Vec3.cross(normal, u, v); // direction of the surface
+        Vec3.add(radius, a, b);
+        Vec3.add(radius, radius, c);
+        Vec3.sub(radius, radius, center3); // direction center -> this triangle
+        dirMetric += Vec3.dot(radius, normal);
+    }
+    return dirMetric < 0;
+}
+
+function meshCenter(mesh: Mesh) {
+    const vertices = mesh.vertexBuffer.ref.value;
+    const n = vertices.length;
+    let x = 0.0;
+    let y = 0.0;
+    let z = 0.0;
+    for (let i = 0; i < vertices.length; i += 3) {
+        x += vertices[i];
+        y += vertices[i + 1];
+        z += vertices[i + 2];
+    }
+    return Vec3.create(x / n, y / n, z / n);
+}
+
+function flattenCoords(x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number>): Float32Array {
+    const n = x.length;
+    const out = new Float32Array(3 * n);
+    for (let i = 0; i < n; i++) {
+        out[3 * i] = x[i];
+        out[3 * i + 1] = y[i];
+        out[3 * i + 2] = z[i];
+    }
+    return out;
+}
+
+/** Get mapping of unique values to the position of their first occurrence */
+function offsetMap(values: ArrayLike<number>) {
+    const result = new Map<number, number>();
+    for (let i = 0; i < values.length; i++) {
+        if (!result.has(values[i])) {
+            result.set(values[i], i);
+        }
+    }
+    return result;
+}
+
+/** Return bounding box */
+export function bbox(mesh: Mesh): Box3D | null { // Is there no function for this?
+    const nVertices = mesh.vertexCount;
+    const coords = mesh.vertexBuffer.ref.value;
+    if (nVertices === 0) {
+        return null;
+    }
+    let minX = coords[0], minY = coords[1], minZ = coords[2];
+    let maxX = minX, maxY = minY, maxZ = minZ;
+    for (let i = 0; i < 3 * nVertices; i += 3) {
+        const x = coords[i], y = coords[i + 1], z = coords[i + 2];
+        if (x < minX) minX = x;
+        if (y < minY) minY = y;
+        if (z < minZ) minZ = z;
+        if (x > maxX) maxX = x;
+        if (y > maxY) maxY = y;
+        if (z > maxZ) maxZ = z;
+    }
+    return Box3D.create(Vec3.create(minX, minY, minZ), Vec3.create(maxX, maxY, maxZ));
+}
+
+/** Example mesh - 1 triangle */
+export function fakeFakeMesh1(): Mesh {
+    const nVertices = 3;
+    const nTriangles = 1;
+    const vertices = new Float32Array([0, 0, 0, 1, 0, 0, 0, 1, 0]);
+    const indices = new Uint32Array([0, 1, 2]);
+    const normals = new Float32Array([0, 0, 1]);
+    const groups = new Float32Array([0]);
+    return Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
+}
+
+/** Example mesh - irregular tetrahedron */
+export function fakeMesh4(): Mesh {
+    const nVertices = 4;
+    const nTriangles = 4;
+    const vertices = new Float32Array([0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1]);
+    const indices = new Uint32Array([0, 2, 1, 0, 1, 3, 1, 2, 3, 2, 0, 3]);
+    const normals = new Float32Array([-1, -1, -1, 1, 0, 0, 0, 1, 0, 0, 0, 1]);
+    const groups = new Float32Array([0, 1, 2, 3]);
+    return Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
+}
+
+/** Return a box-shaped mesh */
+export function meshFromBox(box: [[number, number, number], [number, number, number]], group: number = 0) {
+    const [[x0, y0, z0], [x1, y1, z1]] = box;
+    const vertices = new Float32Array([
+        x0, y0, z0,
+        x1, y0, z0,
+        x0, y1, z0,
+        x1, y1, z0,
+        x0, y0, z1,
+        x1, y0, z1,
+        x0, y1, z1,
+        x1, y1, z1,
+    ]);
+    const indices = new Uint32Array([
+        2, 1, 0, 1, 2, 3,
+        1, 4, 0, 4, 1, 5,
+        3, 5, 1, 5, 3, 7,
+        2, 7, 3, 7, 2, 6,
+        0, 6, 2, 6, 0, 4,
+        4, 7, 6, 7, 4, 5,
+    ]);
+    const groups = new Float32Array([group, group, group, group, group, group, group, group]);
+    const normals = new Float32Array(8);
+    const mesh = Mesh.create(vertices, indices, normals, groups, 8, 12);
+    Mesh.computeNormals(mesh); // normals only necessary if flatShaded==false
+    return mesh;
+}
+
+function sum(array: number[]): number {
+    return array.reduce((a, b) => a + b, 0);
+}
+
+function concatArrays<T extends TypedArray>(t: new (len: number) => T, arrays: T[]): T {
+    const totalLength = arrays.map(a => a.length).reduce((a, b) => a + b, 0);
+    const result: T = new t(totalLength);
+    let offset = 0;
+    for (const array of arrays) {
+        result.set(array, offset);
+        offset += array.length;
+    }
+    return result;
+}
+
+/** Generate random colors (in a cycle) */
+export const ColorGenerator = function* () {
+    const colors = shuffleArray(Object.values(ColorNames));
+    let i = 0;
+    while (true) {
+        yield colors[i];
+        i++;
+        if (i >= colors.length) i = 0;
+    }
+}();
+function shuffleArray<T>(array: T[]): T[] {
+    // Stealed from https://www.w3docs.com/snippets/javascript/how-to-randomize-shuffle-a-javascript-array.html
+    let curId = array.length;
+    // There remain elements to shuffle
+    while (0 !== curId) {
+        // Pick a remaining element
+        const randId = Math.floor(Math.random() * curId);
+        curId -= 1;
+        // Swap it with the current element.
+        const tmp = array[curId];
+        array[curId] = array[randId];
+        array[randId] = tmp;
+    }
+    return array;
+}
+

src/extensions/model-archive/quality-assessment/prop.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -14,6 +15,7 @@ import { CustomPropSymbol } from '../../../mol-script/language/symbol';
 import { Type } from '../../../mol-script/language/type';
 import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+import { AtomicIndex } from '../../../mol-model/structure/model/properties/atomic';
 
 export { QualityAssessment };
 
@@ -71,14 +73,28 @@ namespace QualityAssessment {
             localNames.set(ma_qa_metric.id.value(i), name);
         }
 
+        const residueKey: AtomicIndex.ResidueLabelKey = {
+            label_entity_id: '',
+            label_asym_id: '',
+            label_seq_id: 0,
+            pdbx_PDB_ins_code: undefined,
+        };
+
         for (let i = 0, il = ma_qa_metric_local._rowCount; i < il; i++) {
             if (model_id.value(i) !== model.modelNum) continue;
 
             const labelAsymId = label_asym_id.value(i);
             const entityIndex = index.findEntity(labelAsymId);
-            const rI = index.findResidue(model.entities.data.id.value(entityIndex), labelAsymId, label_seq_id.value(i));
-            const name = localNames.get(metric_id.value(i))!;
-            localMetrics.get(name)!.set(rI, metric_value.value(i));
+
+            residueKey.label_entity_id = model.entities.data.id.value(entityIndex);
+            residueKey.label_asym_id = labelAsymId;
+            residueKey.label_seq_id = label_seq_id.value(i);
+
+            const rI = index.findResidueLabel(residueKey);
+            if (rI >= 0) {
+                const name = localNames.get(metric_id.value(i))!;
+                localMetrics.get(name)!.set(rI, metric_value.value(i));
+            }
         }
 
         return {

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

@@ -29,7 +29,7 @@ export { StructureQualityReport };
 type StructureQualityReport = PropertyWrapper<{
     issues: IndexedCustomProperty.Residue<string[]>,
     issueTypes: string[]
-}| undefined>
+} | undefined>
 
 namespace StructureQualityReport {
     export const DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/';

src/extensions/rcsb/graphql/types.ts

@@ -4,7 +4,7 @@ export type InputMaybe<T> = Maybe<T>;
 export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
 export type MakeOptional<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]?: Maybe<T[SubKey]> };
 export type MakeMaybe<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]: Maybe<T[SubKey]> };
-// Generated on 2022-08-20T16:36:05-07:00
+// Generated on 2023-01-15T10:00:07-08:00
 
 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -343,6 +343,14 @@ export type Citation = {
    *
    */
   readonly journal_abbrev?: Maybe<Scalars['String']>;
+  /**
+   * Full name of the cited journal; relevant for journal articles.
+   *
+   * Examples:
+   * Journal of Molecular Biology
+   *
+   */
+  readonly journal_full?: Maybe<Scalars['String']>;
   /**
    * The American Society for Testing and Materials (ASTM) code
    *  assigned to the journal cited (also referred to as the CODEN
@@ -550,6 +558,7 @@ export type CoreBranchedEntityInstance = {
   readonly rcsb_id: Scalars['String'];
   readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
   readonly rcsb_ligand_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbLigandNeighbors>>>;
+  readonly struct_asym?: Maybe<StructAsym>;
 };
 
 export type CoreChemComp = {
@@ -661,6 +670,7 @@ export type CoreEntry = {
   readonly exptl?: Maybe<ReadonlyArray<Maybe<Exptl>>>;
   readonly exptl_crystal?: Maybe<ReadonlyArray<Maybe<ExptlCrystal>>>;
   readonly exptl_crystal_grow?: Maybe<ReadonlyArray<Maybe<ExptlCrystalGrow>>>;
+  readonly ma_data?: Maybe<ReadonlyArray<Maybe<MaData>>>;
   /** Get all non-polymer (non-solvent) entities for this PDB entry. */
   readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
   readonly pdbx_SG_project?: Maybe<ReadonlyArray<Maybe<PdbxSgProject>>>;
@@ -701,6 +711,7 @@ export type CoreEntry = {
   /** The list of content types associated with this entry. */
   readonly rcsb_associated_holdings?: Maybe<CurrentEntry>;
   readonly rcsb_binding_affinity?: Maybe<ReadonlyArray<Maybe<RcsbBindingAffinity>>>;
+  readonly rcsb_comp_model_provenance?: Maybe<RcsbCompModelProvenance>;
   readonly rcsb_entry_container_identifiers: RcsbEntryContainerIdentifiers;
   readonly rcsb_entry_group_membership?: Maybe<ReadonlyArray<Maybe<RcsbEntryGroupMembership>>>;
   readonly rcsb_entry_info: RcsbEntryInfo;
@@ -713,6 +724,7 @@ export type CoreEntry = {
    *
    */
   readonly rcsb_id: Scalars['String'];
+  readonly rcsb_ma_qa_metric_global?: Maybe<ReadonlyArray<Maybe<RcsbMaQaMetricGlobal>>>;
   readonly rcsb_primary_citation?: Maybe<RcsbPrimaryCitation>;
   readonly refine?: Maybe<ReadonlyArray<Maybe<Refine>>>;
   readonly refine_analyze?: Maybe<ReadonlyArray<Maybe<RefineAnalyze>>>;
@@ -786,6 +798,7 @@ export type CoreNonpolymerEntityInstance = {
   readonly rcsb_nonpolymer_instance_validation_score?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceValidationScore>>>;
   readonly rcsb_nonpolymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerStructConn>>>;
   readonly rcsb_target_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbTargetNeighbors>>>;
+  readonly struct_asym?: Maybe<StructAsym>;
 };
 
 export type CorePfam = {
@@ -919,6 +932,7 @@ export type CorePolymerEntityInstance = {
   readonly rcsb_polymer_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeature>>>;
   readonly rcsb_polymer_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureSummary>>>;
   readonly rcsb_polymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbPolymerStructConn>>>;
+  readonly struct_asym?: Maybe<StructAsym>;
 };
 
 export type CorePubmed = {
@@ -1284,9 +1298,9 @@ export type Em2dCrystalEntity = {
   readonly id: Scalars['String'];
   /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
   readonly image_processing_id: Scalars['String'];
-  /** Unit-cell length a in Angstroms. */
+  /** Unit-cell length a in angstroms. */
   readonly length_a?: Maybe<Scalars['Float']>;
-  /** Unit-cell length b in Angstroms. */
+  /** Unit-cell length b in angstroms. */
   readonly length_b?: Maybe<Scalars['Float']>;
   /** Thickness of 2D crystal */
   readonly length_c?: Maybe<Scalars['Float']>;
@@ -1317,11 +1331,11 @@ export type Em3dCrystalEntity = {
   readonly id: Scalars['String'];
   /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
   readonly image_processing_id: Scalars['String'];
-  /** Unit-cell length a in Angstroms. */
+  /** Unit-cell length a in angstroms. */
   readonly length_a?: Maybe<Scalars['Float']>;
-  /** Unit-cell length b in Angstroms. */
+  /** Unit-cell length b in angstroms. */
   readonly length_b?: Maybe<Scalars['Float']>;
-  /** Unit-cell length c in Angstroms. */
+  /** Unit-cell length c in angstroms. */
   readonly length_c?: Maybe<Scalars['Float']>;
   /**
    * Space group name.
@@ -1482,7 +1496,7 @@ export type Em3dReconstruction = {
    */
   readonly refinement_type?: Maybe<Scalars['String']>;
   /**
-   * The final resolution (in Angstroms)of the 3D reconstruction.
+   * The final resolution (in angstroms)of the 3D reconstruction.
    *
    * Examples:
    * null, null
@@ -1558,7 +1572,7 @@ export type EmDiffractionShell = {
    */
   readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
   /**
-   * High resolution limit for this shell (Angstroms)
+   * High resolution limit for this shell (angstroms)
    *
    * Examples:
    * null
@@ -1568,7 +1582,7 @@ export type EmDiffractionShell = {
   /** Unique identifier for the category em_diffraction_shell */
   readonly id: Scalars['String'];
   /**
-   * Low resolution limit for this shell (Angstroms)
+   * Low resolution limit for this shell (angstroms)
    *
    * Examples:
    * null
@@ -1614,7 +1628,7 @@ export type EmDiffractionStats = {
    */
   readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
   /**
-   * High resolution limit of the structure factor data, in Angstroms
+   * High resolution limit of the structure factor data, in angstroms
    *
    * Examples:
    * null
@@ -1998,12 +2012,12 @@ export type EmImaging = {
   /** The magnification indicated by the microscope readout. */
   readonly nominal_magnification?: Maybe<Scalars['Int']>;
   /**
-   * The specimen temperature maximum (degrees Kelvin) for the duration
+   * The specimen temperature maximum (kelvin) for the duration
    *  of imaging.
    */
   readonly recording_temperature_maximum?: Maybe<Scalars['Float']>;
   /**
-   * The specimen temperature minimum (degrees Kelvin) for the duration
+   * The specimen temperature minimum (kelvin) for the duration
    *  of imaging.
    */
   readonly recording_temperature_minimum?: Maybe<Scalars['Float']>;
@@ -2028,7 +2042,7 @@ export type EmImaging = {
   /** Foreign key to the EM_SPECIMEN category */
   readonly specimen_id?: Maybe<Scalars['String']>;
   /**
-   * The mean specimen stage temperature (degrees Kelvin) during imaging
+   * The mean specimen stage temperature (in kelvin) during imaging
    *  in the microscope.
    */
   readonly temperature?: Maybe<Scalars['Float']>;
@@ -2215,7 +2229,7 @@ export type EmStaining = {
 };
 
 export type EmVitrification = {
-  /** The temperature (in degrees Kelvin) of the sample just prior to vitrification. */
+  /** The temperature (in kelvin) of the sample just prior to vitrification. */
   readonly chamber_temperature?: Maybe<Scalars['Float']>;
   /**
    * This is the name of the cryogen.
@@ -2259,7 +2273,7 @@ export type EmVitrification = {
   /** This data item is a pointer to _em_specimen.id */
   readonly specimen_id: Scalars['String'];
   /**
-   * The vitrification temperature (in degrees Kelvin), e.g.,
+   * The vitrification temperature (in kelvin), e.g.,
    *   temperature of the plunge instrument cryogen bath.
    */
   readonly temp?: Maybe<Scalars['Float']>;
@@ -2364,6 +2378,14 @@ export type EntityPoly = {
    *
    */
   readonly pdbx_seq_one_letter_code_can?: Maybe<Scalars['String']>;
+  /**
+   * Evidence for the assignment of the polymer sequence.
+   *
+   * Allowable values:
+   * depositor provided, derived from coordinates
+   *
+   */
+  readonly pdbx_sequence_evidence_code?: Maybe<Scalars['String']>;
   /**
    * The PDB strand/chain id(s) corresponding to this polymer entity.
    *
@@ -3005,6 +3027,8 @@ export type Entry = {
    *  identifier.
    */
   readonly id: Scalars['String'];
+  /** An identifier for the model collection associated with the entry. */
+  readonly ma_collection_id?: Maybe<Scalars['String']>;
 };
 
 export type Exptl = {
@@ -3263,6 +3287,29 @@ export type InterfacePartnerFeatureFeaturePositions = {
   readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
 };
 
+export type MaData = {
+  /**
+   * The type of data held in the dataset.
+   *
+   * Allowable values:
+   * coevolution MSA, input structure, model coordinates, other, polymeric template library, spatial restraints, target, target-template alignment, template structure
+   *
+   */
+  readonly content_type?: Maybe<Scalars['String']>;
+  /** Details for other content types. */
+  readonly content_type_other_details?: Maybe<Scalars['String']>;
+  /** A unique identifier for the data. */
+  readonly id: Scalars['Int'];
+  /**
+   * An author-given name for the content held in the dataset.
+   *
+   * Examples:
+   * NMR NOE Distances, Target Template Alignment, Coevolution Data
+   *
+   */
+  readonly name?: Maybe<Scalars['String']>;
+};
+
 export type MethodDetails = {
   /** A description of special aspects of the clustering process */
   readonly description?: Maybe<Scalars['String']>;
@@ -4199,7 +4246,7 @@ export type PdbxNmrExptlSampleConditions = {
    */
   readonly pressure_units?: Maybe<Scalars['String']>;
   /**
-   * The temperature (in Kelvin) at which NMR data were
+   * The temperature (in kelvin) at which NMR data were
    *  collected.
    */
   readonly temperature?: Maybe<Scalars['String']>;
@@ -4453,7 +4500,7 @@ export type PdbxPrdAudit = {
    * An identifier for the wwPDB site creating or modifying the molecule.
    *
    * Allowable values:
-   * BMRB, PDBC, PDBJ, PDBe, RCSB
+   * BMRB, PDBC, PDBE, PDBJ, RCSB
    *
    */
   readonly processing_site?: Maybe<Scalars['String']>;
@@ -6817,7 +6864,7 @@ export type Query = {
   readonly assemblies?: Maybe<ReadonlyArray<Maybe<CoreAssembly>>>;
   /** Get an assembly given the PDB ID and ASSEMBLY ID. Here ASSEMBLY ID is '1', '2', '3', etc. or 'deposited' for deposited coordinates. */
   readonly assembly?: Maybe<CoreAssembly>;
-  /** Get a list of PDB branched entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
+  /** Get a list of PDB branched entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. Note that the ENTRY ID part must be upper case. */
   readonly branched_entities?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntity>>>;
   /** Get a PDB branched entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
   readonly branched_entity?: Maybe<CoreBranchedEntity>;
@@ -6841,9 +6888,9 @@ export type Query = {
   readonly group_provenance?: Maybe<GroupProvenance>;
   /** Get a pairwise polymeric interface given the PDB ID, ASSEMBLY ID and INTERFACE ID. */
   readonly interface?: Maybe<CoreInterface>;
-  /** Get a list of pairwise polymeric interfaces given a list of INTERFACE IDs. Here INTERFACE ID is a compound identifier that includes entry_id, assembly_id and interface_id e.g. 1XXX-1.1. */
+  /** Get a list of pairwise polymeric interfaces given a list of INTERFACE IDs. Here INTERFACE ID is a compound identifier that includes entry_id, assembly_id and interface_id e.g. 1XXX-1.1. Note that the ENTRY ID part must be upper case. */
   readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
-  /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
+  /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. Note that the ENTRY ID part must be upper case. */
   readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
   /** Get a PDB non-polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
   readonly nonpolymer_entity?: Maybe<CoreNonpolymerEntity>;
@@ -6851,7 +6898,7 @@ export type Query = {
   readonly nonpolymer_entity_instance?: Maybe<CoreNonpolymerEntityInstance>;
   /** Get a list of PDB non-polymer entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
   readonly nonpolymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntityInstance>>>;
-  /** Get a list of PDB polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
+  /** Get a list of PDB polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. Note that the ENTRY ID part must be upper case. */
   readonly polymer_entities?: Maybe<ReadonlyArray<Maybe<CorePolymerEntity>>>;
   /** Get a PDB polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
   readonly polymer_entity?: Maybe<CorePolymerEntity>;
@@ -8421,6 +8468,31 @@ export type RcsbClusterMembership = {
   readonly identity?: Maybe<Scalars['Int']>;
 };
 
+export type RcsbCompModelProvenance = {
+  /**
+   * Entry identifier corresponding to the computed structure model.
+   *
+   * Examples:
+   * AF-P60325-F1, ma-bak-cepc-0019
+   *
+   */
+  readonly entry_id: Scalars['String'];
+  /**
+   * Source database for the computed structure model.
+   *
+   * Allowable values:
+   * AlphaFoldDB, ModelArchive
+   *
+   */
+  readonly source_db?: Maybe<Scalars['String']>;
+  /** Source filename for the computed structure model. */
+  readonly source_filename?: Maybe<Scalars['String']>;
+  /** Source URL for computed structure model predicted aligned error (PAE) json file. */
+  readonly source_pae_url?: Maybe<Scalars['String']>;
+  /** Source URL for computed structure model file. */
+  readonly source_url?: Maybe<Scalars['String']>;
+};
+
 export type RcsbEntityHostOrganism = {
   /**
    * The beginning polymer sequence position for the polymer section corresponding
@@ -8657,7 +8729,7 @@ export type RcsbEntitySourceOrganism = {
    * A code indicating the provenance of the source organism details for the entity
    *
    * Allowable values:
-   * PDB Primary Data
+   * PDB Primary Data, UniProt
    *
    */
   readonly provenance_source?: Maybe<Scalars['String']>;
@@ -8731,7 +8803,7 @@ export type RcsbEntryContainerIdentifiers = {
    * Entry identifier for the container.
    *
    * Examples:
-   * 1KIP, 4HHB
+   * 4HHB, AF_AFP60325F1, MA_MABAKCEPC0019
    *
    */
   readonly entry_id: Scalars['String'];
@@ -8879,6 +8951,15 @@ export type RcsbEntryInfo = {
    *
    */
   readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
+  /**
+   * This data item identifies secondary structure
+   *  features of nucleic acids in the entry.
+   *
+   * Allowable values:
+   * a-form double helix, b-form double helix, bulge loop, double helix, four-way junction, hairpin loop, internal loop, mismatched base pair, other right-handed double helix, parallel strands, quadruple helix, tetraloop, three-way junction, triple helix, two-way junction, z-form double helix
+   *
+   */
+  readonly ndb_struct_conf_na_feature_combined?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
   /** Bound nonpolymer components in this entry. */
   readonly nonpolymer_bound_components?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
   /** The number of distinct non-polymer entities in the structure entry exclusive of solvent. */
@@ -8955,6 +9036,21 @@ export type RcsbEntryInfo = {
   readonly software_programs_combined?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
   /** The number of distinct solvent entities per deposited structure model. */
   readonly solvent_entity_count?: Maybe<Scalars['Int']>;
+  /**
+   * Indicates if the structure was determined using experimental or computational methods.
+   *
+   * Allowable values:
+   * computational, experimental
+   *
+   */
+  readonly structure_determination_methodology: Scalars['String'];
+  /**
+   * Indicates the priority of the value in _rcsb_entry_info.structure_determination_methodology.
+   *  The lower the number the higher the priority.
+   *  Priority values for "experimental" structures is currently set to 10 and
+   *  the values for "computational" structures is set to 100.
+   */
+  readonly structure_determination_methodology_priority?: Maybe<Scalars['Int']>;
 };
 
 export type RcsbEntryInfoDiffrnResolutionHigh = {
@@ -9294,6 +9390,49 @@ export type RcsbLigandNeighbors = {
   readonly seq_id?: Maybe<Scalars['Int']>;
 };
 
+export type RcsbMaQaMetricGlobal = {
+  readonly ma_qa_metric_global?: Maybe<ReadonlyArray<Maybe<RcsbMaQaMetricGlobalMaQaMetricGlobal>>>;
+  /** The model identifier. */
+  readonly model_id: Scalars['Int'];
+};
+
+export type RcsbMaQaMetricGlobalMaQaMetricGlobal = {
+  /**
+   * Description of the global QA metric.
+   *
+   * Examples:
+   * confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]
+   *
+   */
+  readonly description?: Maybe<Scalars['String']>;
+  /**
+   * Name of the global QA metric.
+   *
+   * Examples:
+   * pLDDT
+   *
+   */
+  readonly name: Scalars['String'];
+  /**
+   * The type of global QA metric.
+   *
+   * Allowable values:
+   * PAE, contact probability, distance, energy, ipTM, normalized score, other, pLDDT, pLDDT all-atom, pLDDT all-atom in [0,1], pLDDT in [0,1], pTM, zscore
+   *
+   */
+  readonly type: Scalars['String'];
+  /** Details for other type of global QA metric. */
+  readonly type_other_details?: Maybe<Scalars['String']>;
+  /**
+   * Value of the global QA metric.
+   *
+   * Examples:
+   * null
+   *
+   */
+  readonly value: Scalars['Float'];
+};
+
 export type RcsbMembraneLineage = {
   /** Hierarchy depth. */
   readonly depth?: Maybe<Scalars['Int']>;
@@ -10332,7 +10471,7 @@ export type RcsbPolymerEntityContainerIdentifiersReferenceSequenceIdentifiers =
    * Source of the reference database assignment
    *
    * Allowable values:
-   * PDB, RCSB, SIFTS
+   * PDB, RCSB, SIFTS, UniProt
    *
    */
   readonly provenance_source?: Maybe<Scalars['String']>;
@@ -10737,7 +10876,7 @@ export type RcsbPolymerInstanceFeature = {
    * A type or category of the feature.
    *
    * Allowable values:
-   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ, ASA
+   * ANGLE_OUTLIER, BEND, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, HELX_LH_PP_P, HELX_RH_3T_P, HELX_RH_AL_P, HELX_RH_PI_P, MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY, MA_QA_METRIC_LOCAL_TYPE_DISTANCE, MA_QA_METRIC_LOCAL_TYPE_ENERGY, MA_QA_METRIC_LOCAL_TYPE_IPTM, MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE, MA_QA_METRIC_LOCAL_TYPE_OTHER, MA_QA_METRIC_LOCAL_TYPE_PAE, MA_QA_METRIC_LOCAL_TYPE_PLDDT, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1], MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1], MA_QA_METRIC_LOCAL_TYPE_PTM, MA_QA_METRIC_LOCAL_TYPE_ZSCORE, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, STRN, TURN_TY1_P, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ, ASA
    *
    */
   readonly type?: Maybe<Scalars['String']>;
@@ -10748,7 +10887,7 @@ export type RcsbPolymerInstanceFeatureAdditionalProperties = {
    * The additional property name.
    *
    * Allowable values:
-   * CATH_DOMAIN_ID, CATH_NAME, ECOD_DOMAIN_ID, ECOD_FAMILY_NAME, OMEGA_ANGLE, PARTNER_ASYM_ID, PARTNER_BOND_DISTANCE, PARTNER_COMP_ID, SCOP2_DOMAIN_ID, SCOP2_FAMILY_ID, SCOP2_FAMILY_NAME, SCOP2_SUPERFAMILY_ID, SCOP2_SUPERFAMILY_NAME, SCOP_DOMAIN_ID, SCOP_NAME, SCOP_SUN_ID, SHEET_SENSE
+   * CATH_DOMAIN_ID, CATH_NAME, ECOD_DOMAIN_ID, ECOD_FAMILY_NAME, MODELCIF_MODEL_ID, OMEGA_ANGLE, PARTNER_ASYM_ID, PARTNER_BOND_DISTANCE, PARTNER_COMP_ID, SCOP2_DOMAIN_ID, SCOP2_FAMILY_ID, SCOP2_FAMILY_NAME, SCOP2_SUPERFAMILY_ID, SCOP2_SUPERFAMILY_NAME, SCOP_DOMAIN_ID, SCOP_NAME, SCOP_SUN_ID, SHEET_SENSE
    *
    */
   readonly name?: Maybe<Scalars['String']>;
@@ -10818,7 +10957,7 @@ export type RcsbPolymerInstanceFeatureSummary = {
    * Type or category of the feature.
    *
    * Allowable values:
-   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SAbDab Antibody Heavy Chain Subclass, SAbDab Antibody Light Chain Subclass, SAbDab Antibody Light Chain Type, SCOP, SCOP2 Family, SCOP2 Superfamily, SCOP2B Superfamily, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+   * ANGLE_OUTLIER, BEND, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, HELX_LH_PP_P, HELX_RH_3T_P, HELX_RH_AL_P, HELX_RH_PI_P, MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY, MA_QA_METRIC_LOCAL_TYPE_DISTANCE, MA_QA_METRIC_LOCAL_TYPE_ENERGY, MA_QA_METRIC_LOCAL_TYPE_IPTM, MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE, MA_QA_METRIC_LOCAL_TYPE_OTHER, MA_QA_METRIC_LOCAL_TYPE_PAE, MA_QA_METRIC_LOCAL_TYPE_PLDDT, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1], MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1], MA_QA_METRIC_LOCAL_TYPE_PTM, MA_QA_METRIC_LOCAL_TYPE_ZSCORE, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, STRN, TURN_TY1_P, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
    *
    */
   readonly type?: Maybe<Scalars['String']>;
@@ -13377,6 +13516,11 @@ export type ReflnsShell = {
 };
 
 export type Software = {
+  /**
+   * This data item is a pointer to _citation.id in the CITATION
+   *  category.
+   */
+  readonly citation_id?: Maybe<Scalars['String']>;
   /**
    * The classification of the program according to its
    *  major function.
@@ -13527,6 +13671,37 @@ export type Struct = {
   readonly title?: Maybe<Scalars['String']>;
 };
 
+export type StructAsym = {
+  /**
+   * This data item is a pointer to _atom_site.pdbx_PDB_strand_id the
+   *  ATOM_SITE category.
+   *
+   * Examples:
+   * 1ABC
+   *
+   */
+  readonly pdbx_PDB_id?: Maybe<Scalars['String']>;
+  /**
+   * This data item is a pointer to _atom_site.ndb_alias_strand_id the
+   *  ATOM_SITE category.
+   */
+  readonly pdbx_alt_id?: Maybe<Scalars['String']>;
+  /**
+   * This data item gives the order of the structural elements in the
+   *  ATOM_SITE category.
+   */
+  readonly pdbx_order?: Maybe<Scalars['Int']>;
+  /**
+   * This data item describes the general type of the structural elements
+   *  in the ATOM_SITE category.
+   *
+   * Allowable values:
+   * ATOMN, ATOMP, ATOMS, HETAC, HETAD, HETAI, HETAIN, HETAS, HETIC
+   *
+   */
+  readonly pdbx_type?: Maybe<Scalars['String']>;
+};
+
 export type StructKeywords = {
   /**
    * Terms characterizing the macromolecular structure.

src/extensions/volumes-and-segmentations/entry-meshes.ts

@@ -0,0 +1,103 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { CreateGroup } from '../../mol-plugin-state/transforms/misc';
+import { ShapeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { setSubtreeVisibility } from '../../mol-plugin/behavior/static/state';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+
+import { BACKGROUND_SEGMENT_VOLUME_THRESHOLD } from '../meshes/mesh-streaming/behavior';
+import { createMeshFromUrl } from '../meshes/mesh-extension';
+
+import { Segment } from './volseg-api/data';
+import { VolsegEntryData } from './entry-root';
+
+
+const DEFAULT_MESH_DETAIL: number | null = 5; // null means worst
+
+
+export class VolsegMeshSegmentationData {
+    private entryData: VolsegEntryData;
+
+    constructor(rootData: VolsegEntryData) {
+        this.entryData = rootData;
+    }
+
+    async loadSegmentation() {
+        const hasMeshes = this.entryData.metadata.meshSegmentIds.length > 0;
+        if (hasMeshes) {
+            await this.showSegments(this.entryData.metadata.allSegmentIds);
+        }
+    }
+
+    updateOpacity(opacity: number) {
+        const visuals = this.entryData.findNodesByTags('mesh-segment-visual');
+        const update = this.entryData.newUpdate();
+        for (const visual of visuals) {
+            update.to(visual).update(ShapeRepresentation3D, p => { (p as any).alpha = opacity; });
+        }
+        return update.commit();
+    }
+
+    async highlightSegment(segment: Segment) {
+        const visuals = this.entryData.findNodesByTags('mesh-segment-visual', `segment-${segment.id}`);
+        for (const visual of visuals) {
+            await PluginCommands.Interactivity.Object.Highlight(this.entryData.plugin, { state: this.entryData.plugin.state.data, ref: visual.transform.ref });
+        }
+    }
+
+    async selectSegment(segment?: number) {
+        if (segment === undefined || segment < 0) return;
+        const visuals = this.entryData.findNodesByTags('mesh-segment-visual', `segment-${segment}`);
+        const reprNode: PluginStateObject.Shape.Representation3D | undefined = visuals[0]?.obj;
+        if (!reprNode) return;
+        const loci = reprNode.data.repr.getAllLoci()[0];
+        if (!loci) return;
+        this.entryData.plugin.managers.interactivity.lociSelects.select({ loci: loci, repr: reprNode.data.repr }, false);
+    }
+
+    /** Make visible the specified set of mesh segments */
+    async showSegments(segments: number[]) {
+        const segmentsToShow = new Set(segments);
+
+        const visuals = this.entryData.findNodesByTags('mesh-segment-visual');
+        for (const visual of visuals) {
+            const theTag = visual.obj?.tags?.find(tag => tag.startsWith('segment-'));
+            if (!theTag) continue;
+            const id = parseInt(theTag.split('-')[1]);
+            const visibility = segmentsToShow.has(id);
+            setSubtreeVisibility(this.entryData.plugin.state.data, visual.transform.ref, !visibility); // true means hide, ¯\_(ツ)_/¯
+            segmentsToShow.delete(id);
+        }
+
+        const segmentsToCreate = this.entryData.metadata.meshSegmentIds.filter(seg => segmentsToShow.has(seg));
+        if (segmentsToCreate.length === 0) return;
+
+        let group = this.entryData.findNodesByTags('mesh-segmentation-group')[0]?.transform.ref;
+        if (!group) {
+            const newGroupNode = await this.entryData.newUpdate().apply(CreateGroup, { label: 'Segmentation', description: 'Mesh' }, { tags: ['mesh-segmentation-group'], state: { isCollapsed: true } }).commit();
+            group = newGroupNode.ref;
+        }
+        const totalVolume = this.entryData.metadata.gridTotalVolume;
+
+        const awaiting = [];
+        for (const seg of segmentsToCreate) {
+            const segment = this.entryData.metadata.getSegment(seg);
+            if (!segment) continue;
+            const detail = this.entryData.metadata.getSufficientMeshDetail(seg, DEFAULT_MESH_DETAIL);
+            const color = segment.colour.length >= 3 ? Color.fromNormalizedArray(segment.colour, 0) : ColorNames.gray;
+            const url = this.entryData.api.meshUrl_Bcif(this.entryData.source, this.entryData.entryId, seg, detail);
+            const label = segment.biological_annotation.name ?? `Segment ${seg}`;
+            const meshPromise = createMeshFromUrl(this.entryData.plugin, url, seg, detail, true, color, group,
+                BACKGROUND_SEGMENT_VOLUME_THRESHOLD * totalVolume, `<b>${label}</b>`, this.entryData.ref);
+            awaiting.push(meshPromise);
+        }
+        for (const promise of awaiting) await promise;
+    }
+}

src/extensions/volumes-and-segmentations/entry-models.ts

@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
+import { CreateGroup } from '../../mol-plugin-state/transforms/misc';
+import { TrajectoryFromMmCif } from '../../mol-plugin-state/transforms/model';
+import { setSubtreeVisibility } from '../../mol-plugin/behavior/static/state';
+import { StateObjectRef, StateObjectSelector } from '../../mol-state';
+
+import { VolsegEntryData } from './entry-root';
+
+
+export class VolsegModelData {
+    private entryData: VolsegEntryData;
+
+    constructor(rootData: VolsegEntryData) {
+        this.entryData = rootData;
+    }
+
+    private async loadPdb(pdbId: string, parent: StateObjectSelector | StateObjectRef) {
+        const url = `https://www.ebi.ac.uk/pdbe/entry-files/download/${pdbId}.bcif`;
+        const dataNode = await this.entryData.plugin.build().to(parent).apply(Download, { url: url, isBinary: true }, { tags: ['fitted-model-data', `pdbid-${pdbId}`] }).commit();
+        const cifNode = await this.entryData.plugin.build().to(dataNode).apply(ParseCif).commit();
+        const trajectoryNode = await this.entryData.plugin.build().to(cifNode).apply(TrajectoryFromMmCif).commit();
+        await this.entryData.plugin.builders.structure.hierarchy.applyPreset(trajectoryNode, 'default', { representationPreset: 'polymer-cartoon' });
+        return dataNode;
+    }
+
+    async showPdbs(pdbIds: string[]) {
+        const segmentsToShow = new Set(pdbIds);
+
+        const visuals = this.entryData.findNodesByTags('fitted-model-data');
+        for (const visual of visuals) {
+            const theTag = visual.obj?.tags?.find(tag => tag.startsWith('pdbid-'));
+            if (!theTag) continue;
+            const id = theTag.split('-')[1];
+            const visibility = segmentsToShow.has(id);
+            setSubtreeVisibility(this.entryData.plugin.state.data, visual.transform.ref, !visibility); // true means hide, ¯\_(ツ)_/¯
+            segmentsToShow.delete(id);
+        }
+
+        const segmentsToCreate = Array.from(segmentsToShow);
+        if (segmentsToCreate.length === 0) return;
+
+        let group = this.entryData.findNodesByTags('fitted-models-group')[0]?.transform.ref;
+        if (!group) {
+            const newGroupNode = await this.entryData.newUpdate().apply(CreateGroup, { label: 'Fitted Models' }, { tags: ['fitted-models-group'], state: { isCollapsed: true } }).commit();
+            group = newGroupNode.ref;
+        }
+
+        const awaiting = [];
+        for (const pdbId of segmentsToCreate) {
+            awaiting.push(this.loadPdb(pdbId, group));
+        }
+        for (const promise of awaiting) await promise;
+    }
+}

src/extensions/volumes-and-segmentations/entry-root.ts

@@ -0,0 +1,377 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { BehaviorSubject, distinctUntilChanged, Subject, throttleTime } from 'rxjs';
+import { VolsegVolumeServerConfig } from '.';
+import { Loci } from '../../mol-model/loci';
+
+import { ShapeGroup } from '../../mol-model/shape';
+import { Volume } from '../../mol-model/volume';
+import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectCell, StateSelection, StateTransform } from '../../mol-state';
+import { shallowEqualObjects } from '../../mol-util';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { MeshlistData } from '../meshes/mesh-extension';
+
+import { DEFAULT_VOLSEG_SERVER, VolumeApiV2 } from './volseg-api/api';
+import { Segment } from './volseg-api/data';
+import { MetadataWrapper } from './volseg-api/utils';
+import { VolsegMeshSegmentationData } from './entry-meshes';
+import { VolsegModelData } from './entry-models';
+import { VolsegLatticeSegmentationData } from './entry-segmentation';
+import { VolsegState, VolsegStateData, VolsegStateParams } from './entry-state';
+import { VolsegVolumeData, SimpleVolumeParamValues, VOLUME_VISUAL_TAG } from './entry-volume';
+import * as ExternalAPIs from './external-api';
+import { VolsegGlobalStateData } from './global-state';
+import { applyEllipsis, Choice, isDefined, lazyGetter, splitEntryId } from './helpers';
+import { type VolsegStateFromEntry } from './transformers';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+
+
+export const MAX_VOXELS = 10 ** 7;
+// export const MAX_VOXELS = 10 ** 2; // DEBUG
+export const BOX: [[number, number, number], [number, number, number]] | null = null;
+// export const BOX: [[number, number, number], [number, number, number]] | null = [[-90, -90, -90], [90, 90, 90]]; // DEBUG
+
+const MAX_ANNOTATIONS_IN_LABEL = 6;
+
+
+const SourceChoice = new Choice({ emdb: 'EMDB', empiar: 'EMPIAR', idr: 'IDR' }, 'emdb');
+export type Source = Choice.Values<typeof SourceChoice>;
+
+
+export function createLoadVolsegParams(plugin?: PluginContext, entrylists: { [source: string]: string[] } = {}) {
+    const defaultVolumeServer = plugin?.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLSEG_SERVER;
+    return {
+        serverUrl: ParamDefinition.Text(defaultVolumeServer),
+        source: ParamDefinition.Mapped(SourceChoice.values[0], SourceChoice.options, src => entryParam(entrylists[src])),
+    };
+}
+function entryParam(entries: string[] = []) {
+    const options: [string, string][] = entries.map(e => [e, e]);
+    options.push(['__custom__', 'Custom']);
+    return ParamDefinition.Group({
+        entryId: ParamDefinition.Select(options[0][0], options, { description: 'Choose an entry from the list, or choose "Custom" and type any entry ID (useful when using other than default server).' }),
+        customEntryId: ParamDefinition.Text('', { hideIf: p => p.entryId !== '__custom__', description: 'Entry identifier, including the source prefix, e.g. "emd-1832"' }),
+    }, { isFlat: true });
+}
+type LoadVolsegParamValues = ParamDefinition.Values<ReturnType<typeof createLoadVolsegParams>>;
+
+export function createVolsegEntryParams(plugin?: PluginContext) {
+    const defaultVolumeServer = plugin?.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLSEG_SERVER;
+    return {
+        serverUrl: ParamDefinition.Text(defaultVolumeServer),
+        source: SourceChoice.PDSelect(),
+        entryId: ParamDefinition.Text('emd-1832', { description: 'Entry identifier, including the source prefix, e.g. "emd-1832"' }),
+    };
+}
+type VolsegEntryParamValues = ParamDefinition.Values<ReturnType<typeof createVolsegEntryParams>>;
+
+export namespace VolsegEntryParamValues {
+    export function fromLoadVolsegParamValues(params: LoadVolsegParamValues): VolsegEntryParamValues {
+        let entryId = (params.source.params as any).entryId;
+        if (entryId === '__custom__') {
+            entryId = (params.source.params as any).customEntryId;
+        }
+        return {
+            serverUrl: params.serverUrl,
+            source: params.source.name as Source,
+            entryId: entryId
+        };
+    }
+}
+
+
+export class VolsegEntry extends PluginStateObject.CreateBehavior<VolsegEntryData>({ name: 'Vol & Seg Entry' }) { }
+
+type VolRepr3DT = typeof StateTransforms.Representation.VolumeRepresentation3D
+
+export class VolsegEntryData extends PluginBehavior.WithSubscribers<VolsegEntryParamValues> {
+    plugin: PluginContext;
+    ref: string = '';
+    api: VolumeApiV2;
+    source: Source;
+    /** Number part of entry ID; e.g. '1832' */
+    entryNumber: string;
+    /** Full entry ID; e.g. 'emd-1832' */
+    entryId: string;
+    metadata: MetadataWrapper;
+    pdbs: string[];
+
+    public readonly volumeData = new VolsegVolumeData(this);
+    private readonly latticeSegmentationData = new VolsegLatticeSegmentationData(this);
+    private readonly meshSegmentationData = new VolsegMeshSegmentationData(this);
+    private readonly modelData = new VolsegModelData(this);
+    private highlightRequest = new Subject<Segment | undefined>();
+
+    private getStateNode = lazyGetter(() => this.plugin.state.data.selectQ(q => q.byRef(this.ref).subtree().ofType(VolsegState))[0] as StateObjectCell<VolsegState, StateTransform<typeof VolsegStateFromEntry>>, 'Missing VolsegState node. Must first create VolsegState for this VolsegEntry.');
+    public currentState = new BehaviorSubject(ParamDefinition.getDefaultValues(VolsegStateParams));
+    public currentVolume = new BehaviorSubject<StateTransform<VolRepr3DT> | undefined>(undefined);
+
+
+    private constructor(plugin: PluginContext, params: VolsegEntryParamValues) {
+        super(plugin, params);
+        this.plugin = plugin;
+        this.api = new VolumeApiV2(params.serverUrl);
+        this.source = params.source;
+        this.entryId = params.entryId;
+        this.entryNumber = splitEntryId(this.entryId).entryNumber;
+    }
+
+    private async initialize() {
+        const metadata = await this.api.getMetadata(this.source, this.entryId);
+        this.metadata = new MetadataWrapper(metadata);
+        this.pdbs = await ExternalAPIs.getPdbIdsForEmdbEntry(this.metadata.raw.grid.general.source_db_id ?? this.entryId);
+        // TODO use Asset?
+    }
+
+    static async create(plugin: PluginContext, params: VolsegEntryParamValues) {
+        const result = new VolsegEntryData(plugin, params);
+        await result.initialize();
+        return result;
+    }
+
+    async register(ref: string) {
+        this.ref = ref;
+        this.plugin.managers.lociLabels.addProvider(this.labelProvider);
+
+        try {
+            const params = this.getStateNode().obj?.data;
+            if (params) {
+                this.currentState.next(params);
+            }
+        } catch {
+            // do nothing
+        }
+
+        const volumeVisual = this.findNodesByTags(VOLUME_VISUAL_TAG)[0];
+        if (volumeVisual) this.currentVolume.next(volumeVisual.transform);
+
+        let volumeRef: string | undefined;
+        this.subscribeObservable(this.plugin.state.data.events.cell.stateUpdated, e => {
+            try { (this.getStateNode()); } catch { return; } // if state not does not exist yet
+            if (e.cell.transform.ref === this.getStateNode().transform.ref) {
+                const newState = this.getStateNode().obj?.data;
+                if (newState && !shallowEqualObjects(newState, this.currentState.value)) { // avoid repeated update
+                    this.currentState.next(newState);
+                }
+            } else if (e.cell.transform.tags?.includes(VOLUME_VISUAL_TAG)) {
+                if (e.ref === volumeRef) {
+                    this.currentVolume.next(e.cell.transform);
+                } else if (StateSelection.findAncestor(this.plugin.state.data.tree, this.plugin.state.data.cells, e.ref, a => a.transform.ref === ref)) {
+                    volumeRef = e.ref;
+                    this.currentVolume.next(e.cell.transform);
+                }
+            }
+        });
+
+        this.subscribeObservable(this.plugin.state.data.events.cell.removed, e => {
+            if (e.ref === volumeRef) {
+                volumeRef = undefined;
+                this.currentVolume.next(undefined);
+            }
+        });
+
+        this.subscribeObservable(this.plugin.behaviors.interaction.click, async e => {
+            const loci = e.current.loci;
+            const clickedSegment = this.getSegmentIdFromLoci(loci);
+            if (clickedSegment === undefined) return;
+            if (clickedSegment === this.currentState.value.selectedSegment) {
+                this.actionSelectSegment(undefined);
+            } else {
+                this.actionSelectSegment(clickedSegment);
+            }
+        });
+
+        this.subscribeObservable(
+            this.highlightRequest.pipe(throttleTime(50, undefined, { leading: true, trailing: true })),
+            async segment => await this.highlightSegment(segment)
+        );
+
+        this.subscribeObservable(
+            this.currentState.pipe(distinctUntilChanged((a, b) => a.selectedSegment === b.selectedSegment)),
+            async state => {
+                if (VolsegGlobalStateData.getGlobalState(this.plugin)?.selectionMode) await this.selectSegment(state.selectedSegment);
+            }
+        );
+    }
+
+    async unregister() {
+        this.plugin.managers.lociLabels.removeProvider(this.labelProvider);
+    }
+
+    async loadVolume() {
+        const result = await this.volumeData.loadVolume();
+        if (result) {
+            const isovalue = result.isovalue.kind === 'relative' ? result.isovalue.relativeValue : result.isovalue.absoluteValue;
+            await this.updateStateNode({ volumeIsovalueKind: result.isovalue.kind, volumeIsovalueValue: isovalue });
+        }
+    }
+
+    async loadSegmentations() {
+        await this.latticeSegmentationData.loadSegmentation();
+        await this.meshSegmentationData.loadSegmentation();
+        await this.actionShowSegments(this.metadata.allSegmentIds);
+    }
+
+
+    actionHighlightSegment(segment?: Segment) {
+        this.highlightRequest.next(segment);
+    }
+
+    async actionToggleSegment(segment: number) {
+        const current = this.currentState.value.visibleSegments.map(seg => seg.segmentId);
+        if (current.includes(segment)) {
+            await this.actionShowSegments(current.filter(s => s !== segment));
+        } else {
+            await this.actionShowSegments([...current, segment]);
+        }
+    }
+
+    async actionToggleAllSegments() {
+        const current = this.currentState.value.visibleSegments.map(seg => seg.segmentId);
+        if (current.length !== this.metadata.allSegments.length) {
+            await this.actionShowSegments(this.metadata.allSegmentIds);
+        } else {
+            await this.actionShowSegments([]);
+        }
+    }
+
+    async actionSelectSegment(segment?: number) {
+        if (segment !== undefined && this.currentState.value.visibleSegments.find(s => s.segmentId === segment) === undefined) {
+            // first make the segment visible if it is not
+            await this.actionToggleSegment(segment);
+        }
+        await this.updateStateNode({ selectedSegment: segment });
+    }
+
+    async actionSetOpacity(opacity: number) {
+        if (opacity === this.getStateNode().obj?.data.segmentOpacity) return;
+        this.latticeSegmentationData.updateOpacity(opacity);
+        this.meshSegmentationData.updateOpacity(opacity);
+
+        await this.updateStateNode({ segmentOpacity: opacity });
+    }
+
+    async actionShowFittedModel(pdbIds: string[]) {
+        await this.modelData.showPdbs(pdbIds);
+        await this.updateStateNode({ visibleModels: pdbIds.map(pdbId => ({ pdbId: pdbId })) });
+    }
+
+    async actionSetVolumeVisual(type: 'isosurface' | 'direct-volume' | 'off') {
+        await this.volumeData.setVolumeVisual(type);
+        await this.updateStateNode({ volumeType: type });
+    }
+
+    async actionUpdateVolumeVisual(params: SimpleVolumeParamValues) {
+        await this.volumeData.updateVolumeVisual(params);
+        await this.updateStateNode({
+            volumeType: params.volumeType,
+            volumeOpacity: params.opacity,
+        });
+    }
+
+
+    private async actionShowSegments(segments: number[]) {
+        await this.latticeSegmentationData.showSegments(segments);
+        await this.meshSegmentationData.showSegments(segments);
+        await this.updateStateNode({ visibleSegments: segments.map(s => ({ segmentId: s })) });
+    }
+
+    private async highlightSegment(segment?: Segment) {
+        await PluginCommands.Interactivity.ClearHighlights(this.plugin);
+        if (segment) {
+            await this.latticeSegmentationData.highlightSegment(segment);
+            await this.meshSegmentationData.highlightSegment(segment);
+        }
+    }
+
+    private async selectSegment(segment: number) {
+        this.plugin.managers.interactivity.lociSelects.deselectAll();
+        await this.latticeSegmentationData.selectSegment(segment);
+        await this.meshSegmentationData.selectSegment(segment);
+        await this.highlightSegment();
+    }
+
+    private async updateStateNode(params: Partial<VolsegStateData>) {
+        const oldParams = this.getStateNode().transform.params;
+        const newParams = { ...oldParams, ...params };
+        const state = this.plugin.state.data;
+        const update = state.build().to(this.getStateNode().transform.ref).update(newParams);
+        await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotUpdateCurrent: true } });
+    }
+
+
+    /** Find the nodes under this entry root which have all of the given tags. */
+    findNodesByTags(...tags: string[]) {
+        return this.plugin.state.data.selectQ(q => {
+            let builder = q.byRef(this.ref).subtree();
+            for (const tag of tags) builder = builder.withTag(tag);
+            return builder;
+        });
+    }
+
+    newUpdate() {
+        if (this.ref !== '') {
+            return this.plugin.build().to(this.ref);
+        } else {
+            return this.plugin.build().toRoot();
+        }
+    }
+
+    private readonly labelProvider: LociLabelProvider = {
+        label: (loci: Loci): string | undefined => {
+            const segmentId = this.getSegmentIdFromLoci(loci);
+            if (segmentId === undefined) return;
+            const segment = this.metadata.getSegment(segmentId);
+            if (!segment) return;
+            const annotLabels = segment.biological_annotation.external_references.map(annot => `${applyEllipsis(annot.label)} [${annot.resource}:${annot.accession}]`);
+            if (annotLabels.length === 0) return;
+            if (annotLabels.length > MAX_ANNOTATIONS_IN_LABEL + 1) {
+                const nHidden = annotLabels.length - MAX_ANNOTATIONS_IN_LABEL;
+                annotLabels.length = MAX_ANNOTATIONS_IN_LABEL;
+                annotLabels.push(`(${nHidden} more annotations, click on the segment to see all)`);
+            }
+            return '<hr class="msp-highlight-info-hr"/>' + annotLabels.filter(isDefined).join('<br/>');
+        }
+    };
+
+    private getSegmentIdFromLoci(loci: Loci): number | undefined {
+        if (Volume.Segment.isLoci(loci) && loci.volume._propertyData.ownerId === this.ref) {
+            if (loci.segments.length === 1) {
+                return loci.segments[0];
+            }
+        }
+        if (ShapeGroup.isLoci(loci)) {
+            const meshData = (loci.shape.sourceData ?? {}) as MeshlistData;
+            if (meshData.ownerId === this.ref && meshData.segmentId !== undefined) {
+                return meshData.segmentId;
+            }
+        }
+    }
+
+    async setTryUseGpu(tryUseGpu: boolean) {
+        await Promise.all([
+            this.volumeData.setTryUseGpu(tryUseGpu),
+            this.latticeSegmentationData.setTryUseGpu(tryUseGpu),
+        ]);
+    }
+    async setSelectionMode(selectSegments: boolean) {
+        if (selectSegments) {
+            await this.selectSegment(this.currentState.value.selectedSegment);
+        } else {
+            this.plugin.managers.interactivity.lociSelects.deselectAll();
+        }
+    }
+
+}
+
+
+

src/extensions/volumes-and-segmentations/entry-segmentation.ts

@@ -0,0 +1,131 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Volume } from '../../mol-model/volume';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
+import { CreateGroup } from '../../mol-plugin-state/transforms/misc';
+import { VolumeFromSegmentationCif } from '../../mol-plugin-state/transforms/volume';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { Color } from '../../mol-util/color';
+
+import { Segment } from './volseg-api/data';
+import { BOX, VolsegEntryData, MAX_VOXELS } from './entry-root';
+import { VolumeVisualParams } from './entry-volume';
+import { VolsegGlobalStateData } from './global-state';
+
+
+const GROUP_TAG = 'lattice-segmentation-group';
+const SEGMENT_VISUAL_TAG = 'lattice-segment-visual';
+
+const DEFAULT_SEGMENT_COLOR = Color.fromNormalizedRgb(0.8, 0.8, 0.8);
+
+
+export class VolsegLatticeSegmentationData {
+    private entryData: VolsegEntryData;
+
+    constructor(rootData: VolsegEntryData) {
+        this.entryData = rootData;
+    }
+
+    async loadSegmentation() {
+        const hasLattices = this.entryData.metadata.raw.grid.segmentation_lattices.segmentation_lattice_ids.length > 0;
+        if (hasLattices) {
+            const url = this.entryData.api.latticeUrl(this.entryData.source, this.entryData.entryId, 0, BOX, MAX_VOXELS);
+            let group = this.entryData.findNodesByTags(GROUP_TAG)[0]?.transform.ref;
+            if (!group) {
+                const newGroupNode = await this.entryData.newUpdate().apply(CreateGroup,
+                    { label: 'Segmentation', description: 'Lattice' }, { tags: [GROUP_TAG], state: { isCollapsed: true } }).commit();
+                group = newGroupNode.ref;
+            }
+            const segmentLabels = this.entryData.metadata.allSegments.map(seg => ({ id: seg.id, label: seg.biological_annotation.name ? `<b>${seg.biological_annotation.name}</b>` : '' }));
+            const volumeNode = await this.entryData.newUpdate().to(group)
+                .apply(Download, { url, isBinary: true, label: `Segmentation Data: ${url}` })
+                .apply(ParseCif)
+                .apply(VolumeFromSegmentationCif, { blockHeader: 'SEGMENTATION_DATA', segmentLabels: segmentLabels, ownerId: this.entryData.ref })
+                .commit();
+            const volumeData = volumeNode.data as Volume;
+            const segmentation = Volume.Segmentation.get(volumeData);
+            const segmentIds: number[] = Array.from(segmentation?.segments.keys() ?? []);
+            await this.entryData.newUpdate().to(volumeNode)
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.entryData.plugin, volumeData, {
+                    type: 'segment',
+                    typeParams: { tryUseGpu: VolsegGlobalStateData.getGlobalState(this.entryData.plugin)?.tryUseGpu },
+                    color: 'volume-segment',
+                    colorParams: { palette: this.createPalette(segmentIds) },
+                }), { tags: [SEGMENT_VISUAL_TAG] }).commit();
+        }
+    }
+
+    private createPalette(segmentIds: number[]) {
+        const colorMap = new Map<number, Color>();
+        for (const segment of this.entryData.metadata.allSegments) {
+            const color = Color.fromNormalizedArray(segment.colour, 0);
+            colorMap.set(segment.id, color);
+        }
+        if (colorMap.size === 0) return undefined;
+        for (const segid of segmentIds) {
+            colorMap.get(segid);
+        }
+        const colors = segmentIds.map(segid => colorMap.get(segid) ?? DEFAULT_SEGMENT_COLOR);
+        return { name: 'colors' as const, params: { list: { kind: 'set' as const, colors: colors } } };
+    }
+
+    async updateOpacity(opacity: number) {
+        const reprs = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG);
+        const update = this.entryData.newUpdate();
+        for (const s of reprs) {
+            update.to(s).update(StateTransforms.Representation.VolumeRepresentation3D, p => { p.type.params.alpha = opacity; });
+        }
+        return await update.commit();
+    }
+    private makeLoci(segments: number[]) {
+        const vis = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG)[0];
+        if (!vis) return undefined;
+        const repr = vis.obj?.data.repr;
+        const wholeLoci = repr.getAllLoci()[0];
+        if (!wholeLoci || !Volume.Segment.isLoci(wholeLoci)) return undefined;
+        return { loci: Volume.Segment.Loci(wholeLoci.volume, segments), repr: repr };
+    }
+    async highlightSegment(segment: Segment) {
+        const segmentLoci = this.makeLoci([segment.id]);
+        if (!segmentLoci) return;
+        this.entryData.plugin.managers.interactivity.lociHighlights.highlight(segmentLoci, false);
+    }
+    async selectSegment(segment?: number) {
+        if (segment === undefined || segment < 0) return;
+        const segmentLoci = this.makeLoci([segment]);
+        if (!segmentLoci) return;
+        this.entryData.plugin.managers.interactivity.lociSelects.select(segmentLoci, false);
+    }
+
+    /** Make visible the specified set of lattice segments */
+    async showSegments(segments: number[]) {
+        const repr = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG)[0];
+        if (!repr) return;
+        const selectedSegment = this.entryData.currentState.value.selectedSegment;
+        const mustReselect = segments.includes(selectedSegment) && !repr.params?.values.type.params.segments.includes(selectedSegment);
+        const update = this.entryData.newUpdate();
+        update.to(repr).update(StateTransforms.Representation.VolumeRepresentation3D, p => { p.type.params.segments = segments; });
+        await update.commit();
+        if (mustReselect) {
+            await this.selectSegment(this.entryData.currentState.value.selectedSegment);
+        }
+    }
+
+    async setTryUseGpu(tryUseGpu: boolean) {
+        const visuals = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG);
+        for (const visual of visuals) {
+            const oldParams: VolumeVisualParams = visual.transform.params;
+            if (oldParams.type.params.tryUseGpu === !tryUseGpu) {
+                const newParams = { ...oldParams, type: { ...oldParams.type, params: { ...oldParams.type.params, tryUseGpu: tryUseGpu } } };
+                const update = this.entryData.newUpdate().to(visual.transform.ref).update(newParams);
+                await PluginCommands.State.Update(this.entryData.plugin, { state: this.entryData.plugin.state.data, tree: update, options: { doNotUpdateCurrent: true } });
+            }
+        }
+    }
+}

src/extensions/volumes-and-segmentations/entry-state.ts

@@ -0,0 +1,33 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+import { Choice } from './helpers';
+
+
+export const VolumeTypeChoice = new Choice({ 'isosurface': 'Isosurface', 'direct-volume': 'Direct volume', 'off': 'Off' }, 'isosurface');
+export type VolumeType = Choice.Values<typeof VolumeTypeChoice>
+
+
+export const VolsegStateParams = {
+    volumeType: VolumeTypeChoice.PDSelect(),
+    volumeIsovalueKind: PD.Select('relative', [['relative', 'Relative'], ['absolute', 'Absolute']]),
+    volumeIsovalueValue: PD.Numeric(1),
+    volumeOpacity: PD.Numeric(0.2, { min: 0, max: 1, step: 0.05 }),
+    segmentOpacity: PD.Numeric(1, { min: 0, max: 1, step: 0.05 }),
+    selectedSegment: PD.Numeric(-1, { step: 1 }),
+    visibleSegments: PD.ObjectList({ segmentId: PD.Numeric(0) }, s => s.segmentId.toString()),
+    visibleModels: PD.ObjectList({ pdbId: PD.Text('') }, s => s.pdbId.toString()),
+};
+export type VolsegStateData = PD.Values<typeof VolsegStateParams>;
+
+
+export class VolsegState extends PluginStateObject.Create<VolsegStateData>({ name: 'Vol & Seg Entry State', typeClass: 'Data' }) { }
+
+
+export const VOLSEG_STATE_FROM_ENTRY_TRANSFORMER_NAME = 'volseg-state-from-entry'; // defined here to avoid cyclic dependency

src/extensions/volumes-and-segmentations/entry-volume.ts

@@ -0,0 +1,191 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Vec2 } from '../../mol-math/linear-algebra';
+import { Volume } from '../../mol-model/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 { Download } from '../../mol-plugin-state/transforms/data';
+import { CreateGroup } from '../../mol-plugin-state/transforms/misc';
+import { setSubtreeVisibility } from '../../mol-plugin/behavior/static/state';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { StateObjectSelector } from '../../mol-state';
+import { Color } from '../../mol-util/color';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+import { BOX, VolsegEntryData, MAX_VOXELS } from './entry-root';
+import { VolsegStateParams, VolumeTypeChoice } from './entry-state';
+import * as ExternalAPIs from './external-api';
+import { VolsegGlobalStateData } from './global-state';
+
+
+const GROUP_TAG = 'volume-group';
+export const VOLUME_VISUAL_TAG = 'volume-visual';
+
+const DIRECT_VOLUME_RELATIVE_PEAK_HALFWIDTH = 0.5;
+
+
+export type VolumeVisualParams = ReturnType<typeof createVolumeRepresentationParams>;
+
+interface VolumeStats { min: number, max: number, mean: number, sigma: number };
+
+
+export const SimpleVolumeParams = {
+    volumeType: VolumeTypeChoice.PDSelect(),
+    opacity: PD.Numeric(0.2, { min: 0, max: 1, step: 0.05 }, { hideIf: p => p.volumeType === 'off' }),
+};
+export type SimpleVolumeParamValues = PD.Values<typeof SimpleVolumeParams>;
+
+
+export class VolsegVolumeData {
+    private entryData: VolsegEntryData;
+    private visualTypeParamCache: { [type: string]: any } = {};
+
+    constructor(rootData: VolsegEntryData) {
+        this.entryData = rootData;
+    }
+
+    async loadVolume() {
+        const hasVolumes = this.entryData.metadata.raw.grid.volumes.volume_downsamplings.length > 0;
+        if (hasVolumes) {
+            const isoLevelPromise = ExternalAPIs.tryGetIsovalue(this.entryData.metadata.raw.grid.general.source_db_id ?? this.entryData.entryId);
+            let group = this.entryData.findNodesByTags(GROUP_TAG)[0]?.transform.ref;
+            if (!group) {
+                const newGroupNode = await this.entryData.newUpdate().apply(CreateGroup, { label: 'Volume' }, { tags: [GROUP_TAG], state: { isCollapsed: true } }).commit();
+                group = newGroupNode.ref;
+            }
+            const url = this.entryData.api.volumeUrl(this.entryData.source, this.entryData.entryId, BOX, MAX_VOXELS);
+            const data = await this.entryData.newUpdate().to(group).apply(Download, { url, isBinary: true, label: `Volume Data: ${url}` }).commit();
+            const parsed = await this.entryData.plugin.dataFormats.get('dscif')!.parse(this.entryData.plugin, data);
+            const volumeNode: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[0] ?? parsed.volume;
+            const volumeData = volumeNode.cell!.obj!.data;
+
+            const volumeType = VolsegStateParams.volumeType.defaultValue;
+            let isovalue = await isoLevelPromise;
+            if (!isovalue) {
+                const stats = volumeData.grid.stats;
+                const maxRelative = (stats.max - stats.mean) / stats.sigma;
+                if (maxRelative > 1) {
+                    isovalue = { kind: 'relative', value: 1.0 };
+                } else {
+                    isovalue = { kind: 'relative', value: maxRelative * 0.5 };
+                }
+            }
+
+            const adjustedIsovalue = Volume.adjustedIsoValue(volumeData, isovalue.value, isovalue.kind);
+            const visualParams = this.createVolumeVisualParams(volumeData, volumeType);
+            this.changeIsovalueInVolumeVisualParams(visualParams, adjustedIsovalue, volumeData.grid.stats);
+
+            await this.entryData.newUpdate()
+                .to(volumeNode)
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, visualParams, { tags: [VOLUME_VISUAL_TAG], state: { isHidden: volumeType === 'off' } })
+                .commit();
+            return { isovalue: adjustedIsovalue };
+        }
+    }
+
+    async setVolumeVisual(type: 'isosurface' | 'direct-volume' | 'off') {
+        const visual = this.entryData.findNodesByTags(VOLUME_VISUAL_TAG)[0];
+        if (!visual) return;
+        const oldParams: VolumeVisualParams = visual.transform.params;
+        this.visualTypeParamCache[oldParams.type.name] = oldParams.type.params;
+        if (type === 'off') {
+            setSubtreeVisibility(this.entryData.plugin.state.data, visual.transform.ref, true); // true means hide, ¯\_(ツ)_/¯
+        } else {
+            setSubtreeVisibility(this.entryData.plugin.state.data, visual.transform.ref, false); // true means hide, ¯\_(ツ)_/¯
+            if (oldParams.type.name === type) return;
+            const newParams: VolumeVisualParams = {
+                ...oldParams,
+                type: {
+                    name: type,
+                    params: this.visualTypeParamCache[type] ?? oldParams.type.params,
+                }
+            };
+            const volumeStats = visual.obj?.data.sourceData.grid.stats;
+            if (!volumeStats) throw new Error(`Cannot get volume stats from volume visual ${visual.transform.ref}`);
+            this.changeIsovalueInVolumeVisualParams(newParams, undefined, volumeStats);
+            const update = this.entryData.newUpdate().to(visual.transform.ref).update(newParams);
+            await PluginCommands.State.Update(this.entryData.plugin, { state: this.entryData.plugin.state.data, tree: update, options: { doNotUpdateCurrent: true } });
+        }
+    }
+
+    async updateVolumeVisual(newParams: SimpleVolumeParamValues) {
+        const { volumeType, opacity } = newParams;
+        const visual = this.entryData.findNodesByTags(VOLUME_VISUAL_TAG)[0];
+        if (!visual) return;
+        const oldVisualParams: VolumeVisualParams = visual.transform.params;
+        this.visualTypeParamCache[oldVisualParams.type.name] = oldVisualParams.type.params;
+
+        if (volumeType === 'off') {
+            setSubtreeVisibility(this.entryData.plugin.state.data, visual.transform.ref, true); // true means hide, ¯\_(ツ)_/¯
+        } else {
+            setSubtreeVisibility(this.entryData.plugin.state.data, visual.transform.ref, false); // true means hide, ¯\_(ツ)_/¯
+            const newVisualParams: VolumeVisualParams = {
+                ...oldVisualParams,
+                type: {
+                    name: volumeType,
+                    params: this.visualTypeParamCache[volumeType] ?? oldVisualParams.type.params,
+                }
+            };
+            newVisualParams.type.params.alpha = opacity;
+            const volumeStats = visual.obj?.data.sourceData.grid.stats;
+            if (!volumeStats) throw new Error(`Cannot get volume stats from volume visual ${visual.transform.ref}`);
+            this.changeIsovalueInVolumeVisualParams(newVisualParams, undefined, volumeStats);
+            const update = this.entryData.newUpdate().to(visual.transform.ref).update(newVisualParams);
+            await PluginCommands.State.Update(this.entryData.plugin, { state: this.entryData.plugin.state.data, tree: update, options: { doNotUpdateCurrent: true } });
+        }
+    }
+
+    async setTryUseGpu(tryUseGpu: boolean) {
+        const visuals = this.entryData.findNodesByTags(VOLUME_VISUAL_TAG);
+        for (const visual of visuals) {
+            const oldParams: VolumeVisualParams = visual.transform.params;
+            if (oldParams.type.params.tryUseGpu === !tryUseGpu) {
+                const newParams = { ...oldParams, type: { ...oldParams.type, params: { ...oldParams.type.params, tryUseGpu: tryUseGpu } } };
+                const update = this.entryData.newUpdate().to(visual.transform.ref).update(newParams);
+                await PluginCommands.State.Update(this.entryData.plugin, { state: this.entryData.plugin.state.data, tree: update, options: { doNotUpdateCurrent: true } });
+            }
+        }
+    }
+
+    private getIsovalueFromState(): Volume.IsoValue {
+        const { volumeIsovalueKind, volumeIsovalueValue } = this.entryData.currentState.value;
+        return volumeIsovalueKind === 'relative'
+            ? Volume.IsoValue.relative(volumeIsovalueValue)
+            : Volume.IsoValue.absolute(volumeIsovalueValue);
+    }
+
+    private createVolumeVisualParams(volume: Volume, type: 'isosurface' | 'direct-volume' | 'off'): VolumeVisualParams {
+        if (type === 'off') type = 'isosurface';
+        return createVolumeRepresentationParams(this.entryData.plugin, volume, {
+            type: type,
+            typeParams: { alpha: 0.2, tryUseGpu: VolsegGlobalStateData.getGlobalState(this.entryData.plugin)?.tryUseGpu },
+            color: 'uniform',
+            colorParams: { value: Color(0x121212) },
+        });
+    }
+
+    private changeIsovalueInVolumeVisualParams(params: VolumeVisualParams, isovalue: Volume.IsoValue | undefined, stats: VolumeStats) {
+        isovalue ??= this.getIsovalueFromState();
+        switch (params.type.name) {
+            case 'isosurface':
+                params.type.params.isoValue = isovalue;
+                params.type.params.tryUseGpu = VolsegGlobalStateData.getGlobalState(this.entryData.plugin)?.tryUseGpu;
+                break;
+            case 'direct-volume':
+                const absIso = Volume.IsoValue.toAbsolute(isovalue, stats).absoluteValue;
+                const fractIso = (absIso - stats.min) / (stats.max - stats.min);
+                const peakHalfwidth = DIRECT_VOLUME_RELATIVE_PEAK_HALFWIDTH * stats.sigma / (stats.max - stats.min);
+                params.type.params.controlPoints = [
+                    Vec2.create(Math.max(fractIso - peakHalfwidth, 0), 0),
+                    Vec2.create(fractIso, 1),
+                    Vec2.create(Math.min(fractIso + peakHalfwidth, 1), 0),
+                ];
+                break;
+        }
+    }
+}

src/extensions/volumes-and-segmentations/external-api.ts

@@ -0,0 +1,51 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { splitEntryId } from './helpers';
+
+
+/** Try to get author-defined contour value for isosurface from EMDB API. Return relative value 1.0, if not applicable or fails.  */
+export async function tryGetIsovalue(entryId: string): Promise<{ kind: 'absolute' | 'relative', value: number } | undefined> {
+    const split = splitEntryId(entryId);
+    if (split.source === 'emdb') {
+        try {
+            const response = await fetch(`https://www.ebi.ac.uk/emdb/api/entry/map/${split.entryNumber}`);
+            const json = await response.json();
+            const contours: any[] = json?.map?.contour_list?.contour;
+            if (contours && contours.length > 0) {
+                const theContour = contours.find(c => c.primary) || contours[0];
+                if (theContour.level === undefined) throw new Error('EMDB API response missing contour level.');
+                return { kind: 'absolute', value: theContour.level };
+            }
+        } catch {
+            // do nothing
+        }
+    }
+    return undefined;
+}
+
+export async function getPdbIdsForEmdbEntry(entryId: string): Promise<string[]> {
+    const split = splitEntryId(entryId);
+    const result = [];
+    if (split.source === 'emdb') {
+        entryId = entryId.toUpperCase();
+        const apiUrl = `https://www.ebi.ac.uk/pdbe/api/emdb/entry/fitted/${entryId}`;
+        try {
+            const response = await fetch(apiUrl);
+            if (response.ok) {
+                const json = await response.json();
+                const jsonEntry = json[entryId] ?? [];
+                for (const record of jsonEntry) {
+                    const pdbs = record?.fitted_emdb_id_list?.pdb_id ?? [];
+                    result.push(...pdbs);
+                }
+            }
+        } catch (ex) {
+            // do nothing
+        }
+    }
+    return result;
+}

src/extensions/volumes-and-segmentations/global-state.ts

@@ -0,0 +1,65 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { BehaviorSubject } from 'rxjs';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { PluginContext } from '../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { VolsegEntry } from './entry-root';
+import { isDefined } from './helpers';
+
+
+export const VolsegGlobalStateParams = {
+    tryUseGpu: PD.Boolean(true, { description: 'Attempt using GPU for faster rendering. \nCaution: with some hardware setups, this might render some objects incorrectly or not at all.' }),
+    selectionMode: PD.Boolean(true, { description: 'Allow selecting/deselecting a segment by clicking on it.' }),
+};
+export type VolsegGlobalStateParamValues = PD.Values<typeof VolsegGlobalStateParams>;
+
+
+export class VolsegGlobalState extends PluginStateObject.CreateBehavior<VolsegGlobalStateData>({ name: 'Vol & Seg Global State' }) { }
+
+export class VolsegGlobalStateData extends PluginBehavior.WithSubscribers<VolsegGlobalStateParamValues> {
+    private ref: string;
+    currentState = new BehaviorSubject(PD.getDefaultValues(VolsegGlobalStateParams));
+
+    constructor(plugin: PluginContext, params: VolsegGlobalStateParamValues) {
+        super(plugin, params);
+        this.currentState.next(params);
+    }
+
+    register(ref: string) {
+        this.ref = ref;
+    }
+    unregister() {
+        this.ref = '';
+    }
+    isRegistered() {
+        return this.ref !== '';
+    }
+    async updateState(plugin: PluginContext, state: Partial<VolsegGlobalStateParamValues>) {
+        const oldState = this.currentState.value;
+
+        const promises = [];
+        const allEntries = plugin.state.data.selectQ(q => q.ofType(VolsegEntry)).map(cell => cell.obj?.data).filter(isDefined);
+        if (state.tryUseGpu !== undefined && state.tryUseGpu !== oldState.tryUseGpu) {
+            for (const entry of allEntries) {
+                promises.push(entry.setTryUseGpu(state.tryUseGpu));
+            }
+        }
+        if (state.selectionMode !== undefined && state.selectionMode !== oldState.selectionMode) {
+            for (const entry of allEntries) {
+                promises.push(entry.setSelectionMode(state.selectionMode));
+            }
+        }
+        await Promise.all(promises);
+        await plugin.build().to(this.ref).update(state).commit();
+    }
+
+    static getGlobalState(plugin: PluginContext): VolsegGlobalStateParamValues | undefined {
+        return plugin.state.data.selectQ(q => q.ofType(VolsegGlobalState))[0]?.obj?.data.currentState.value;
+    }
+}

src/extensions/volumes-and-segmentations/helpers.ts

@@ -0,0 +1,163 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Volume } from '../../mol-model/volume';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { setSubtreeVisibility } from '../../mol-plugin/behavior/static/state';
+import { StateBuilder, StateObjectSelector, StateTransformer } from '../../mol-state';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { Source } from './entry-root';
+
+
+/** Split entry ID (e.g. 'emd-1832') into source ('emdb') and number ('1832') */
+export function splitEntryId(entryId: string) {
+    const PREFIX_TO_SOURCE: { [prefix: string]: Source } = { 'emd': 'emdb' };
+    const [prefix, entry] = entryId.split('-');
+    return {
+        source: PREFIX_TO_SOURCE[prefix] ?? prefix,
+        entryNumber: entry
+    };
+}
+
+/** Create entry ID (e.g. 'emd-1832') for a combination of source ('emdb') and number ('1832') */
+export function createEntryId(source: Source, entryNumber: string | number) {
+    const SOURCE_TO_PREFIX: { [prefix: string]: string } = { 'emdb': 'emd' };
+    const prefix = SOURCE_TO_PREFIX[source] ?? source;
+    return `${prefix}-${entryNumber}`;
+}
+
+
+
+/**
+ * Represents a set of values to choose from, with a default value. Example:
+ * ```
+ * export const MyChoice = new Choice({ yes: 'I agree', no: 'Nope' }, 'yes');
+ * export type MyChoiceType = Choice.Values<typeof MyChoice>; // 'yes'|'no'
+ * ```
+ */
+export class Choice<T extends string, D extends T> {
+    readonly defaultValue: D;
+    readonly options: [T, string][];
+    private readonly nameDict: { [value in T]: string };
+    constructor(opts: { [value in T]: string }, defaultValue: D) {
+        this.defaultValue = defaultValue;
+        this.options = Object.keys(opts).map(k => [k as T, opts[k as T]]);
+        this.nameDict = opts;
+    }
+    PDSelect(defaultValue?: T, info?: ParamDefinition.Info): ParamDefinition.Select<T> {
+        return ParamDefinition.Select<T>(defaultValue ?? this.defaultValue, this.options, info);
+    }
+    prettyName(value: T): string {
+        return this.nameDict[value];
+    }
+    get values(): T[] {
+        return this.options.map(([value, pretty]) => value);
+    }
+}
+export namespace Choice {
+    export type Values<T extends Choice<any, any>> = T extends Choice<infer R, any> ? R : any;
+}
+
+
+export function isDefined<T>(x: T | undefined): x is T {
+    return x !== undefined;
+}
+
+
+export class NodeManager {
+    private nodes: { [key: string]: StateObjectSelector };
+
+    constructor() {
+        this.nodes = {};
+    }
+
+    private static nodeExists(node: StateObjectSelector): boolean {
+        try {
+            return node.checkValid();
+        } catch {
+            return false;
+        }
+    }
+
+    public getNode(key: string): StateObjectSelector | undefined {
+        const node = this.nodes[key];
+        if (node && !NodeManager.nodeExists(node)) {
+            delete this.nodes[key];
+            return undefined;
+        }
+        return node;
+    }
+
+    public getNodes(): StateObjectSelector[] {
+        return Object.keys(this.nodes).map(key => this.getNode(key)).filter(node => node) as StateObjectSelector[];
+    }
+
+    public deleteAllNodes(update: StateBuilder.Root) {
+        for (const node of this.getNodes()) {
+            update.delete(node);
+        }
+        this.nodes = {};
+    }
+
+    public hideAllNodes() {
+        for (const node of this.getNodes()) {
+            setSubtreeVisibility(node.state!, node.ref, true); // hide
+        }
+    }
+
+    public async showNode(key: string, factory: () => StateObjectSelector | Promise<StateObjectSelector>, forceVisible: boolean = true) {
+        let node = this.getNode(key);
+        if (node) {
+            if (forceVisible) {
+                setSubtreeVisibility(node.state!, node.ref, false); // show
+            }
+        } else {
+            node = await factory();
+            this.nodes[key] = node;
+        }
+        return node;
+    }
+}
+
+
+
+const CreateTransformer = StateTransformer.builderFactory('volseg');
+
+export const CreateVolume = CreateTransformer({
+    name: 'create-transformer',
+    from: PluginStateObject.Root,
+    to: PluginStateObject.Volume.Data,
+    params: {
+        label: ParamDefinition.Text('Volume', { isHidden: true }),
+        description: ParamDefinition.Text('', { isHidden: true }),
+        volume: ParamDefinition.Value<Volume>(undefined as any, { isHidden: true }),
+    }
+})({
+    apply({ params }) {
+        return new PluginStateObject.Volume.Data(params.volume, { label: params.label, description: params.description });
+    }
+});
+
+
+
+export function applyEllipsis(name: string, max_chars: number = 60) {
+    if (name.length <= max_chars) return name;
+    const beginning = name.substring(0, max_chars);
+    let lastSpace = beginning.lastIndexOf(' ');
+    if (lastSpace === -1) return beginning + '...';
+    if (lastSpace > 0 && ',;.'.includes(name.charAt(lastSpace - 1))) lastSpace--;
+    return name.substring(0, lastSpace) + '...';
+}
+
+
+export function lazyGetter<T>(getter: () => T, errorIfUndefined?: string) {
+    let value: T | undefined = undefined;
+    return () => {
+        if (value === undefined) value = getter();
+        if (errorIfUndefined && value === undefined) throw new Error(errorIfUndefined);
+        return value;
+    };
+}

src/extensions/volumes-and-segmentations/index.ts

@@ -0,0 +1,102 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { PluginStateObject as SO } from '../../mol-plugin-state/objects';
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { PluginConfigItem } from '../../mol-plugin/config';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateAction } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { DEFAULT_VOLSEG_SERVER, VolumeApiV2 } from './volseg-api/api';
+
+import { VolsegEntryData, VolsegEntryParamValues, createLoadVolsegParams } from './entry-root';
+import { VolsegGlobalState } from './global-state';
+import { createEntryId } from './helpers';
+import { VolsegEntryFromRoot, VolsegGlobalStateFromRoot, VolsegStateFromEntry } from './transformers';
+import { VolsegUI } from './ui';
+
+
+const DEBUGGING = window.location.hostname === 'localhost';
+
+export const VolsegVolumeServerConfig = {
+    // DefaultServer: new PluginConfigItem('volseg-volume-server', DEFAULT_VOLUME_SERVER_V2),
+    DefaultServer: new PluginConfigItem('volseg-volume-server', DEBUGGING ? 'http://localhost:9000/v2' : DEFAULT_VOLSEG_SERVER),
+};
+
+
+export const Volseg = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'volseg',
+    category: 'misc',
+    display: {
+        name: 'Volseg',
+        description: 'Volseg'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+        register() {
+            this.ctx.state.data.actions.add(LoadVolseg);
+            this.ctx.customStructureControls.set('volseg', VolsegUI as any);
+            this.initializeEntryLists(); // do not await
+
+            const entries = new Map<string, VolsegEntryData>();
+            this.subscribeObservable(this.ctx.state.data.events.cell.created, o => {
+                if (o.cell.obj instanceof VolsegEntryData) entries.set(o.ref, o.cell.obj);
+            });
+
+            this.subscribeObservable(this.ctx.state.data.events.cell.removed, o => {
+                if (entries.has(o.ref)) {
+                    entries.get(o.ref)!.dispose();
+                    entries.delete(o.ref);
+                }
+            });
+        }
+        unregister() {
+            this.ctx.state.data.actions.remove(LoadVolseg);
+            this.ctx.customStructureControls.delete('volseg');
+        }
+        private async initializeEntryLists() {
+            const apiUrl = this.ctx.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLSEG_SERVER;
+            const api = new VolumeApiV2(apiUrl);
+            const entryLists = await api.getEntryList(10 ** 6);
+            Object.values(entryLists).forEach(l => l.sort());
+            (this.ctx.customState as any).volsegAvailableEntries = entryLists;
+        }
+    }
+});
+
+
+export const LoadVolseg = StateAction.build({
+    display: { name: 'Load Volume & Segmentation' },
+    from: SO.Root,
+    params: (a, plugin: PluginContext) => {
+        const res = createLoadVolsegParams(plugin, (plugin.customState as any).volsegAvailableEntries);
+        return res;
+    },
+})(({ params, state }, ctx: PluginContext) => Task.create('Loading Volume & Segmentation', taskCtx => {
+    return state.transaction(async () => {
+        const entryParams = VolsegEntryParamValues.fromLoadVolsegParamValues(params);
+        if (entryParams.entryId.trim().length === 0) {
+            alert('Must specify Entry Id!');
+            throw new Error('Specify Entry Id');
+        }
+        if (!entryParams.entryId.includes('-')) {
+            // add source prefix if the user omitted it (e.g. 1832 -> emd-1832)
+            entryParams.entryId = createEntryId(entryParams.source, entryParams.entryId);
+        }
+        ctx.behaviors.layout.leftPanelTabName.next('data');
+
+        const globalStateNode = ctx.state.data.selectQ(q => q.ofType(VolsegGlobalState))[0];
+        if (!globalStateNode) {
+            await state.build().toRoot().apply(VolsegGlobalStateFromRoot, {}, { state: { isGhost: !DEBUGGING } }).commit();
+        }
+
+        const entryNode = await state.build().toRoot().apply(VolsegEntryFromRoot, entryParams).commit();
+        await state.build().to(entryNode).apply(VolsegStateFromEntry, {}, { state: { isGhost: !DEBUGGING } }).commit();
+        if (entryNode.data) {
+            await entryNode.data.loadVolume();
+            await entryNode.data.loadSegmentations();
+        }
+    }).runInContext(taskCtx);
+}));

src/extensions/volumes-and-segmentations/transformers.ts

@@ -0,0 +1,70 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateTransformer } from '../../mol-state';
+import { Task } from '../../mol-task';
+
+import { VolsegEntry, VolsegEntryData, createVolsegEntryParams } from './entry-root';
+import { VolsegState, VolsegStateParams, VOLSEG_STATE_FROM_ENTRY_TRANSFORMER_NAME } from './entry-state';
+import { VolsegGlobalState, VolsegGlobalStateData, VolsegGlobalStateParams } from './global-state';
+
+
+export const VolsegEntryFromRoot = PluginStateTransform.BuiltIn({
+    name: 'volseg-entry-from-root',
+    display: { name: 'Vol & Seg Entry', description: 'Vol & Seg Entry' },
+    from: PluginStateObject.Root,
+    to: VolsegEntry,
+    params: (a, plugin: PluginContext) => createVolsegEntryParams(plugin),
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Load Vol & Seg Entry', async () => {
+            const data = await VolsegEntryData.create(plugin, params);
+            return new VolsegEntry(data, { label: data.entryId, description: 'Vol & Seg Entry' });
+        });
+    },
+    update({ b, oldParams, newParams }) {
+        Object.assign(newParams, oldParams);
+        console.error('Changing params of existing VolsegEntry node is not allowed');
+        return StateTransformer.UpdateResult.Unchanged;
+    }
+});
+
+
+export const VolsegStateFromEntry = PluginStateTransform.BuiltIn({
+    name: VOLSEG_STATE_FROM_ENTRY_TRANSFORMER_NAME,
+    display: { name: 'Vol & Seg Entry State', description: 'Vol & Seg Entry State' },
+    from: VolsegEntry,
+    to: VolsegState,
+    params: VolsegStateParams,
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Create Vol & Seg Entry State', async () => {
+            return new VolsegState(params, { label: 'State' });
+        });
+    }
+});
+
+
+export const VolsegGlobalStateFromRoot = PluginStateTransform.BuiltIn({
+    name: 'volseg-global-state-from-root',
+    display: { name: 'Vol & Seg Global State', description: 'Vol & Seg Global State' },
+    from: PluginStateObject.Root,
+    to: VolsegGlobalState,
+    params: VolsegGlobalStateParams,
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Create Vol & Seg Global State', async () => {
+            const data = new VolsegGlobalStateData(plugin, params);
+            return new VolsegGlobalState(data, { label: 'Global State', description: 'Vol & Seg Global State' });
+        });
+    },
+    update({ b, oldParams, newParams }) {
+        b.data.currentState.next(newParams);
+        return StateTransformer.UpdateResult.Updated;
+    }
+});

src/extensions/volumes-and-segmentations/ui.tsx

@@ -0,0 +1,264 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { useCallback, useEffect, useRef, useState } from 'react';
+
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button, ControlRow, ExpandGroup, IconButton } from '../../mol-plugin-ui/controls/common';
+import * as Icons from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { Slider } from '../../mol-plugin-ui/controls/slider';
+import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { UpdateTransformControl } from '../../mol-plugin-ui/state/update-transform';
+import { PluginContext } from '../../mol-plugin/context';
+import { shallowEqualArrays } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { sleep } from '../../mol-util/sleep';
+
+import { VolsegEntry, VolsegEntryData } from './entry-root';
+import { SimpleVolumeParams, SimpleVolumeParamValues } from './entry-volume';
+import { VolsegGlobalState, VolsegGlobalStateData, VolsegGlobalStateParams } from './global-state';
+import { isDefined } from './helpers';
+
+
+interface VolsegUIData {
+    globalState?: VolsegGlobalStateData,
+    availableNodes: VolsegEntry[],
+    activeNode?: VolsegEntry,
+}
+namespace VolsegUIData {
+    export function changeAvailableNodes(data: VolsegUIData, newNodes: VolsegEntry[]): VolsegUIData {
+        const newActiveNode = newNodes.length > data.availableNodes.length ?
+            newNodes[newNodes.length - 1]
+            : newNodes.find(node => node.data.ref === data.activeNode?.data.ref) ?? newNodes[0];
+        return { ...data, availableNodes: newNodes, activeNode: newActiveNode };
+    }
+    export function changeActiveNode(data: VolsegUIData, newActiveRef: string): VolsegUIData {
+        const newActiveNode = data.availableNodes.find(node => node.data.ref === newActiveRef) ?? data.availableNodes[0];
+        return { ...data, availableNodes: data.availableNodes, activeNode: newActiveNode };
+    }
+    export function equals(data1: VolsegUIData, data2: VolsegUIData) {
+        return shallowEqualArrays(data1.availableNodes, data2.availableNodes) && data1.activeNode === data2.activeNode && data1.globalState === data2.globalState;
+    }
+}
+
+export class VolsegUI extends CollapsableControls<{}, { data: VolsegUIData }> {
+    protected defaultState(): CollapsableState & { data: VolsegUIData } {
+        return {
+            header: 'Volume & Segmentation',
+            isCollapsed: true,
+            brand: { accent: 'orange', svg: Icons.ExtensionSvg },
+            data: {
+                globalState: undefined,
+                availableNodes: [],
+                activeNode: undefined,
+            }
+        };
+    }
+    protected renderControls(): JSX.Element | null {
+        return <VolsegControls plugin={this.plugin} data={this.state.data} setData={d => this.setState({ data: d })} />;
+    }
+    componentDidMount(): void {
+        this.setState({ isHidden: true, isCollapsed: false });
+        this.subscribe(this.plugin.state.data.events.changed, e => {
+            const nodes = e.state.selectQ(q => q.ofType(VolsegEntry)).map(cell => cell?.obj).filter(isDefined);
+            const isHidden = nodes.length === 0;
+            const newData = VolsegUIData.changeAvailableNodes(this.state.data, nodes);
+            if (!this.state.data.globalState?.isRegistered()) {
+                const globalState = e.state.selectQ(q => q.ofType(VolsegGlobalState))[0]?.obj?.data;
+                if (globalState) newData.globalState = globalState;
+            }
+            if (!VolsegUIData.equals(this.state.data, newData) || this.state.isHidden !== isHidden) {
+                this.setState({ data: newData, isHidden: isHidden });
+            }
+        });
+    }
+}
+
+
+function VolsegControls({ plugin, data, setData }: { plugin: PluginContext, data: VolsegUIData, setData: (d: VolsegUIData) => void }) {
+    const entryData = data.activeNode?.data;
+    if (!entryData) {
+        return <p>No data!</p>;
+    }
+    if (!data.globalState) {
+        return <p>No global state!</p>;
+    }
+
+    const params = {
+        /** Reference to the active VolsegEntry node */
+        entry: PD.Select(data.activeNode!.data.ref, data.availableNodes.map(entry => [entry.data.ref, entry.data.entryId]))
+    };
+    const values: PD.Values<typeof params> = {
+        entry: data.activeNode!.data.ref,
+    };
+
+    const globalState = useBehavior(data.globalState.currentState);
+
+    return <>
+        <ParameterControls params={params} values={values} onChangeValues={next => setData(VolsegUIData.changeActiveNode(data, next.entry))} />
+
+        <ExpandGroup header='Global options'>
+            <WaitingParameterControls params={VolsegGlobalStateParams} values={globalState} onChangeValues={async next => await data.globalState?.updateState(plugin, next)} />
+        </ExpandGroup>
+
+        <VolsegEntryControls entryData={entryData} key={entryData.ref} />
+    </>;
+}
+
+function VolsegEntryControls({ entryData }: { entryData: VolsegEntryData }) {
+    const state = useBehavior(entryData.currentState);
+
+    const allSegments = entryData.metadata.allSegments;
+    const selectedSegment = entryData.metadata.getSegment(state.selectedSegment);
+    const visibleSegments = state.visibleSegments.map(seg => seg.segmentId);
+    const visibleModels = state.visibleModels.map(model => model.pdbId);
+    const allPdbs = entryData.pdbs;
+
+    return <>
+        {/* Title */}
+        <div style={{ fontWeight: 'bold', padding: 8, paddingTop: 6, paddingBottom: 4, overflow: 'hidden' }}>
+            {entryData.metadata.raw.annotation?.name ?? 'Unnamed Annotation'}
+        </div>
+
+        {/* Fitted models */}
+        {allPdbs.length > 0 && <ExpandGroup header='Fitted models in PDB' initiallyExpanded>
+            {allPdbs.map(pdb =>
+                <WaitingButton key={pdb} onClick={() => entryData.actionShowFittedModel(visibleModels.includes(pdb) ? [] : [pdb])}
+                    style={{ fontWeight: visibleModels.includes(pdb) ? 'bold' : undefined, textAlign: 'left', marginTop: 1 }}>
+                    {pdb}
+                </WaitingButton>
+            )}
+        </ExpandGroup>}
+
+        {/* Volume */}
+        <VolumeControls entryData={entryData} />
+        <ExpandGroup header='Segmentation data' initiallyExpanded>
+            {/* Segment opacity slider */}
+            <ControlRow label='Opacity' control={
+                <WaitingSlider min={0} max={1} value={state.segmentOpacity} step={0.05} onChange={async v => await entryData.actionSetOpacity(v)} />
+            } />
+
+            {/* Segment toggles */}
+            {allSegments.length > 0 && <>
+                <WaitingButton onClick={async () => { await sleep(20); await entryData.actionToggleAllSegments(); }} style={{ marginTop: 1 }}>
+                    Toggle All segments
+                </WaitingButton>
+                <div style={{ maxHeight: 200, overflow: 'hidden', overflowY: 'auto', marginBlock: 1 }}>
+                    {allSegments.map(segment =>
+                        <div style={{ display: 'flex', marginBottom: 1 }} key={segment.id}
+                            onMouseEnter={() => entryData.actionHighlightSegment(segment)}
+                            onMouseLeave={() => entryData.actionHighlightSegment()}>
+                            <Button onClick={() => entryData.actionSelectSegment(segment !== selectedSegment ? segment.id : undefined)}
+                                style={{ fontWeight: segment.id === selectedSegment?.id ? 'bold' : undefined, marginRight: 1, flexGrow: 1, textAlign: 'left' }}>
+                                <div title={segment.biological_annotation.name ?? 'Unnamed segment'} style={{ maxWidth: 240, whiteSpace: 'nowrap', overflow: 'hidden', textOverflow: 'ellipsis' }}>
+                                    {segment.biological_annotation.name ?? 'Unnamed segment'} ({segment.id})
+                                </div>
+                            </Button>
+                            <IconButton svg={visibleSegments.includes(segment.id) ? Icons.VisibilityOutlinedSvg : Icons.VisibilityOffOutlinedSvg}
+                                onClick={() => entryData.actionToggleSegment(segment.id)} />
+                        </div>
+                    )}
+                </div>
+            </>}
+        </ExpandGroup>
+
+        {/* Segment annotations */}
+        <ExpandGroup header='Selected segment annotation' initiallyExpanded>
+            <div style={{ paddingTop: 4, paddingRight: 8, maxHeight: 300, overflow: 'hidden', overflowY: 'auto' }}>
+                {!selectedSegment && 'No segment selected'}
+                {selectedSegment && <b>Segment {selectedSegment.id}:<br />{selectedSegment.biological_annotation.name ?? 'Unnamed segment'}</b>}
+                {selectedSegment?.biological_annotation.external_references.map(ref =>
+                    <p key={ref.id} style={{ marginTop: 4 }}>
+                        <small>{ref.resource}:{ref.accession}</small><br />
+                        <b>{capitalize(ref.label)}</b><br />
+                        {ref.description}
+                    </p>)}
+            </div>
+        </ExpandGroup>
+    </>;
+}
+
+function VolumeControls({ entryData }: { entryData: VolsegEntryData }) {
+    const vol = useBehavior(entryData.currentVolume);
+    if (!vol) return null;
+
+    const volumeValues: SimpleVolumeParamValues = {
+        volumeType: vol.state.isHidden ? 'off' : vol.params?.type.name as any,
+        opacity: vol.params?.type.params.alpha,
+    };
+
+    return <ExpandGroup header='Volume data' initiallyExpanded>
+        <WaitingParameterControls params={SimpleVolumeParams} values={volumeValues} onChangeValues={async next => { await sleep(20); await entryData.actionUpdateVolumeVisual(next); }} />
+        <ExpandGroup header='Detailed Volume Params' headerStyle={{ marginTop: 1 }}>
+            <UpdateTransformControl state={entryData.plugin.state.data} transform={vol} customHeader='none' />
+        </ExpandGroup>
+    </ExpandGroup>;
+}
+
+type ComponentParams<T extends React.Component<any, any, any> | ((props: any) => JSX.Element)> =
+    T extends React.Component<infer P, any, any> ? P : T extends (props: infer P) => JSX.Element ? P : never;
+
+function WaitingSlider({ value, onChange, ...etc }: { value: number, onChange: (value: number) => any } & ComponentParams<Slider>) {
+    const [changing, sliderValue, execute] = useAsyncChange(value);
+
+    return <Slider value={sliderValue} disabled={changing} onChange={newValue => execute(onChange, newValue)} {...etc} />;
+}
+
+function WaitingButton({ onClick, ...etc }: { onClick: () => any } & ComponentParams<typeof Button>) {
+    const [changing, _, execute] = useAsyncChange(undefined);
+
+    return <Button disabled={changing} onClick={() => execute(onClick, undefined)} {...etc}>
+        {etc.children}
+    </Button>;
+}
+
+function WaitingParameterControls<T extends PD.Params>({ values, onChangeValues, ...etc }: { values: PD.ValuesFor<T>, onChangeValues: (values: PD.ValuesFor<T>) => any } & ComponentParams<ParameterControls<T>>) {
+    const [changing, currentValues, execute] = useAsyncChange(values);
+
+    return <ParameterControls isDisabled={changing} values={currentValues} onChangeValues={newValue => execute(onChangeValues, newValue)} {...etc} />;
+}
+
+function capitalize(text: string) {
+    const first = text.charAt(0);
+    const rest = text.slice(1);
+    return first.toUpperCase() + rest;
+}
+
+function useAsyncChange<T>(initialValue: T) {
+    const [isExecuting, setIsExecuting] = useState(false);
+    const [value, setValue] = useState(initialValue);
+    const isMounted = useRef(false);
+
+    useEffect(() => setValue(initialValue), [initialValue]);
+
+    useEffect(() => {
+        isMounted.current = true;
+        return () => { isMounted.current = false; };
+    }, []);
+
+    const execute = useCallback(
+        async (func: (val: T) => Promise<any>, val: T) => {
+            setIsExecuting(true);
+            setValue(val);
+            try {
+                await func(val);
+            } catch (err) {
+                if (isMounted.current) {
+                    setValue(initialValue);
+                }
+                throw err;
+            } finally {
+                if (isMounted.current) {
+                    setIsExecuting(false);
+                }
+            }
+        },
+        []
+    );
+
+    return [isExecuting, value, execute] as const;
+}

src/extensions/volumes-and-segmentations/volseg-api/api.ts

@@ -0,0 +1,65 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { type Metadata } from './data';
+
+
+export const DEFAULT_VOLSEG_SERVER = 'https://molstarvolseg.ncbr.muni.cz/v2';
+
+
+export class VolumeApiV2 {
+    public volumeServerUrl: string;
+
+    public constructor(volumeServerUrl: string = DEFAULT_VOLSEG_SERVER) {
+        this.volumeServerUrl = volumeServerUrl.replace(/\/$/, ''); // trim trailing slash
+    }
+
+    public entryListUrl(maxEntries: number, keyword?: string): string {
+        return `${this.volumeServerUrl}/list_entries/${maxEntries}/${keyword ?? ''}`;
+    }
+
+    public metadataUrl(source: string, entryId: string): string {
+        return `${this.volumeServerUrl}/${source}/${entryId}/metadata`;
+    }
+    public volumeUrl(source: string, entryId: string, box: [[number, number, number], [number, number, number]] | null, maxPoints: number): string {
+        if (box) {
+            const [[a1, a2, a3], [b1, b2, b3]] = box;
+            return `${this.volumeServerUrl}/${source}/${entryId}/volume/box/${a1}/${a2}/${a3}/${b1}/${b2}/${b3}?max_points=${maxPoints}`;
+        } else {
+            return `${this.volumeServerUrl}/${source}/${entryId}/volume/cell?max_points=${maxPoints}`;
+        }
+    }
+    public latticeUrl(source: string, entryId: string, segmentation: number, box: [[number, number, number], [number, number, number]] | null, maxPoints: number): string {
+        if (box) {
+            const [[a1, a2, a3], [b1, b2, b3]] = box;
+            return `${this.volumeServerUrl}/${source}/${entryId}/segmentation/box/${segmentation}/${a1}/${a2}/${a3}/${b1}/${b2}/${b3}?max_points=${maxPoints}`;
+        } else {
+            return `${this.volumeServerUrl}/${source}/${entryId}/segmentation/cell/${segmentation}?max_points=${maxPoints}`;
+        }
+    }
+    public meshUrl_Json(source: string, entryId: string, segment: number, detailLevel: number): string {
+        return `${this.volumeServerUrl}/${source}/${entryId}/mesh/${segment}/${detailLevel}`;
+    }
+
+    public meshUrl_Bcif(source: string, entryId: string, segment: number, detailLevel: number): string {
+        return `${this.volumeServerUrl}/${source}/${entryId}/mesh_bcif/${segment}/${detailLevel}`;
+    }
+    public volumeInfoUrl(source: string, entryId: string): string {
+        return `${this.volumeServerUrl}/${source}/${entryId}/volume_info`;
+    }
+
+    public async getEntryList(maxEntries: number, keyword?: string): Promise<{ [source: string]: string[] }> {
+        const response = await fetch(this.entryListUrl(maxEntries, keyword));
+        return await response.json();
+    }
+
+    public async getMetadata(source: string, entryId: string): Promise<Metadata> {
+        const url = this.metadataUrl(source, entryId);
+        const response = await fetch(url);
+        if (!response.ok) throw new Error(`Failed to fetch metadata from ${url}`);
+        return await response.json();
+    }
+}

src/extensions/volumes-and-segmentations/volseg-api/data.ts

@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+export interface Metadata {
+    grid: {
+        general: {
+            details: string,
+            source_db_name: string,
+            source_db_id: string,
+        },
+        volumes: Volumes,
+        segmentation_lattices: SegmentationLattices,
+        segmentation_meshes: SegmentationMeshes,
+    },
+    annotation: Annotation | null,
+}
+
+export interface Volumes {
+    volume_downsamplings: number[],
+    voxel_size: { [downsampling: number]: Vector3 },
+    origin: Vector3,
+    grid_dimensions: Vector3,
+    sampled_grid_dimensions: { [downsampling: number]: Vector3 },
+    mean: { [downsampling: number]: number },
+    std: { [downsampling: number]: number },
+    min: { [downsampling: number]: number },
+    max: { [downsampling: number]: number },
+    volume_force_dtype: string,
+}
+
+export interface SegmentationLattices {
+    segmentation_lattice_ids: number[],
+    segmentation_downsamplings: { [lattice: number]: number[] },
+}
+
+export interface SegmentationMeshes {
+    mesh_component_numbers: {
+        segment_ids?: {
+            [segId: number]: {
+                detail_lvls: {
+                    [detail: number]: {
+                        mesh_ids: {
+                            [meshId: number]: {
+                                num_triangles: number,
+                                num_vertices: number
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    detail_lvl_to_fraction: {
+        [lvl: number]: number
+    }
+}
+
+export interface Annotation {
+    name: string,
+    details: string,
+    segment_list: Segment[],
+}
+
+export interface Segment {
+    id: number,
+    colour: number[],
+    biological_annotation: BiologicalAnnotation,
+}
+
+export interface BiologicalAnnotation {
+    name: string,
+    external_references: ExternalReference[]
+}
+
+export interface ExternalReference {
+    id: number, resource: string, accession: string, label: string,
+    description: string
+}
+
+type Vector3 = [number, number, number];

src/extensions/volumes-and-segmentations/volseg-api/utils.ts

@@ -0,0 +1,74 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { Color } from '../../../mol-util/color';
+import { Metadata, Segment } from './data';
+
+
+export class MetadataWrapper {
+    raw: Metadata;
+    private segmentMap?: { [id: number]: Segment };
+
+    constructor(rawMetadata: Metadata) {
+        this.raw = rawMetadata;
+    }
+
+    get allSegments() {
+        return this.raw.annotation?.segment_list ?? [];
+    }
+
+    get allSegmentIds() {
+        return this.allSegments.map(segment => segment.id);
+    }
+
+    getSegment(segmentId: number): Segment | undefined {
+        if (!this.segmentMap) {
+            this.segmentMap = {};
+            for (const segment of this.allSegments) {
+                this.segmentMap[segment.id] = segment;
+            }
+        }
+        return this.segmentMap[segmentId];
+    }
+
+    getSegmentColor(segmentId: number): Color | undefined {
+        const colorArray = this.getSegment(segmentId)?.colour;
+        return colorArray ? Color.fromNormalizedArray(colorArray, 0) : undefined;
+    }
+
+    /** Get the list of detail levels available for the given mesh segment. */
+    getMeshDetailLevels(segmentId: number): number[] {
+        const segmentIds = this.raw.grid.segmentation_meshes.mesh_component_numbers.segment_ids;
+        if (!segmentIds) return [];
+        const details = segmentIds[segmentId].detail_lvls;
+        return Object.keys(details).map(s => parseInt(s));
+    }
+
+    /** Get the worst available detail level that is not worse than preferredDetail.
+     * If preferredDetail is null, get the worst detail level overall.
+     * (worse = greater number) */
+    getSufficientMeshDetail(segmentId: number, preferredDetail: number | null) {
+        let availDetails = this.getMeshDetailLevels(segmentId);
+        if (preferredDetail !== null) {
+            availDetails = availDetails.filter(det => det <= preferredDetail);
+        }
+        return Math.max(...availDetails);
+    }
+
+    /** IDs of all segments available as meshes */
+    get meshSegmentIds() {
+        const segmentIds = this.raw.grid.segmentation_meshes.mesh_component_numbers.segment_ids;
+        if (!segmentIds) return [];
+        return Object.keys(segmentIds).map(s => parseInt(s));
+    }
+
+    get gridTotalVolume() {
+        const [vx, vy, vz] = this.raw.grid.volumes.voxel_size[1];
+        const [gx, gy, gz] = this.raw.grid.volumes.grid_dimensions;
+        return vx * vy * vz * gx * gy * gz;
+    }
+
+}

src/mol-canvas3d/camera.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -119,11 +119,11 @@ class Camera implements ICamera {
         return Camera.targetDistance(radius, this.state.fov, this.viewport.width, this.viewport.height);
     }
 
-    getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot> {
+    getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3, snapshot?: Partial<Camera.Snapshot>): Partial<Camera.Snapshot> {
         const r = Math.max(radius, 0.01);
         const targetDistance = this.getTargetDistance(r);
 
-        Vec3.sub(this.deltaDirection, this.target, this.position);
+        Vec3.sub(this.deltaDirection, snapshot?.target ?? this.target, snapshot?.position ?? this.position);
         if (dir) Vec3.matchDirection(this.deltaDirection, dir, this.deltaDirection);
         Vec3.setMagnitude(this.deltaDirection, this.deltaDirection, targetDistance);
         Vec3.sub(this.newPosition, target, this.deltaDirection);
@@ -137,6 +137,18 @@ class Camera implements ICamera {
         return state;
     }
 
+    getCenter(target: Vec3, radius?: number): Partial<Camera.Snapshot> {
+        Vec3.sub(this.deltaDirection, this.target, this.position);
+        Vec3.sub(this.newPosition, target, this.deltaDirection);
+
+        const state = Camera.copySnapshot(Camera.createDefaultSnapshot(), this.state);
+        state.target = Vec3.clone(target);
+        state.position = Vec3.clone(this.newPosition);
+        if (radius) state.radius = Math.max(radius, 0.01);
+
+        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);
@@ -160,6 +172,10 @@ class Camera implements ICamera {
         }
     }
 
+    center(target: Vec3, durationMs?: number) {
+        this.setState(this.getCenter(target), durationMs);
+    }
+
     /** Transform point into 2D window coordinates. */
     project(out: Vec4, point: Vec3) {
         return cameraProject(out, point, this.viewport, this.projectionView);

src/mol-canvas3d/canvas3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -31,7 +31,7 @@ import { PickData } from './passes/pick';
 import { PickHelper } from './passes/pick';
 import { ImagePass, ImageProps } from './passes/image';
 import { Sphere3D } from '../mol-math/geometry';
-import { isDebugMode, isTimingMode } from '../mol-util/debug';
+import { addConsoleStatsProvider, isDebugMode, isTimingMode, removeConsoleStatsProvider } from '../mol-util/debug';
 import { CameraHelperParams } from './helper/camera-helper';
 import { produce } from 'immer';
 import { HandleHelperParams } from './helper/handle-helper';
@@ -120,6 +120,7 @@ interface Canvas3DContext {
 
 namespace Canvas3DContext {
     export const DefaultAttribs = {
+        powerPreference: 'high-performance' as WebGLContextAttributes['powerPreference'],
         failIfMajorPerformanceCaveat: false,
         /** true by default to avoid issues with Safari (Jan 2021) */
         antialias: true,
@@ -140,8 +141,9 @@ namespace Canvas3DContext {
 
         if (a.enableWboit && a.enableDpoit) throw new Error('Multiple transparency methods not allowed.');
 
-        const { failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
+        const { powerPreference, failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
         const gl = getGLContext(canvas, {
+            powerPreference,
             failIfMajorPerformanceCaveat,
             antialias,
             preserveDrawingBuffer,
@@ -258,6 +260,7 @@ interface Canvas3D {
     notifyDidDraw: boolean,
     readonly didDraw: BehaviorSubject<now.Timestamp>
     readonly commited: BehaviorSubject<now.Timestamp>
+    readonly commitQueueSize: BehaviorSubject<number>
     readonly reprCount: BehaviorSubject<number>
     readonly resized: BehaviorSubject<any>
 
@@ -304,6 +307,7 @@ namespace Canvas3D {
         let startTime = now();
         const didDraw = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
         const commited = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
+        const commitQueueSize = new BehaviorSubject<number>(0);
 
         const { gl, contextRestored } = webgl;
 
@@ -438,7 +442,7 @@ namespace Canvas3D {
                     cam = stereoCamera;
                 }
 
-                if (isTimingMode) webgl.timer.mark('Canvas3D.render');
+                if (isTimingMode) webgl.timer.mark('Canvas3D.render', true);
                 const ctx = { renderer, camera: cam, scene, helper };
                 if (MultiSamplePass.isEnabled(p.multiSample)) {
                     const forceOn = !cameraChanged && markingUpdated && !controls.isAnimating;
@@ -591,7 +595,11 @@ namespace Canvas3D {
             // snapshot the current bounding sphere of visible objects
             Sphere3D.copy(oldBoundingSphereVisible, scene.boundingSphereVisible);
 
-            if (!scene.commit(isSynchronous ? void 0 : sceneCommitTimeoutMs)) return false;
+            if (!scene.commit(isSynchronous ? void 0 : sceneCommitTimeoutMs)) {
+                commitQueueSize.next(scene.commitQueueSize);
+                return false;
+            }
+            commitQueueSize.next(0);
 
             if (helper.debug.isEnabled) helper.debug.update();
             if (!p.camera.manualReset && (reprCount.value === 0 || shouldResetCamera())) {
@@ -621,6 +629,8 @@ namespace Canvas3D {
                 attribute: `${(attribute / 1024 / 1024).toFixed(3)} MiB`,
                 elements: `${(elements / 1024 / 1024).toFixed(3)} MiB`,
             });
+
+            console.log(webgl.timer.formatedStats());
         }
 
         function add(repr: Representation.Any) {
@@ -726,6 +736,8 @@ namespace Canvas3D {
             resized.next(+new Date());
         }
 
+        addConsoleStatsProvider(consoleStats);
+
         return {
             webgl,
 
@@ -788,6 +800,7 @@ namespace Canvas3D {
             set notifyDidDraw(v: boolean) { notifyDidDraw = v; },
             didDraw,
             commited,
+            commitQueueSize,
             reprCount,
             resized,
             setProps: (properties, doNotRequestDraw = false) => {
@@ -903,6 +916,8 @@ namespace Canvas3D {
                 controls.dispose();
                 renderer.dispose();
                 interactionHelper.dispose();
+
+                removeConsoleStatsProvider(consoleStats);
             }
         };
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,6 +11,8 @@ 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 { Text } from '../../mol-geo/geometry/text/text';
+import { TextBuilder } from '../../mol-geo/geometry/text/text-builder';
 import { GraphicsRenderObject } from '../../mol-gl/render-object';
 import { Scene } from '../../mol-gl/scene';
 import { WebGLContext } from '../../mol-gl/webgl/context';
@@ -23,19 +25,36 @@ 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 { assertUnreachable } from '../../mol-util/type-helpers';
 import { Camera, ICamera } from '../camera';
 import { Viewport } from '../camera/util';
 
 // TODO add scale line/grid
 
 const AxesParams = {
-    ...Mesh.Params,
-    alpha: { ...Mesh.Params.alpha, defaultValue: 0.51 },
-    ignoreLight: { ...Mesh.Params.ignoreLight, defaultValue: true },
+    alpha: PD.Numeric(0.51, { min: 0, max: 1, step: 0.01 }, { isEssential: true, label: 'Opacity' }),
     colorX: PD.Color(ColorNames.red, { isEssential: true }),
     colorY: PD.Color(ColorNames.green, { isEssential: true }),
     colorZ: PD.Color(ColorNames.blue, { isEssential: true }),
     scale: PD.Numeric(0.33, { min: 0.1, max: 2, step: 0.1 }, { isEssential: true }),
+    location: PD.Select('bottom-left', PD.arrayToOptions(['bottom-left', 'bottom-right', 'top-left', 'top-right'] as const)),
+    locationOffsetX: PD.Numeric(0),
+    locationOffsetY: PD.Numeric(0),
+    originColor: PD.Color(ColorNames.grey),
+    radiusScale: PD.Numeric(0.075, { min: 0.01, max: 0.3, step: 0.001 }),
+    showPlanes: PD.Boolean(true),
+    planeColorXY: PD.Color(ColorNames.grey, { label: 'Plane Color XY' }),
+    planeColorXZ: PD.Color(ColorNames.grey, { label: 'Plane Color XZ' }),
+    planeColorYZ: PD.Color(ColorNames.grey, { label: 'Plane Color YZ' }),
+    showLabels: PD.Boolean(false),
+    labelX: PD.Text('X'),
+    labelY: PD.Text('Y'),
+    labelZ: PD.Text('Z'),
+    labelColorX: PD.Color(ColorNames.grey),
+    labelColorY: PD.Color(ColorNames.grey),
+    labelColorZ: PD.Color(ColorNames.grey),
+    labelOpacity: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+    labelScale: PD.Numeric(0.25, { min: 0.1, max: 1.0, step: 0.01 }),
 };
 type AxesParams = typeof AxesParams
 type AxesProps = PD.Values<AxesParams>
@@ -56,7 +75,9 @@ export class CameraHelper {
         axes: { name: 'off', params: {} }
     };
 
-    private renderObject: GraphicsRenderObject | undefined;
+    private meshRenderObject: GraphicsRenderObject | undefined;
+    private textRenderObject: GraphicsRenderObject | undefined;
+    private pixelRatio = 1;
 
     constructor(private webgl: WebGLContext, props: Partial<CameraHelperProps> = {}) {
         this.scene = Scene.create(webgl, GraphicsRenderVariantsBlended);
@@ -74,9 +95,20 @@ export class CameraHelper {
                 p.axes.name = props.axes.name;
                 if (props.axes.name === 'on') {
                     this.scene.clear();
-                    const params = { ...props.axes.params, scale: props.axes.params.scale * this.webgl.pixelRatio };
-                    this.renderObject = createAxesRenderObject(params);
-                    this.scene.add(this.renderObject);
+                    this.pixelRatio = this.webgl.pixelRatio;
+                    const params = {
+                        ...props.axes.params,
+                        scale: props.axes.params.scale * this.pixelRatio,
+                        labelScale: props.axes.params.labelScale * this.pixelRatio,
+                    };
+                    this.meshRenderObject = createMeshRenderObject(params);
+                    this.scene.add(this.meshRenderObject);
+                    if (props.axes.params.showLabels) {
+                        this.textRenderObject = createTextRenderObject(params);
+                        this.scene.add(this.textRenderObject);
+                    } else {
+                        this.textRenderObject = undefined;
+                    }
                     this.scene.commit();
 
                     Vec3.set(this.camera.position, 0, 0, params.scale * 200);
@@ -94,19 +126,29 @@ export class CameraHelper {
 
     getLoci(pickingId: PickingId) {
         const { objectId, groupId, instanceId } = pickingId;
-        if (!this.renderObject || objectId !== this.renderObject.id || groupId === CameraHelperAxis.None) return EmptyLoci;
+        if ((
+            (!this.meshRenderObject || objectId !== this.meshRenderObject.id) &&
+            (!this.textRenderObject || objectId !== this.textRenderObject.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;
+        if (this.meshRenderObject) {
+            const groupCount = this.meshRenderObject.values.uGroupCount.ref.value;
+            for (const { groupId, instanceId } of loci.elements) {
+                const idx = instanceId * groupCount + groupId;
+                if (apply(Interval.ofSingleton(idx))) changed = true;
+            }
+        }
+        if (this.textRenderObject) {
+            const groupCount = this.textRenderObject.values.uGroupCount.ref.value;
+            for (const { groupId, instanceId } of loci.elements) {
+                const idx = instanceId * groupCount + groupId;
+                if (apply(Interval.ofSingleton(idx))) changed = true;
+            }
         }
         return changed;
     };
@@ -117,42 +159,82 @@ export class CameraHelper {
             if (!isCameraAxesLoci(loci)) return false;
             if (loci.data !== this) return false;
         }
-        return Visual.mark(this.renderObject, loci, action, this.eachGroup);
+        return (
+            Visual.mark(this.meshRenderObject, loci, action, this.eachGroup) ||
+            Visual.mark(this.textRenderObject, loci, action, this.eachGroup)
+        );
     }
 
     update(camera: ICamera) {
-        if (!this.renderObject) return;
+        if (!this.meshRenderObject || this.props.axes.name === 'off') return;
+
+        if (this.pixelRatio !== this.webgl.pixelRatio) {
+            this.setProps(this.props);
+        }
 
         updateCamera(this.camera, camera.viewport, camera.viewOffset);
         Mat4.extractRotation(this.scene.view, camera.view);
 
-        const r = this.renderObject.values.boundingSphere.ref.value.radius;
-        Mat4.setTranslation(this.scene.view, Vec3.create(
-            -camera.viewport.width / 2 + r,
-            -camera.viewport.height / 2 + r,
-            0
-        ));
+        const r = this.textRenderObject
+            ? this.textRenderObject.values.boundingSphere.ref.value.radius
+            : this.meshRenderObject.values.boundingSphere.ref.value.radius;
+        const l = this.props.axes.params.location;
+        const ox = this.props.axes.params.locationOffsetX * this.pixelRatio;
+        const oy = this.props.axes.params.locationOffsetY * this.pixelRatio;
+        if (l === 'bottom-left') {
+            Mat4.setTranslation(this.scene.view, Vec3.create(
+                -camera.viewport.width / 2 + r + ox,
+                -camera.viewport.height / 2 + r + oy,
+                0
+            ));
+        } else if (l === 'bottom-right') {
+            Mat4.setTranslation(this.scene.view, Vec3.create(
+                camera.viewport.width / 2 - r - ox,
+                -camera.viewport.height / 2 + r + oy,
+                0
+            ));
+        } else if (l === 'top-left') {
+            Mat4.setTranslation(this.scene.view, Vec3.create(
+                -camera.viewport.width / 2 + r + ox,
+                camera.viewport.height / 2 - r - oy,
+                0
+            ));
+        } else if (l === 'top-right') {
+            Mat4.setTranslation(this.scene.view, Vec3.create(
+                camera.viewport.width / 2 - r - ox,
+                camera.viewport.height / 2 - r - oy,
+                0
+            ));
+        } else {
+            assertUnreachable(l);
+        }
     }
 }
 
-export const enum CameraHelperAxis {
+export enum CameraHelperAxis {
     None = 0,
     X,
     Y,
     Z,
     XY,
     XZ,
-    YZ
+    YZ,
+    Origin
 }
 
-function getAxisLabel(axis: number) {
+function getAxisLabel(axis: number, cameraHelper: CameraHelper) {
+    const a = cameraHelper.props.axes;
+    const x = a.name === 'on' ? a.params.labelX : 'X';
+    const y = a.name === 'on' ? a.params.labelY : 'Y';
+    const z = a.name === 'on' ? a.params.labelZ : 'Z';
     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';
+        case CameraHelperAxis.X: return `${x} Axis`;
+        case CameraHelperAxis.Y: return `${y} Axis`;
+        case CameraHelperAxis.Z: return `${z} Axis`;
+        case CameraHelperAxis.XY: return `${x}${y} Plane`;
+        case CameraHelperAxis.XZ: return `${x}${z} Plane`;
+        case CameraHelperAxis.YZ: return `${y}${z} Plane`;
+        case CameraHelperAxis.Origin: return 'Origin';
         default: return 'Axes';
     }
 }
@@ -160,7 +242,7 @@ function getAxisLabel(axis: number) {
 function CameraAxesLoci(cameraHelper: CameraHelper, groupId: number, instanceId: number) {
     return DataLoci('camera-axes', cameraHelper, [{ groupId, instanceId }],
         void 0 /** bounding sphere */,
-        () => getAxisLabel(groupId));
+        () => getAxisLabel(groupId, cameraHelper));
 }
 export type CameraAxesLoci = ReturnType<typeof CameraAxesLoci>
 export function isCameraAxesLoci(x: Loci): x is CameraAxesLoci {
@@ -197,15 +279,17 @@ function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.Vie
     Mat4.ortho(camera.projection, left, right, top, bottom, near, far);
 }
 
-function createAxesMesh(scale: number, mesh?: Mesh) {
+function createAxesMesh(props: AxesProps, mesh?: Mesh) {
     const state = MeshBuilder.createState(512, 256, mesh);
-    const radius = 0.075 * 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 scale = 100 * props.scale;
+    const radius = props.radiusScale * scale;
+    const textScale = props.showLabels ? 100 * props.labelScale / 3 : 0;
+    const x = Vec3.scale(Vec3(), Vec3.unitX, scale - textScale);
+    const y = Vec3.scale(Vec3(), Vec3.unitY, scale - textScale);
+    const z = Vec3.scale(Vec3(), Vec3.unitZ, scale - textScale);
     const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments: 32 };
 
-    state.currentGroup = CameraHelperAxis.None;
+    state.currentGroup = CameraHelperAxis.Origin;
     addSphere(state, Vec3.origin, radius, 2);
 
     state.currentGroup = CameraHelperAxis.X;
@@ -220,50 +304,102 @@ function createAxesMesh(scale: number, mesh?: Mesh) {
     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);
+    if (props.showPlanes) {
+        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.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.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);
+        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);
 }
 
-function getAxesShape(props: AxesProps, shape?: Shape<Mesh>) {
+function getAxesMeshShape(props: AxesProps, shape?: Shape<Mesh>) {
     const scale = 100 * props.scale;
-    const mesh = createAxesMesh(scale, shape?.geometry);
+    const mesh = createAxesMesh(props, shape?.geometry);
     mesh.setBoundingSphere(Sphere3D.create(Vec3.create(scale / 2, scale / 2, scale / 2), scale + scale / 4));
     const getColor = (groupId: number) => {
         switch (groupId) {
-            case 1: return props.colorX;
-            case 2: return props.colorY;
-            case 3: return props.colorZ;
+            case CameraHelperAxis.X: return props.colorX;
+            case CameraHelperAxis.Y: return props.colorY;
+            case CameraHelperAxis.Z: return props.colorZ;
+            case CameraHelperAxis.XY: return props.planeColorXY;
+            case CameraHelperAxis.XZ: return props.planeColorXZ;
+            case CameraHelperAxis.YZ: return props.planeColorYZ;
+            case CameraHelperAxis.Origin: return props.originColor;
             default: return ColorNames.grey;
         }
     };
-    return Shape.create('axes', {}, mesh, getColor, () => 1, () => '');
+    return Shape.create('axes-mesh', {}, mesh, getColor, () => 1, () => '');
 }
 
-function createAxesRenderObject(props: AxesProps) {
-    const shape = getAxesShape(props);
-    return Shape.createRenderObject(shape, props);
-}
+function createMeshRenderObject(props: AxesProps) {
+    const shape = getAxesMeshShape(props);
+    return Shape.createRenderObject(shape, {
+        ...PD.getDefaultValues(Mesh.Params),
+        ...props,
+        ignoreLight: true,
+    });
+}
+
+//
+
+function createAxesText(props: AxesProps, text?: Text) {
+    const builder = TextBuilder.create(props, 8, 8, text);
+    const scale = 100 * props.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 textScale = 100 * props.labelScale;
+    builder.add(props.labelX, x[0], x[1], x[2], 0.0, textScale, CameraHelperAxis.X);
+    builder.add(props.labelY, y[0], y[1], y[2], 0.0, textScale, CameraHelperAxis.Y);
+    builder.add(props.labelZ, z[0], z[1], z[2], 0.0, textScale, CameraHelperAxis.Z);
+
+    return builder.getText();
+}
+
+function getAxesTextShape(props: AxesProps, shape?: Shape<Text>) {
+    const scale = 100 * props.scale;
+    const text = createAxesText(props, shape?.geometry);
+    text.setBoundingSphere(Sphere3D.create(Vec3.create(scale / 2, scale / 2, scale / 2), scale));
+    const getColor = (groupId: number) => {
+        switch (groupId) {
+            case CameraHelperAxis.X: return props.labelColorX;
+            case CameraHelperAxis.Y: return props.labelColorY;
+            case CameraHelperAxis.Z: return props.labelColorZ;
+            default: return ColorNames.grey;
+        }
+    };
+    return Shape.create('axes-text', {}, text, getColor, () => 1, () => '');
+}
+
+function createTextRenderObject(props: AxesProps) {
+    const shape = getAxesTextShape(props);
+    return Shape.createRenderObject(shape, {
+        ...PD.getDefaultValues(Text.Params),
+        ...props,
+        alpha: props.labelOpacity,
+    });
+}

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -54,6 +54,7 @@ export class HandleHelper {
     };
 
     private renderObject: GraphicsRenderObject | undefined;
+    private pixelRatio = 1;
 
     private _transform = Mat4();
     getBoundingSphere(out: Sphere3D, instanceId: number) {
@@ -71,7 +72,11 @@ export class HandleHelper {
                 p.handle.name = props.handle.name;
                 if (props.handle.name === 'on') {
                     this.scene.clear();
-                    const params = { ...props.handle.params, scale: props.handle.params.scale * this.webgl.pixelRatio };
+                    this.pixelRatio = this.webgl.pixelRatio;
+                    const params = {
+                        ...props.handle.params,
+                        scale: props.handle.params.scale * this.webgl.pixelRatio
+                    };
                     this.renderObject = createHandleRenderObject(params);
                     this.scene.add(this.renderObject);
                     this.scene.commit();
@@ -91,6 +96,10 @@ export class HandleHelper {
     update(camera: Camera, position: Vec3, rotation: Mat3) {
         if (!this.renderObject) return;
 
+        if (this.pixelRatio !== this.webgl.pixelRatio) {
+            this.setProps(this.props);
+        }
+
         Mat4.setTranslation(this.renderObject.values.aTransform.ref.value as unknown as Mat4, position);
         Mat4.fromMat3(this.renderObject.values.aTransform.ref.value as unknown as Mat4, rotation);
 

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

@@ -19,7 +19,7 @@ type HoverEvent = import('../canvas3d').Canvas3D.HoverEvent
 type DragEvent = import('../canvas3d').Canvas3D.DragEvent
 type ClickEvent = import('../canvas3d').Canvas3D.ClickEvent
 
-const enum InputEvent { Move, Click, Drag }
+enum InputEvent { Move, Click, Drag }
 
 const tmpPosA = Vec3();
 const tmpPos = Vec3();

src/mol-canvas3d/passes/draw.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 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>
@@ -142,7 +142,7 @@ export class DrawPass {
         }
 
         if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
                 this.depthTargetTransparent.bind();
                 renderer.clearDepth(true);
                 if (scene.opacityAverage < 1) {
@@ -150,7 +150,7 @@ export class DrawPass {
                 }
             }
 
-            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
+            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
         }
 
         this.depthTextureOpaque.detachFramebuffer(this.colorTarget.framebuffer, 'depth');
@@ -196,7 +196,7 @@ export class DrawPass {
         }
 
         if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
                 this.depthTargetTransparent.bind();
                 renderer.clearDepth(true);
                 if (scene.opacityAverage < 1) {
@@ -204,7 +204,7 @@ export class DrawPass {
                 }
             }
 
-            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
+            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
         }
 
         // render transparent primitives and volumes
@@ -260,7 +260,7 @@ export class DrawPass {
                     this.colorTarget.depthRenderbuffer?.detachFramebuffer(this.postprocessing.target.framebuffer);
                 }
 
-                if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
+                if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
                     this.depthTargetTransparent.bind();
                     renderer.clearDepth(true);
                     if (scene.opacityAverage < 1) {
@@ -268,7 +268,7 @@ export class DrawPass {
                     }
                 }
 
-                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
+                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
 
                 if (!this.packedDepth) {
                     this.depthTextureOpaque.attachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
@@ -312,7 +312,7 @@ export class DrawPass {
 
         const { x, y, width, height } = camera.viewport;
         renderer.setViewport(x, y, width, height);
-        renderer.update(camera);
+        renderer.update(camera, scene);
 
         if (transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
             this.drawTarget.bind();
@@ -360,7 +360,7 @@ export class DrawPass {
         }
         if (helper.camera.isEnabled) {
             helper.camera.update(camera);
-            renderer.update(helper.camera.camera);
+            renderer.update(helper.camera.camera, helper.camera.scene);
             renderer.renderBlended(helper.camera.scene, helper.camera.camera);
         }
 

src/mol-canvas3d/passes/marking.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -27,6 +27,8 @@ export const MarkingParams = {
     highlightEdgeColor: PD.Color(Color.darken(Color.fromNormalizedRgb(1.0, 0.4, 0.6), 1.0)),
     selectEdgeColor: PD.Color(Color.darken(Color.fromNormalizedRgb(0.2, 1.0, 0.1), 1.0)),
     edgeScale: PD.Numeric(1, { min: 1, max: 3, step: 1 }, { description: 'Thickness of the edge.' }),
+    highlightEdgeStrength: PD.Numeric(1.0, { min: 0, max: 1, step: 0.1 }),
+    selectEdgeStrength: PD.Numeric(1.0, { min: 0, max: 1, step: 0.1 }),
     ghostEdgeStrength: PD.Numeric(0.3, { min: 0, max: 1, step: 0.1 }, { description: 'Opacity of the hidden edges that are covered by other geometry. When set to 1, one less geometry render pass is done.' }),
     innerEdgeFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Factor to multiply the inner edge color with - for added contrast.' }),
 };
@@ -101,7 +103,7 @@ export class MarkingPass {
     }
 
     update(props: MarkingProps) {
-        const { highlightEdgeColor, selectEdgeColor, edgeScale, innerEdgeFactor, ghostEdgeStrength } = props;
+        const { highlightEdgeColor, selectEdgeColor, edgeScale, innerEdgeFactor, ghostEdgeStrength, highlightEdgeStrength, selectEdgeStrength } = props;
 
         const { values: edgeValues } = this.edge;
         const _edgeScale = Math.round(edgeScale * this.webgl.pixelRatio);
@@ -113,8 +115,10 @@ export class MarkingPass {
         const { values: overlayValues } = this.overlay;
         ValueCell.update(overlayValues.uHighlightEdgeColor, Color.toVec3Normalized(overlayValues.uHighlightEdgeColor.ref.value, highlightEdgeColor));
         ValueCell.update(overlayValues.uSelectEdgeColor, Color.toVec3Normalized(overlayValues.uSelectEdgeColor.ref.value, selectEdgeColor));
-        ValueCell.update(overlayValues.uInnerEdgeFactor, innerEdgeFactor);
-        ValueCell.update(overlayValues.uGhostEdgeStrength, ghostEdgeStrength);
+        ValueCell.updateIfChanged(overlayValues.uInnerEdgeFactor, innerEdgeFactor);
+        ValueCell.updateIfChanged(overlayValues.uGhostEdgeStrength, ghostEdgeStrength);
+        ValueCell.updateIfChanged(overlayValues.uHighlightEdgeStrength, highlightEdgeStrength);
+        ValueCell.updateIfChanged(overlayValues.uSelectEdgeStrength, selectEdgeStrength);
     }
 
     render(viewport: Viewport, target: RenderTarget | undefined) {
@@ -170,6 +174,8 @@ const OverlaySchema = {
     uTexSizeInv: UniformSpec('v2'),
     uHighlightEdgeColor: UniformSpec('v3'),
     uSelectEdgeColor: UniformSpec('v3'),
+    uHighlightEdgeStrength: UniformSpec('f'),
+    uSelectEdgeStrength: UniformSpec('f'),
     uGhostEdgeStrength: UniformSpec('f'),
     uInnerEdgeFactor: UniformSpec('f'),
 };
@@ -186,6 +192,8 @@ function getOverlayRenderable(ctx: WebGLContext, edgeTexture: Texture): OverlayR
         uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)),
         uHighlightEdgeColor: ValueCell.create(Vec3()),
         uSelectEdgeColor: ValueCell.create(Vec3()),
+        uHighlightEdgeStrength: ValueCell.create(1),
+        uSelectEdgeStrength: ValueCell.create(1),
         uGhostEdgeStrength: ValueCell.create(0),
         uInnerEdgeFactor: ValueCell.create(0),
     };

src/mol-canvas3d/passes/pick.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -172,7 +172,7 @@ export class PickPass {
 
     private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: 'pick' | 'depth', pickType: number) {
         renderer.clear(false);
-        renderer.update(camera);
+        renderer.update(camera, scene);
         renderer.renderPick(scene.primitives, camera, variant, null, pickType);
 
         if (helper.handle.isEnabled) {
@@ -181,7 +181,7 @@ export class PickPass {
 
         if (helper.camera.isEnabled) {
             helper.camera.update(camera);
-            renderer.update(helper.camera.camera);
+            renderer.update(helper.camera.camera, helper.camera.scene);
             renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null, pickType);
         }
     }
@@ -291,7 +291,7 @@ export class PickHelper {
     }
 
     private render(camera: Camera | StereoCamera) {
-        if (isTimingMode) this.webgl.timer.mark('PickHelper.render');
+        if (isTimingMode) this.webgl.timer.mark('PickHelper.render', true);
         const { pickX, pickY, pickWidth, pickHeight, halfPickWidth } = this;
         const { renderer, scene, helper } = this;
 

src/mol-canvas3d/passes/postprocessing.ts

@@ -1,8 +1,9 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 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>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
 
 import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
@@ -30,6 +31,8 @@ import { SmaaParams, SmaaPass } from './smaa';
 import { isTimingMode } from '../../mol-util/debug';
 import { BackgroundParams, BackgroundPass } from './background';
 import { AssetManager } from '../../mol-util/assets';
+import { Light } from '../../mol-gl/renderer';
+import { shadows_frag } from '../../mol-gl/shader/shadows.frag';
 
 const OutlinesSchema = {
     ...QuadSchema,
@@ -42,10 +45,12 @@ const OutlinesSchema = {
     uFar: UniformSpec('f'),
 
     uMaxPossibleViewZDiff: UniformSpec('f'),
+
+    dTransparentOutline: DefineSpec('boolean'),
 };
 type OutlinesRenderable = ComputeRenderable<Values<typeof OutlinesSchema>>
 
-function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture): OutlinesRenderable {
+function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture, transparentOutline: boolean): OutlinesRenderable {
     const width = depthTextureOpaque.getWidth();
     const height = depthTextureOpaque.getHeight();
 
@@ -60,6 +65,8 @@ function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, d
         uFar: ValueCell.create(10000),
 
         uMaxPossibleViewZDiff: ValueCell.create(0.5),
+
+        dTransparentOutline: ValueCell.create(transparentOutline),
     };
 
     const schema = { ...OutlinesSchema };
@@ -69,6 +76,64 @@ function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, d
     return createComputeRenderable(renderItem, values);
 }
 
+const ShadowsSchema = {
+    ...QuadSchema,
+    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    uProjection: UniformSpec('m4'),
+    uInvProjection: UniformSpec('m4'),
+    uBounds: UniformSpec('v4'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+
+    dSteps: DefineSpec('number'),
+    uMaxDistance: UniformSpec('f'),
+    uTolerance: UniformSpec('f'),
+    uBias: UniformSpec('f'),
+
+    uLightDirection: UniformSpec('v3[]'),
+    uLightColor: UniformSpec('v3[]'),
+    dLightCount: DefineSpec('number'),
+};
+type ShadowsRenderable = ComputeRenderable<Values<typeof ShadowsSchema>>
+
+function getShadowsRenderable(ctx: WebGLContext, depthTexture: Texture): ShadowsRenderable {
+    const width = depthTexture.getWidth();
+    const height = depthTexture.getHeight();
+
+    const values: Values<typeof ShadowsSchema> = {
+        ...QuadValues,
+        tDepth: ValueCell.create(depthTexture),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
+
+        uProjection: ValueCell.create(Mat4.identity()),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+        uBounds: ValueCell.create(Vec4()),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+
+        dSteps: ValueCell.create(1),
+        uMaxDistance: ValueCell.create(3.0),
+        uTolerance: ValueCell.create(1.0),
+        uBias: ValueCell.create(0.6),
+
+        uLightDirection: ValueCell.create([]),
+        uLightColor: ValueCell.create([]),
+        dLightCount: ValueCell.create(0),
+    };
+
+    const schema = { ...ShadowsSchema };
+    const shaderCode = ShaderCode('shadows', quad_vert, shadows_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
 const SsaoSchema = {
     ...QuadSchema,
     tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
@@ -204,6 +269,7 @@ const PostprocessingSchema = {
     tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tShadows: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tOutlines: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     uTexSize: UniformSpec('v2'),
 
@@ -217,23 +283,30 @@ const PostprocessingSchema = {
     uTransparentBackground: UniformSpec('b'),
 
     uMaxPossibleViewZDiff: UniformSpec('f'),
+    uInvProjection: UniformSpec('m4'),
 
     dOcclusionEnable: DefineSpec('boolean'),
     uOcclusionOffset: UniformSpec('v2'),
 
+    dShadowEnable: DefineSpec('boolean'),
+
     dOutlineEnable: DefineSpec('boolean'),
     dOutlineScale: DefineSpec('number'),
     uOutlineThreshold: UniformSpec('f'),
+
+    dTransparentOutline: DefineSpec('boolean'),
 };
 type PostprocessingRenderable = ComputeRenderable<Values<typeof PostprocessingSchema>>
 
-function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture): PostprocessingRenderable {
+
+function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, shadowsTexture: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture, transparentOutline: boolean): PostprocessingRenderable {
     const values: Values<typeof PostprocessingSchema> = {
         ...QuadValues,
         tSsaoDepth: ValueCell.create(ssaoDepthTexture),
         tColor: ValueCell.create(colorTexture),
         tDepthOpaque: ValueCell.create(depthTextureOpaque),
         tDepthTransparent: ValueCell.create(depthTextureTransparent),
+        tShadows: ValueCell.create(shadowsTexture),
         tOutlines: ValueCell.create(outlinesTexture),
         uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
 
@@ -247,13 +320,18 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
         uTransparentBackground: ValueCell.create(false),
 
         uMaxPossibleViewZDiff: ValueCell.create(0.5),
+        uInvProjection: ValueCell.create(Mat4.identity()),
 
         dOcclusionEnable: ValueCell.create(true),
         uOcclusionOffset: ValueCell.create(Vec2.create(0, 0)),
 
+        dShadowEnable: ValueCell.create(false),
+
         dOutlineEnable: ValueCell.create(false),
         dOutlineScale: ValueCell.create(1),
         uOutlineThreshold: ValueCell.create(0.33),
+
+        dTransparentOutline: ValueCell.create(transparentOutline),
     };
 
     const schema = { ...PostprocessingSchema };
@@ -274,11 +352,21 @@ export const PostprocessingParams = {
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
+    shadow: PD.MappedStatic('off', {
+        on: PD.Group({
+            steps: PD.Numeric(1, { min: 1, max: 64, step: 1 }),
+            bias: PD.Numeric(0.6, { min: 0.0, max: 1.0, step: 0.01 }),
+            maxDistance: PD.Numeric(3, { min: 0, max: 256, step: 1 }),
+            tolerance: PD.Numeric(1.0, { min: 0.0, max: 10.0, step: 0.1 }),
+        }),
+        off: PD.Group({})
+    }, { cycle: true, description: 'Simplistic shadows' }),
     outline: PD.MappedStatic('off', {
         on: PD.Group({
             scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
             threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
             color: PD.Color(Color(0x000000)),
+            includeTransparent: PD.Boolean(true, { description: 'Whether to show outline for transparent objects' }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' }),
@@ -289,15 +377,16 @@ export const PostprocessingParams = {
     }, { options: [['fxaa', 'FXAA'], ['smaa', 'SMAA'], ['off', 'Off']], description: 'Smooth pixel edges' }),
     background: PD.Group(BackgroundParams, { isFlat: true }),
 };
+
 export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
 
 export class PostprocessingPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.occlusion.name === 'on' || props.outline.name === 'on' || props.background.variant.name !== 'off';
+        return props.occlusion.name === 'on' || props.shadow.name === 'on' || props.outline.name === 'on' || props.background.variant.name !== 'off';
     }
 
-    static isOutlineEnabled(props: PostprocessingProps) {
-        return props.outline.name === 'on';
+    static isTransparentOutlineEnabled(props: PostprocessingProps) {
+        return props.outline.name === 'on' && props.outline.params.includeTransparent;
     }
 
     readonly target: RenderTarget;
@@ -305,6 +394,9 @@ export class PostprocessingPass {
     private readonly outlinesTarget: RenderTarget;
     private readonly outlinesRenderable: OutlinesRenderable;
 
+    private readonly shadowsTarget: RenderTarget;
+    private readonly shadowsRenderable: ShadowsRenderable;
+
     private readonly ssaoFramebuffer: Framebuffer;
     private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
     private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;
@@ -348,7 +440,10 @@ export class PostprocessingPass {
         this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
 
         this.outlinesTarget = webgl.createRenderTarget(width, height, false);
-        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent);
+        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent, true);
+
+        this.shadowsTarget = webgl.createRenderTarget(width, height, false);
+        this.shadowsRenderable = getShadowsRenderable(webgl, depthTextureOpaque);
 
         this.ssaoFramebuffer = webgl.resources.framebuffer();
         this.ssaoBlurFirstPassFramebuffer = webgl.resources.framebuffer();
@@ -357,7 +452,9 @@ export class PostprocessingPass {
         const sw = Math.floor(width * this.ssaoScale);
         const sh = Math.floor(height * this.ssaoScale);
 
-        this.downsampledDepthTarget = webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear');
+        this.downsampledDepthTarget = drawPass.packedDepth
+            ? webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear', 'rgba')
+            : webgl.createRenderTarget(sw, sh, false, 'float32', 'linear', webgl.isWebGL2 ? 'alpha' : 'rgba');
         this.downsampleDepthRenderable = createCopyRenderable(webgl, depthTextureOpaque);
 
         this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
@@ -370,10 +467,10 @@ export class PostprocessingPass {
 
         this.ssaoDepthTexture.attachFramebuffer(this.ssaoBlurSecondPassFramebuffer, 'color0');
 
-        this.ssaoRenderable = getSsaoRenderable(webgl, this.downsampleFactor === 1 ? depthTextureOpaque : this.downsampledDepthTarget.texture);
+        this.ssaoRenderable = getSsaoRenderable(webgl, this.ssaoScale === 1 ? depthTextureOpaque : this.downsampledDepthTarget.texture);
         this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
         this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
-        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.outlinesTarget.texture, this.ssaoDepthTexture);
+        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.shadowsTarget.texture, this.outlinesTarget.texture, this.ssaoDepthTexture, true);
 
         this.background = new BackgroundPass(webgl, assetManager, width, height);
     }
@@ -389,12 +486,14 @@ export class PostprocessingPass {
             const sh = Math.floor(height * this.ssaoScale);
             this.target.setSize(width, height);
             this.outlinesTarget.setSize(width, height);
+            this.shadowsTarget.setSize(width, height);
             this.downsampledDepthTarget.setSize(sw, sh);
             this.ssaoDepthTexture.define(sw, sh);
             this.ssaoDepthBlurProxyTexture.define(sw, sh);
 
             ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
             ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.shadowsRenderable.values.uTexSize, Vec2.set(this.shadowsRenderable.values.uTexSize.ref.value, width, height));
             ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
@@ -404,25 +503,29 @@ export class PostprocessingPass {
         }
     }
 
-    private updateState(camera: ICamera, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
+    private updateState(camera: ICamera, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light) {
+        let needsUpdateShadows = false;
         let needsUpdateMain = false;
         let needsUpdateSsao = false;
         let needsUpdateSsaoBlur = false;
+        let needsUpdateOutlines = false;
 
         const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
         const outlinesEnabled = props.outline.name === 'on';
+        const shadowsEnabled = props.shadow.name === 'on';
         const occlusionEnabled = props.occlusion.name === 'on';
 
         const invProjection = Mat4.identity();
         Mat4.invert(invProjection, camera.projection);
 
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        const v = camera.viewport;
+
         if (props.occlusion.name === 'on') {
             ValueCell.update(this.ssaoRenderable.values.uProjection, camera.projection);
             ValueCell.update(this.ssaoRenderable.values.uInvProjection, invProjection);
 
-            const [w, h] = this.renderable.values.uTexSize.ref.value;
             const b = this.ssaoRenderable.values.uBounds;
-            const v = camera.viewport;
             const s = this.ssaoScale;
             Vec4.set(b.ref.value,
                 Math.floor(v.x * s) / (w * s),
@@ -482,7 +585,7 @@ export class PostprocessingPass {
                 this.ssaoDepthBlurProxyTexture.define(sw, sh);
 
                 if (this.ssaoScale === 1) {
-                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.drawPass.depthTextureTransparent);
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.drawPass.depthTextureOpaque);
                 } else {
                     ValueCell.update(this.ssaoRenderable.values.tDepth, this.downsampledDepthTarget.texture);
                 }
@@ -494,11 +597,44 @@ export class PostprocessingPass {
             }
         }
 
+        if (props.shadow.name === 'on') {
+            ValueCell.update(this.shadowsRenderable.values.uProjection, camera.projection);
+            ValueCell.update(this.shadowsRenderable.values.uInvProjection, invProjection);
+
+            Vec4.set(this.shadowsRenderable.values.uBounds.ref.value,
+                v.x / w,
+                v.y / h,
+                (v.x + v.width) / w,
+                (v.y + v.height) / h
+            );
+            ValueCell.update(this.shadowsRenderable.values.uBounds, this.shadowsRenderable.values.uBounds.ref.value);
+
+            ValueCell.updateIfChanged(this.shadowsRenderable.values.uNear, camera.near);
+            ValueCell.updateIfChanged(this.shadowsRenderable.values.uFar, camera.far);
+            ValueCell.updateIfChanged(this.shadowsRenderable.values.dOrthographic, orthographic);
+
+            ValueCell.updateIfChanged(this.shadowsRenderable.values.uMaxDistance, props.shadow.params.maxDistance);
+            ValueCell.updateIfChanged(this.shadowsRenderable.values.uTolerance, props.shadow.params.tolerance);
+            ValueCell.updateIfChanged(this.shadowsRenderable.values.uBias, props.shadow.params.bias);
+            if (this.shadowsRenderable.values.dSteps.ref.value !== props.shadow.params.steps) {
+                ValueCell.update(this.shadowsRenderable.values.dSteps, props.shadow.params.steps);
+                needsUpdateShadows = true;
+            }
+
+            ValueCell.update(this.shadowsRenderable.values.uLightDirection, light.direction);
+            ValueCell.update(this.shadowsRenderable.values.uLightColor, light.color);
+            if (this.shadowsRenderable.values.dLightCount.ref.value !== light.count) {
+                ValueCell.update(this.shadowsRenderable.values.dLightCount, light.count);
+                needsUpdateShadows = true;
+            }
+        }
+
         if (props.outline.name === 'on') {
-            let { threshold } = props.outline.params;
+            let { threshold, includeTransparent } = props.outline.params;
+            const transparentOutline = includeTransparent ?? true;
             // orthographic needs lower threshold
             if (camera.state.mode === 'orthographic') threshold /= 5;
-            const factor = Math.pow(1000, threshold) / 1000;
+            const factor = Math.pow(1000, threshold / 10) / 1000;
             // use radiusMax for stable outlines when zooming
             const maxPossibleViewZDiff = factor * camera.state.radiusMax;
             const outlineScale = props.outline.params.scale - 1;
@@ -506,12 +642,18 @@ export class PostprocessingPass {
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
+            if (this.renderable.values.dTransparentOutline.ref.value !== transparentOutline) { needsUpdateOutlines = true; }
+            ValueCell.updateIfChanged(this.outlinesRenderable.values.dTransparentOutline, transparentOutline);
 
             ValueCell.update(this.renderable.values.uOutlineColor, Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, props.outline.params.color));
 
             ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
+            ValueCell.update(this.renderable.values.uInvProjection, invProjection);
+
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) { needsUpdateMain = true; }
             ValueCell.updateIfChanged(this.renderable.values.dOutlineScale, outlineScale);
+            if (this.renderable.values.dTransparentOutline.ref.value !== transparentOutline) { needsUpdateMain = true; }
+            ValueCell.updateIfChanged(this.renderable.values.dTransparentOutline, transparentOutline);
         }
 
         ValueCell.updateIfChanged(this.renderable.values.uFar, camera.far);
@@ -522,11 +664,22 @@ export class PostprocessingPass {
         ValueCell.updateIfChanged(this.renderable.values.uTransparentBackground, transparentBackground);
         if (this.renderable.values.dOrthographic.ref.value !== orthographic) { needsUpdateMain = true; }
         ValueCell.updateIfChanged(this.renderable.values.dOrthographic, orthographic);
+
         if (this.renderable.values.dOutlineEnable.ref.value !== outlinesEnabled) { needsUpdateMain = true; }
         ValueCell.updateIfChanged(this.renderable.values.dOutlineEnable, outlinesEnabled);
+        if (this.renderable.values.dShadowEnable.ref.value !== shadowsEnabled) { needsUpdateMain = true; }
+        ValueCell.updateIfChanged(this.renderable.values.dShadowEnable, shadowsEnabled);
         if (this.renderable.values.dOcclusionEnable.ref.value !== occlusionEnabled) { needsUpdateMain = true; }
         ValueCell.updateIfChanged(this.renderable.values.dOcclusionEnable, occlusionEnabled);
 
+        if (needsUpdateOutlines) {
+            this.outlinesRenderable.update();
+        }
+
+        if (needsUpdateShadows) {
+            this.shadowsRenderable.update();
+        }
+
         if (needsUpdateSsao) {
             this.ssaoRenderable.update();
         }
@@ -564,15 +717,20 @@ export class PostprocessingPass {
         this.transparentBackground = value;
     }
 
-    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
+    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light) {
         if (isTimingMode) this.webgl.timer.mark('PostprocessingPass.render');
-        this.updateState(camera, transparentBackground, backgroundColor, props);
+        this.updateState(camera, transparentBackground, backgroundColor, props, light);
 
         if (props.outline.name === 'on') {
             this.outlinesTarget.bind();
             this.outlinesRenderable.render();
         }
 
+        if (props.shadow.name === 'on') {
+            this.shadowsTarget.bind();
+            this.shadowsRenderable.render();
+        }
+
         // don't render occlusion if offset is given,
         // which will reuse the existing occlusion
         if (props.occlusion.name === 'on' && this.occlusionOffset[0] === 0 && this.occlusionOffset[1] === 0) {

src/mol-data/db/column.ts

@@ -93,20 +93,35 @@ namespace Column {
         return !!v && !!(v as Column<any>).schema && !!(v as Column<any>).value;
     }
 
-    export const enum ValueKind {
+    // Value kinds are accessed very of often
+    // Using a const enum is an internal optimization and is defined separately to better support
+    // compiling with isolatedModules flag in 3rd party use-cases of Mol*.
+    export const enum ValueKinds {
+        /** Defined value (= 0) */
         Present = 0,
-        /** Expressed in CIF as `.` */
+        /** Expressed in CIF as `.` (= 1) */
         NotPresent = 1,
-        /** Expressed in CIF as `?` */
+        /** Expressed in CIF as `?` (= 2) */
         Unknown = 2
     }
 
+    export const ValueKind = {
+        /** Defined value (= 0) */
+        Present: ValueKinds.Present,
+        /** Expressed in CIF as `.` (= 1) */
+        NotPresent: ValueKinds.NotPresent,
+        /** Expressed in CIF as `?` (= 2) */
+        Unknown: ValueKinds.Unknown
+    } as const;
+    export type ValueKind = (typeof ValueKind)[keyof typeof ValueKinds];
+
+
     export function Undefined<T extends Schema>(rowCount: number, schema: T): Column<T['T']> {
-        return constColumn(schema['T'], rowCount, schema, ValueKind.NotPresent);
+        return constColumn(schema['T'], rowCount, schema, ValueKinds.NotPresent);
     }
 
     export function ofConst<T extends Schema>(v: T['T'], rowCount: number, type: T): Column<T['T']> {
-        return constColumn(v, rowCount, type, ValueKind.Present);
+        return constColumn(v, rowCount, type, ValueKinds.Present);
     }
 
     export function ofLambda<T extends Schema>(spec: LambdaSpec<T>): Column<T['T']> {
@@ -256,7 +271,7 @@ function constColumn<T extends Column.Schema>(v: T['T'], rowCount: number, schem
     return {
         schema: schema,
         __array: void 0,
-        isDefined: valueKind === Column.ValueKind.Present,
+        isDefined: valueKind === Column.ValueKinds.Present,
         rowCount,
         value,
         valueKind: row => valueKind,
@@ -276,7 +291,7 @@ function lambdaColumn<T extends Column.Schema>({ value, valueKind, areValuesEqua
         isDefined: true,
         rowCount,
         value,
-        valueKind: valueKind ? valueKind : row => Column.ValueKind.Present,
+        valueKind: valueKind ? valueKind : row => Column.ValueKinds.Present,
         toArray: params => {
             const { array, start } = ColumnHelpers.createArray(rowCount, params);
             for (let i = 0, _i = array.length; i < _i; i++) array[i] = value(i + start);
@@ -304,7 +319,7 @@ function arrayColumn<T extends Column.Schema>({ array, schema, valueKind }: Colu
         isDefined: true,
         rowCount,
         value,
-        valueKind: valueKind ? valueKind : row => Column.ValueKind.Present,
+        valueKind: valueKind ? valueKind : row => Column.ValueKinds.Present,
         toArray: schema.valueType === 'str'
             ? (schema as Column.Schema.Str).transform === 'lowercase'
                 ? params => {

src/mol-data/db/table.ts

@@ -85,7 +85,7 @@ namespace Table {
                 rowCount,
                 schema: schema[k],
                 value: r => rows[r][k],
-                valueKind: r => typeof rows[r][k] === 'undefined' ? Column.ValueKind.NotPresent : Column.ValueKind.Present
+                valueKind: r => typeof rows[r][k] === 'undefined' ? Column.ValueKinds.NotPresent : Column.ValueKinds.Present
             });
         }
         return ret as R;
@@ -267,7 +267,7 @@ namespace Table {
             StringBuilder.write(sb, '|');
             for (let i = 0; i < cols.length; i++) {
                 const c = table[cols[i]];
-                if (c.valueKind(r) === Column.ValueKind.Present) {
+                if (c.valueKind(r) === Column.ValueKinds.Present) {
                     StringBuilder.write(sb, c.value(r));
                     StringBuilder.write(sb, '|');
                 } else {

src/mol-geo/geometry/base.ts

@@ -132,8 +132,8 @@ export namespace BaseGeometry {
         ValueCell.updateIfChanged(values.uBumpiness, props.material.bumpiness);
 
         const clip = Clip.getClip(props.clip);
-        ValueCell.update(values.dClipObjectCount, clip.objects.count);
-        ValueCell.update(values.dClipVariant, clip.variant);
+        ValueCell.updateIfChanged(values.dClipObjectCount, clip.objects.count);
+        ValueCell.updateIfChanged(values.dClipVariant, clip.variant);
         ValueCell.update(values.uClipObjectType, clip.objects.type);
         ValueCell.update(values.uClipObjectInvert, clip.objects.invert);
         ValueCell.update(values.uClipObjectPosition, clip.objects.position);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -158,6 +158,7 @@ export namespace Cylinders {
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
+        solidInterior: PD.Boolean(true, BaseGeometry.ShadingCategory),
         bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
         bumpAmplitude: PD.Numeric(1, { min: 0, max: 5, step: 0.1 }, BaseGeometry.ShadingCategory),
     };
@@ -213,7 +214,7 @@ export namespace Cylinders {
 
         const padding = getMaxSize(size) * props.sizeFactor;
         const invariantBoundingSphere = Sphere3D.clone(cylinders.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('cylinders'),
@@ -245,6 +246,7 @@ export namespace Cylinders {
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
             dTransparentBackfaces: ValueCell.create(props.transparentBackfaces),
+            dSolidInterior: ValueCell.create(props.solidInterior),
             uBumpFrequency: ValueCell.create(props.bumpFrequency),
             uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
         };
@@ -263,13 +265,14 @@ export namespace Cylinders {
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
         ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
+        ValueCell.updateIfChanged(values.dSolidInterior, props.solidInterior);
         ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
 
     function updateBoundingSphere(values: CylindersValues, cylinders: Cylinders) {
         const invariantBoundingSphere = Sphere3D.clone(cylinders.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

src/mol-geo/geometry/direct-volume/direct-volume.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -223,7 +223,7 @@ export namespace DirectVolume {
         const counts = { drawCount: VolumeBox.indices.length, vertexCount: x * y * z, groupCount, instanceCount };
 
         const invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         const controlPoints = getControlPointsFromVec2Array(props.controlPoints);
         const transferTex = createTransferFunctionTexture(controlPoints);
@@ -295,7 +295,7 @@ export namespace DirectVolume {
 
     function updateBoundingSphere(values: DirectVolumeValues, directVolume: DirectVolume) {
         const invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -154,7 +154,7 @@ namespace Image {
         const counts = { drawCount: QuadIndices.length, vertexCount: QuadPositions.length / 3, groupCount, instanceCount };
 
         const invariantBoundingSphere = Sphere3D.clone(image.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('image'),
@@ -199,7 +199,7 @@ namespace Image {
 
     function updateBoundingSphere(values: ImageValues, image: Image) {
         const invariantBoundingSphere = Sphere3D.clone(image.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -219,7 +219,7 @@ export namespace Lines {
         const counts = { drawCount: lines.lineCount * 2 * 3, vertexCount: lines.lineCount * 4, groupCount, instanceCount };
 
         const invariantBoundingSphere = Sphere3D.clone(lines.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('lines'),
@@ -263,7 +263,7 @@ export namespace Lines {
 
     function updateBoundingSphere(values: LinesValues, lines: Lines) {
         const invariantBoundingSphere = Sphere3D.clone(lines.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -680,7 +680,7 @@ export namespace Mesh {
         const counts = { drawCount: mesh.triangleCount * 3, vertexCount: mesh.vertexCount, groupCount, instanceCount };
 
         const invariantBoundingSphere = Sphere3D.clone(mesh.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('mesh'),
@@ -735,7 +735,7 @@ export namespace Mesh {
 
     function updateBoundingSphere(values: MeshValues, mesh: Mesh) {
         const invariantBoundingSphere = Sphere3D.clone(mesh.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

src/mol-geo/geometry/overpaint-data.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -21,6 +21,7 @@ export type OverpaintData = {
     uOverpaintGridDim: ValueCell<Vec3>,
     uOverpaintGridTransform: ValueCell<Vec4>,
     dOverpaintType: ValueCell<string>,
+    uOverpaintStrength: ValueCell<number>,
 }
 
 export function applyOverpaintColor(array: Uint8Array, start: number, end: number, color: Color) {
@@ -54,6 +55,7 @@ export function createOverpaint(count: number, type: OverpaintType, overpaintDat
             uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dOverpaintType: ValueCell.create(type),
+            uOverpaintStrength: ValueCell.create(1),
         };
     }
 }
@@ -74,6 +76,7 @@ export function createEmptyOverpaint(overpaintData?: OverpaintData): OverpaintDa
             uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dOverpaintType: ValueCell.create('groupInstance'),
+            uOverpaintStrength: ValueCell.create(1),
         };
     }
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -181,7 +181,7 @@ export namespace Points {
         const counts = { drawCount: points.pointCount, vertexCount: points.pointCount, groupCount, instanceCount };
 
         const invariantBoundingSphere = Sphere3D.clone(points.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('points'),
@@ -222,7 +222,7 @@ export namespace Points {
 
     function updateBoundingSphere(values: PointsValues, points: Points) {
         const invariantBoundingSphere = Sphere3D.clone(points.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -130,6 +130,7 @@ export namespace Spheres {
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
+        solidInterior: PD.Boolean(true, BaseGeometry.ShadingCategory),
         bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
         bumpAmplitude: PD.Numeric(1, { min: 0, max: 5, step: 0.1 }, BaseGeometry.ShadingCategory),
     };
@@ -183,7 +184,7 @@ export namespace Spheres {
 
         const padding = spheres.boundingSphere.radius ? getMaxSize(size) * props.sizeFactor : 0;
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), spheres.boundingSphere, padding);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('spheres'),
@@ -212,6 +213,7 @@ export namespace Spheres {
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
             dTransparentBackfaces: ValueCell.create(props.transparentBackfaces),
+            dSolidInterior: ValueCell.create(props.solidInterior),
             uBumpFrequency: ValueCell.create(props.bumpFrequency),
             uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
         };
@@ -230,6 +232,7 @@ export namespace Spheres {
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
         ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
+        ValueCell.updateIfChanged(values.dSolidInterior, props.solidInterior);
         ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
@@ -239,7 +242,7 @@ export namespace Spheres {
             ? getMaxSize(values) * values.uSizeFactor.ref.value
             : 0;
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), spheres.boundingSphere, padding);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

src/mol-geo/geometry/substance-data.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -21,6 +21,7 @@ export type SubstanceData = {
     uSubstanceGridDim: ValueCell<Vec3>,
     uSubstanceGridTransform: ValueCell<Vec4>,
     dSubstanceType: ValueCell<string>,
+    uSubstanceStrength: ValueCell<number>,
 }
 
 export function applySubstanceMaterial(array: Uint8Array, start: number, end: number, material: Material) {
@@ -54,6 +55,7 @@ export function createSubstance(count: number, type: SubstanceType, substanceDat
             uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dSubstanceType: ValueCell.create(type),
+            uSubstanceStrength: ValueCell.create(1),
         };
     }
 }
@@ -74,6 +76,7 @@ export function createEmptySubstance(substanceData?: SubstanceData): SubstanceDa
             uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dSubstanceType: ValueCell.create('groupInstance'),
+            uSubstanceStrength: ValueCell.create(1),
         };
     }
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -223,7 +223,7 @@ export namespace Text {
 
         const padding = getPadding(text.mappingBuffer.ref.value, text.depthBuffer.ref.value, text.charCount, getMaxSize(size));
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), text.boundingSphere, padding);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('text'),
@@ -290,7 +290,7 @@ export namespace Text {
     function updateBoundingSphere(values: TextValues, text: Text) {
         const padding = getPadding(values.aMapping.ref.value, values.aDepth.ref.value, text.charCount, getMaxSize(values));
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), text.boundingSphere, padding);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -7,7 +7,7 @@
 import { ValueCell } from '../../../mol-util';
 import { createComputeRenderable, ComputeRenderable } from '../../../mol-gl/renderable';
 import { WebGLContext } from '../../../mol-gl/webgl/context';
-import { Texture } from '../../../mol-gl/webgl/texture';
+import { isNullTexture, Texture } from '../../../mol-gl/webgl/texture';
 import { ShaderCode } from '../../../mol-gl/shader-code';
 import { createComputeRenderItem } from '../../../mol-gl/webgl/render-item';
 import { ValueSpec, AttributeSpec, UniformSpec, TextureSpec, Values, DefineSpec } from '../../../mol-gl/renderable/schema';
@@ -267,7 +267,7 @@ export function calcTextureMeshColorSmoothing(input: ColorSmoothingInput, resolu
 
     const [dx, dy, dz] = gridDim;
     const { texDimX: width, texDimY: height, texCols } = getTexture2dSize(gridDim);
-    // console.log({ width, height, texCols, dim, resolution });
+    // console.log({ width, height, texCols, gridDim, resolution });
 
     if (!webgl.namedFramebuffers[ColorAccumulateName]) {
         webgl.namedFramebuffers[ColorAccumulateName] = webgl.resources.framebuffer();
@@ -363,7 +363,9 @@ export function calcTextureMeshColorSmoothing(input: ColorSmoothingInput, resolu
     // normalize
 
     if (isTimingMode) webgl.timer.mark('ColorNormalize.render');
-    if (!texture) texture = resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+    if (!texture || isNullTexture(texture)) {
+        texture = resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+    }
     texture.define(width, height);
 
     const normalizeRenderable = getNormalizeRenderable(webgl, accumulateTexture, countTexture);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -7,7 +7,7 @@
 import { ValueCell } from '../../../mol-util';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { LocationIterator } from '../../../mol-geo/util/location-iterator';
+import { LocationIterator, PositionLocation } from '../../../mol-geo/util/location-iterator';
 import { TransformData } from '../transform-data';
 import { createColors } from '../color-data';
 import { createMarkers } from '../marker-data';
@@ -20,11 +20,12 @@ import { createEmptyTransparency } from '../transparency-data';
 import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
 import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
 import { createNullTexture, Texture } from '../../../mol-gl/webgl/texture';
-import { Vec2, Vec4 } from '../../../mol-math/linear-algebra';
+import { Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
 import { createEmptyClipping } from '../clipping-data';
 import { NullLocation } from '../../../mol-model/location';
 import { createEmptySubstance } from '../substance-data';
 import { RenderableState } from '../../../mol-gl/renderable';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
 
 export interface TextureMesh {
     readonly kind: 'texture-mesh',
@@ -43,7 +44,10 @@ export interface TextureMesh {
 
     readonly boundingSphere: Sphere3D
 
-    readonly meta: { [k: string]: unknown }
+    readonly meta: {
+        webgl?: WebGLContext
+        [k: string]: unknown
+    }
 }
 
 export namespace TextureMesh {
@@ -131,9 +135,42 @@ export namespace TextureMesh {
         updateBoundingSphere,
         createRenderableState,
         updateRenderableState,
-        createPositionIterator: () => LocationIterator(1, 1, 1, () => NullLocation)
+        createPositionIterator,
     };
 
+    const TextureMeshName = 'texture-mesh';
+
+    function createPositionIterator(textureMesh: TextureMesh, transform: TransformData): LocationIterator {
+        const webgl = textureMesh.meta.webgl;
+        if (!webgl) return LocationIterator(1, 1, 1, () => NullLocation);
+
+        if (!webgl.namedFramebuffers[TextureMeshName]) {
+            webgl.namedFramebuffers[TextureMeshName] = webgl.resources.framebuffer();
+        }
+        const framebuffer = webgl.namedFramebuffers[TextureMeshName];
+        const [width, height] = textureMesh.geoTextureDim.ref.value;
+        const vertices = new Float32Array(width * height * 4);
+        framebuffer.bind();
+        textureMesh.vertexTexture.ref.value.attachFramebuffer(framebuffer, 0);
+        webgl.readPixels(0, 0, width, height, vertices);
+
+        const groupCount = textureMesh.vertexCount;
+        const instanceCount = transform.instanceCount.ref.value;
+        const location = PositionLocation();
+        const p = location.position;
+        const v = vertices;
+        const m = transform.aTransform.ref.value;
+        const getLocation = (groupIndex: number, instanceIndex: number) => {
+            if (instanceIndex < 0) {
+                Vec3.fromArray(p, v, groupIndex * 4);
+            } else {
+                Vec3.transformMat4Offset(p, v, m, 0, groupIndex * 4, instanceIndex * 16);
+            }
+            return location;
+        };
+        return LocationIterator(groupCount, instanceCount, 1, getLocation);
+    }
+
     function createValues(textureMesh: TextureMesh, transform: TransformData, locationIt: LocationIterator, theme: Theme, props: PD.Values<Params>): TextureMeshValues {
         const { instanceCount, groupCount } = locationIt;
         const positionIt = Utils.createPositionIterator(textureMesh, transform);
@@ -150,7 +187,7 @@ export namespace TextureMesh {
         const counts = { drawCount: textureMesh.vertexCount, vertexCount: textureMesh.vertexCount, groupCount, instanceCount };
 
         const invariantBoundingSphere = Sphere3D.clone(textureMesh.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
 
         return {
             dGeometryType: ValueCell.create('textureMesh'),
@@ -207,7 +244,7 @@ export namespace TextureMesh {
 
     function updateBoundingSphere(values: TextureMeshValues, textureMesh: TextureMesh) {
         const invariantBoundingSphere = Sphere3D.clone(textureMesh.boundingSphere);
-        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
+        const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
 
         if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
             ValueCell.update(values.boundingSphere, boundingSphere);

src/mol-geo/geometry/transparency-data.ts

@@ -21,6 +21,7 @@ export type TransparencyData = {
     uTransparencyGridDim: ValueCell<Vec3>,
     uTransparencyGridTransform: ValueCell<Vec4>,
     dTransparencyType: ValueCell<string>,
+    uTransparencyStrength: ValueCell<number>,
 }
 
 export function applyTransparencyValue(array: Uint8Array, start: number, end: number, value: number) {
@@ -63,6 +64,7 @@ export function createTransparency(count: number, type: TransparencyType, transp
             uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dTransparencyType: ValueCell.create(type),
+            uTransparencyStrength: ValueCell.create(1),
         };
     }
 }
@@ -84,6 +86,7 @@ export function createEmptyTransparency(transparencyData?: TransparencyData): Tr
             uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dTransparencyType: ValueCell.create('groupInstance'),
+            uTransparencyStrength: ValueCell.create(1),
         };
     }
 }

src/mol-gl/commit-queue.ts

@@ -19,6 +19,10 @@ export class CommitQueue {
         return this.removeList.count === 0 && this.addList.count === 0;
     }
 
+    get size() {
+        return this.removeMap.size + this.addMap.size;
+    }
+
     add(o: GraphicsRenderObject) {
         if (this.removeMap.has(o)) {
             const a = this.removeMap.get(o)!;

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

@@ -204,8 +204,7 @@ export function createHistogramPyramid(ctx: WebGLContext, inputTexture: Texture,
     // return at least a count of one to avoid issues downstram
     const count = Math.max(1, getHistopyramidSum(ctx, levelTexturesFramebuffers[0].texture));
     const height = Math.ceil(count / Math.pow(2, levels));
-    // const scale = Vec2.create(maxSize / inputTexture.width, maxSize / inputTexture.height);
-    // console.log('height', height, 'finalCount', count, 'scale', scale);
+    // console.log({ height, count, scale });
 
     return { pyramidTex, count, height, levels, scale };
 }

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

@@ -142,9 +142,7 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
 
     if (isWebGL2(gl)) {
         if (!vertexTexture) {
-            vertexTexture = extensions.colorBufferHalfFloat && extensions.textureHalfFloat
-                ? resources.texture('image-float16', 'rgba', 'fp16', 'nearest')
-                : resources.texture('image-float32', 'rgba', 'float', 'nearest');
+            vertexTexture = resources.texture('image-float32', 'rgba', 'float', 'nearest');
         }
 
         if (!groupTexture) {
@@ -199,9 +197,9 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
     gl.finish();
     if (isTimingMode) ctx.timer.markEnd('createIsosurfaceBuffers');
 
-    // printTextureImage(readTexture(ctx, vertexTexture, new Float32Array(width * height * 4)), { scale: 0.75 });
-    // printTextureImage(readTexture(ctx, groupTexture, new Uint8Array(width * height * 4)), { scale: 0.75 });
-    // printTextureImage(readTexture(ctx, normalTexture, new Float32Array(width * height * 4)), { scale: 0.75 });
+    // printTextureImage(readTexture(ctx, vertexTexture, new Float32Array(width * height * 4)), { scale: 0.75, normalize: true });
+    // printTextureImage(readTexture(ctx, groupTexture, new Uint8Array(width * height * 4)), { scale: 0.75, normalize: true });
+    // printTextureImage(readTexture(ctx, normalTexture, new Float32Array(width * height * 4)), { scale: 0.75, normalize: true });
 
     return { vertexTexture, groupTexture, normalTexture, vertexCount: count };
 }

src/mol-gl/renderable/cylinders.ts

@@ -27,6 +27,7 @@ export const CylindersSchema = {
     dIgnoreLight: DefineSpec('boolean'),
     dXrayShaded: DefineSpec('boolean'),
     dTransparentBackfaces: DefineSpec('string', ['off', 'on', 'opaque']),
+    dSolidInterior: DefineSpec('boolean'),
     uBumpFrequency: UniformSpec('f', 'material'),
     uBumpAmplitude: UniformSpec('f', 'material'),
 };

src/mol-gl/renderable/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Gianluca Tomasello <giagitom@gmail.com>
@@ -152,9 +152,12 @@ export const GlobalUniformSchema = {
 
     uHighlightColor: UniformSpec('v3'),
     uSelectColor: UniformSpec('v3'),
+    uDimColor: UniformSpec('v3'),
     uHighlightStrength: UniformSpec('f'),
     uSelectStrength: UniformSpec('f'),
+    uDimStrength: UniformSpec('f'),
     uMarkerPriority: UniformSpec('i'),
+    uMarkerAverage: UniformSpec('f'),
 
     uXrayEdgeFalloff: UniformSpec('f'),
 
@@ -229,6 +232,7 @@ export const OverpaintSchema = {
     uOverpaintGridTransform: UniformSpec('v4'),
     tOverpaintGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
     dOverpaintType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
+    uOverpaintStrength: UniformSpec('f', 'material'),
 } as const;
 export type OverpaintSchema = typeof OverpaintSchema
 export type OverpaintValues = Values<OverpaintSchema>
@@ -242,7 +246,8 @@ export const TransparencySchema = {
     uTransparencyGridDim: UniformSpec('v3'),
     uTransparencyGridTransform: UniformSpec('v4'),
     tTransparencyGrid: TextureSpec('texture', 'alpha', 'ubyte', 'linear'),
-    dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance'])
+    dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
+    uTransparencyStrength: UniformSpec('f', 'material'),
 } as const;
 export type TransparencySchema = typeof TransparencySchema
 export type TransparencyValues = Values<TransparencySchema>
@@ -256,6 +261,7 @@ export const SubstanceSchema = {
     uSubstanceGridTransform: UniformSpec('v4'),
     tSubstanceGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
     dSubstanceType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
+    uSubstanceStrength: UniformSpec('f', 'material'),
 } as const;
 export type SubstanceSchema = typeof SubstanceSchema
 export type SubstanceValues = Values<SubstanceSchema>

src/mol-gl/renderable/spheres.ts

@@ -24,6 +24,7 @@ export const SpheresSchema = {
     dIgnoreLight: DefineSpec('boolean'),
     dXrayShaded: DefineSpec('boolean'),
     dTransparentBackfaces: DefineSpec('string', ['off', 'on', 'opaque']),
+    dSolidInterior: DefineSpec('boolean'),
     uBumpFrequency: UniformSpec('f', 'material'),
     uBumpAmplitude: UniformSpec('f', 'material'),
 };

src/mol-gl/renderable/util.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,6 +10,10 @@ import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
 import { TextureFilter } from '../webgl/texture';
 import { arrayMinMax } from '../../mol-util/array';
 
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3fromArray = Vec3.fromArray;
+const v3transformMat4Offset = Vec3.transformMat4Offset;
+
 export function calculateTextureInfo(n: number, itemSize: number) {
     n = Math.max(n, 2); // observed issues with 1 pixel textures
     const sqN = Math.sqrt(n);
@@ -137,21 +141,21 @@ export function calculateInvariantBoundingSphere(position: Float32Array, positio
 
     boundaryHelper.reset();
     for (let i = 0, _i = positionCount * 3; i < _i; i += step) {
-        Vec3.fromArray(v, position, i);
+        v3fromArray(v, position, i);
         boundaryHelper.includePosition(v);
     }
     boundaryHelper.finishedIncludeStep();
     for (let i = 0, _i = positionCount * 3; i < _i; i += step) {
-        Vec3.fromArray(v, position, i);
+        v3fromArray(v, position, i);
         boundaryHelper.radiusPosition(v);
     }
 
     const sphere = boundaryHelper.getSphere();
 
-    if (positionCount <= 98) {
+    if (positionCount <= 14) {
         const extrema: Vec3[] = [];
         for (let i = 0, _i = positionCount * 3; i < _i; i += step) {
-            extrema.push(Vec3.fromArray(Vec3(), position, i));
+            extrema.push(v3fromArray(Vec3(), position, i));
         }
         Sphere3D.setExtrema(sphere, extrema);
     }
@@ -161,9 +165,9 @@ export function calculateInvariantBoundingSphere(position: Float32Array, positio
 
 const _mat4 = Mat4();
 
-export function calculateTransformBoundingSphere(invariantBoundingSphere: Sphere3D, transform: Float32Array, transformCount: number): Sphere3D {
+export function calculateTransformBoundingSphere(invariantBoundingSphere: Sphere3D, transform: Float32Array, transformCount: number, transformOffset: number): Sphere3D {
     if (transformCount === 1) {
-        Mat4.fromArray(_mat4, transform, 0);
+        Mat4.fromArray(_mat4, transform, transformOffset);
         const s = Sphere3D.clone(invariantBoundingSphere);
         return Mat4.isIdentity(_mat4) ? s : Sphere3D.transform(s, s, _mat4);
     }
@@ -174,28 +178,28 @@ export function calculateTransformBoundingSphere(invariantBoundingSphere: Sphere
     const { center, radius, extrema } = invariantBoundingSphere;
 
     // only use extrema if there are not too many transforms
-    if (extrema && transformCount < 50) {
+    if (extrema && transformCount <= 14) {
         for (let i = 0, _i = transformCount; i < _i; ++i) {
             for (const e of extrema) {
-                Vec3.transformMat4Offset(v, e, transform, 0, 0, i * 16);
+                v3transformMat4Offset(v, e, transform, 0, 0, i * 16 + transformOffset);
                 boundaryHelper.includePosition(v);
             }
         }
         boundaryHelper.finishedIncludeStep();
         for (let i = 0, _i = transformCount; i < _i; ++i) {
             for (const e of extrema) {
-                Vec3.transformMat4Offset(v, e, transform, 0, 0, i * 16);
+                v3transformMat4Offset(v, e, transform, 0, 0, i * 16 + transformOffset);
                 boundaryHelper.radiusPosition(v);
             }
         }
     } else {
         for (let i = 0, _i = transformCount; i < _i; ++i) {
-            Vec3.transformMat4Offset(v, center, transform, 0, 0, i * 16);
+            v3transformMat4Offset(v, center, transform, 0, 0, i * 16 + transformOffset);
             boundaryHelper.includePositionRadius(v, radius);
         }
         boundaryHelper.finishedIncludeStep();
         for (let i = 0, _i = transformCount; i < _i; ++i) {
-            Vec3.transformMat4Offset(v, center, transform, 0, 0, i * 16);
+            v3transformMat4Offset(v, center, transform, 0, 0, i * 16 + transformOffset);
             boundaryHelper.radiusPositionRadius(v, radius);
         }
     }
@@ -205,7 +209,7 @@ export function calculateTransformBoundingSphere(invariantBoundingSphere: Sphere
 
 export function calculateBoundingSphere(position: Float32Array, positionCount: number, transform: Float32Array, transformCount: number, padding = 0, stepFactor = 1): { boundingSphere: Sphere3D, invariantBoundingSphere: Sphere3D } {
     const invariantBoundingSphere = calculateInvariantBoundingSphere(position, positionCount, stepFactor);
-    const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform, transformCount);
+    const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform, transformCount, 0);
     Sphere3D.expand(boundingSphere, boundingSphere, padding);
     Sphere3D.expand(invariantBoundingSphere, invariantBoundingSphere, padding);
     return { boundingSphere, invariantBoundingSphere };

src/mol-gl/renderer.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Gianluca Tomasello <giagitom@gmail.com>
@@ -38,14 +38,14 @@ export interface RendererStats {
     instancedDrawCount: number
 }
 
-export const enum PickType {
+export enum PickType {
     None = 0,
     Object = 1,
     Instance = 2,
     Group = 3,
 }
 
-export const enum MarkingType {
+export enum MarkingType {
     None = 0,
     Depth = 1,
     Mask = 2,
@@ -54,10 +54,11 @@ export const enum MarkingType {
 interface Renderer {
     readonly stats: RendererStats
     readonly props: Readonly<RendererProps>
+    readonly light: Readonly<Light>
 
     clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void
     clearDepth: (packed?: boolean) => void
-    update: (camera: ICamera) => void
+    update: (camera: ICamera, scene: Scene) => void
 
     renderPick: (group: Scene.Group, camera: ICamera, variant: 'pick' | 'depth', depthTexture: Texture | null, pickType: PickType) => void
     renderDepth: (group: Scene.Group, camera: ICamera, depthTexture: Texture | null) => void
@@ -96,29 +97,31 @@ export const RendererParams = {
     colorMarker: PD.Boolean(true, { description: 'Enable color marker' }),
     highlightColor: PD.Color(Color.fromNormalizedRgb(1.0, 0.4, 0.6)),
     selectColor: PD.Color(Color.fromNormalizedRgb(0.2, 1.0, 0.1)),
+    dimColor: PD.Color(Color.fromNormalizedRgb(1.0, 1.0, 1.0)),
     highlightStrength: PD.Numeric(0.3, { min: 0.0, max: 1.0, step: 0.1 }),
     selectStrength: PD.Numeric(0.3, { min: 0.0, max: 1.0, step: 0.1 }),
+    dimStrength: PD.Numeric(0.0, { min: 0.0, max: 1.0, step: 0.1 }),
     markerPriority: PD.Select(1, [[1, 'Highlight'], [2, 'Select']]),
 
     xrayEdgeFalloff: PD.Numeric(1, { min: 0.0, max: 3.0, step: 0.1 }),
 
     light: PD.ObjectList({
-        inclination: PD.Numeric(180, { min: 0, max: 180, step: 1 }),
-        azimuth: PD.Numeric(0, { min: 0, max: 360, step: 1 }),
+        inclination: PD.Numeric(150, { min: 0, max: 180, step: 1 }),
+        azimuth: PD.Numeric(320, { min: 0, max: 360, step: 1 }),
         color: PD.Color(Color.fromNormalizedRgb(1.0, 1.0, 1.0)),
-        intensity: PD.Numeric(0.6, { min: 0.0, max: 1.0, step: 0.01 }),
+        intensity: PD.Numeric(0.6, { min: 0.0, max: 5.0, step: 0.01 }),
     }, o => Color.toHexString(o.color), { defaultValue: [{
-        inclination: 180,
-        azimuth: 0,
+        inclination: 150,
+        azimuth: 320,
         color: Color.fromNormalizedRgb(1.0, 1.0, 1.0),
         intensity: 0.6
     }] }),
     ambientColor: PD.Color(Color.fromNormalizedRgb(1.0, 1.0, 1.0)),
-    ambientIntensity: PD.Numeric(0.4, { min: 0.0, max: 1.0, step: 0.01 }),
+    ambientIntensity: PD.Numeric(0.4, { min: 0.0, max: 2.0, step: 0.01 }),
 };
 export type RendererProps = PD.Values<typeof RendererParams>
 
-type Light = {
+export type Light = {
     count: number
     direction: number[]
     color: number[]
@@ -231,9 +234,12 @@ namespace Renderer {
 
             uHighlightColor: ValueCell.create(Color.toVec3Normalized(Vec3(), p.highlightColor)),
             uSelectColor: ValueCell.create(Color.toVec3Normalized(Vec3(), p.selectColor)),
+            uDimColor: ValueCell.create(Color.toVec3Normalized(Vec3(), p.dimColor)),
             uHighlightStrength: ValueCell.create(p.highlightStrength),
             uSelectStrength: ValueCell.create(p.selectStrength),
+            uDimStrength: ValueCell.create(p.dimStrength),
             uMarkerPriority: ValueCell.create(p.markerPriority),
+            uMarkerAverage: ValueCell.create(0),
 
             uXrayEdgeFalloff: ValueCell.create(p.xrayEdgeFalloff),
         };
@@ -328,7 +334,7 @@ namespace Renderer {
             r.render(variant, sharedTexturesList.length);
         };
 
-        const update = (camera: ICamera) => {
+        const update = (camera: ICamera, scene: Scene) => {
             ValueCell.update(globalUniforms.uView, camera.view);
             ValueCell.update(globalUniforms.uInvView, Mat4.invert(invView, camera.view));
             ValueCell.update(globalUniforms.uProjection, camera.projection);
@@ -345,13 +351,15 @@ namespace Renderer {
             ValueCell.updateIfChanged(globalUniforms.uFogFar, camera.fogFar);
             ValueCell.updateIfChanged(globalUniforms.uFogNear, camera.fogNear);
             ValueCell.updateIfChanged(globalUniforms.uTransparentBackground, transparentBackground);
+
+            ValueCell.updateIfChanged(globalUniforms.uMarkerAverage, scene.markerAverage);
         };
 
         const updateInternal = (group: Scene.Group, camera: ICamera, depthTexture: Texture | null, renderMask: Mask, markingDepthTest: boolean) => {
             arrayMapUpsert(sharedTexturesList, 'tDepth', depthTexture || emptyDepthTexture);
 
             ValueCell.update(globalUniforms.uModel, group.view);
-            ValueCell.update(globalUniforms.uModelView, Mat4.mul(modelView, group.view, camera.view));
+            ValueCell.update(globalUniforms.uModelView, Mat4.mul(modelView, camera.view, group.view));
             ValueCell.update(globalUniforms.uInvModelView, Mat4.invert(invModelView, modelView));
             ValueCell.update(globalUniforms.uModelViewProjection, Mat4.mul(modelViewProjection, modelView, camera.projection));
             ValueCell.update(globalUniforms.uInvModelViewProjection, Mat4.invert(invModelViewProjection, modelViewProjection));
@@ -754,6 +762,10 @@ namespace Renderer {
                     p.selectColor = props.selectColor;
                     ValueCell.update(globalUniforms.uSelectColor, Color.toVec3Normalized(globalUniforms.uSelectColor.ref.value, p.selectColor));
                 }
+                if (props.dimColor !== undefined && props.dimColor !== p.dimColor) {
+                    p.dimColor = props.dimColor;
+                    ValueCell.update(globalUniforms.uDimColor, Color.toVec3Normalized(globalUniforms.uDimColor.ref.value, p.dimColor));
+                }
                 if (props.highlightStrength !== undefined && props.highlightStrength !== p.highlightStrength) {
                     p.highlightStrength = props.highlightStrength;
                     ValueCell.update(globalUniforms.uHighlightStrength, p.highlightStrength);
@@ -762,6 +774,10 @@ namespace Renderer {
                     p.selectStrength = props.selectStrength;
                     ValueCell.update(globalUniforms.uSelectStrength, p.selectStrength);
                 }
+                if (props.dimStrength !== undefined && props.dimStrength !== p.dimStrength) {
+                    p.dimStrength = props.dimStrength;
+                    ValueCell.update(globalUniforms.uDimStrength, p.dimStrength);
+                }
                 if (props.markerPriority !== undefined && props.markerPriority !== p.markerPriority) {
                     p.markerPriority = props.markerPriority;
                     ValueCell.update(globalUniforms.uMarkerPriority, p.markerPriority);
@@ -827,6 +843,9 @@ namespace Renderer {
                     instancedDrawCount: stats.instancedDrawCount,
                 };
             },
+            get light(): Light {
+                return light;
+            },
             dispose: () => {
                 // TODO
             }

src/mol-gl/scene.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -77,6 +77,7 @@ interface Scene extends Object3D {
     remove: (o: GraphicsRenderObject) => void
     commit: (maxTimeMs?: number) => boolean
     readonly needsCommit: boolean
+    readonly commitQueueSize: number
     has: (o: GraphicsRenderObject) => boolean
     clear: () => void
     forEach: (callbackFn: (value: GraphicsRenderable, key: GraphicsRenderObject) => void) => void
@@ -105,6 +106,10 @@ namespace Scene {
         let boundingSphereDirty = true;
         let boundingSphereVisibleDirty = true;
 
+        let markerAverageDirty = true;
+        let opacityAverageDirty = true;
+        let hasOpaqueDirty = true;
+
         let markerAverage = 0;
         let opacityAverage = 0;
         let hasOpaque = false;
@@ -165,9 +170,9 @@ namespace Scene {
             }
 
             renderables.sort(renderableSort);
-            markerAverage = calculateMarkerAverage();
-            opacityAverage = calculateOpacityAverage();
-            hasOpaque = calculateHasOpaque();
+            markerAverageDirty = true;
+            opacityAverageDirty = true;
+            hasOpaqueDirty = true;
             return true;
         }
 
@@ -189,9 +194,9 @@ namespace Scene {
             const newVisibleHash = computeVisibleHash();
             if (newVisibleHash !== visibleHash) {
                 boundingSphereVisibleDirty = true;
-                markerAverage = calculateMarkerAverage();
-                opacityAverage = calculateOpacityAverage();
-                hasOpaque = calculateHasOpaque();
+                markerAverageDirty = true;
+                opacityAverageDirty = true;
+                hasOpaqueDirty = true;
                 visibleHash = newVisibleHash;
                 return true;
             } else {
@@ -268,13 +273,14 @@ namespace Scene {
                 } else {
                     syncVisibility();
                 }
-                markerAverage = calculateMarkerAverage();
-                opacityAverage = calculateOpacityAverage();
-                hasOpaque = calculateHasOpaque();
+                markerAverageDirty = true;
+                opacityAverageDirty = true;
+                hasOpaqueDirty = true;
             },
             add: (o: GraphicsRenderObject) => commitQueue.add(o),
             remove: (o: GraphicsRenderObject) => commitQueue.remove(o),
             commit: (maxTime = Number.MAX_VALUE) => commit(maxTime),
+            get commitQueueSize() { return commitQueue.size; },
             get needsCommit() { return !commitQueue.isEmpty; },
             has: (o: GraphicsRenderObject) => {
                 return renderableMap.has(o);
@@ -311,12 +317,24 @@ namespace Scene {
                 return boundingSphereVisible;
             },
             get markerAverage() {
+                if (markerAverageDirty) {
+                    markerAverage = calculateMarkerAverage();
+                    markerAverageDirty = false;
+                }
                 return markerAverage;
             },
             get opacityAverage() {
+                if (opacityAverageDirty) {
+                    opacityAverage = calculateOpacityAverage();
+                    opacityAverageDirty = false;
+                }
                 return opacityAverage;
             },
             get hasOpaque() {
+                if (hasOpaqueDirty) {
+                    hasOpaque = calculateHasOpaque();
+                    hasOpaqueDirty = false;
+                }
                 return hasOpaque;
             },
         };

src/mol-gl/shader/chunks/apply-light-color.glsl.ts

@@ -12,7 +12,7 @@ export const apply_light_color = `
     gl_FragColor = material;
 #else
     #ifdef bumpEnabled
-        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {
+        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0 && bumpiness > 0.0) {
             normal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);
         }
     #endif

src/mol-gl/shader/chunks/apply-marker-color.glsl.ts

@@ -1,4 +1,5 @@
 export const apply_marker_color = `
+
 #if defined(dColorMarker)
     if (marker > 0.0) {
         if ((uMarkerPriority == 1 && marker != 2.0) || (uMarkerPriority != 1 && marker == 1.0)) {
@@ -8,6 +9,9 @@ export const apply_marker_color = `
             gl_FragColor.rgb = mix(gl_FragColor.rgb, uSelectColor, uSelectStrength);
             gl_FragColor.a = max(gl_FragColor.a, uSelectStrength * 0.002); // for direct-volume rendering
         }
+    } else if (uMarkerAverage > 0.0) {
+        gl_FragColor.rgb = mix(gl_FragColor.rgb, uDimColor, uDimStrength);
+        gl_FragColor.a = max(gl_FragColor.a, uDimStrength * 0.002); // for direct-volume rendering
     }
 #endif
 `;

src/mol-gl/shader/chunks/assign-color-varying.glsl.ts

@@ -42,6 +42,7 @@ export const assign_color_varying = `
         #else
             vOverpaint.rgb = mix(vColor.rgb, vOverpaint.rgb, vOverpaint.a);
         #endif
+        vOverpaint *= uOverpaintStrength;
     #endif
 
     #ifdef dSubstance
@@ -58,6 +59,7 @@ export const assign_color_varying = `
 
         // pre-mix to avoid artifacts due to empty substance
         vSubstance.rgb = mix(vec3(uMetalness, uRoughness, uBumpiness), vSubstance.rgb, vSubstance.a);
+        vSubstance *= uSubstanceStrength;
     #endif
 #elif defined(dRenderVariant_pick)
     #ifdef requiredDrawBuffers
@@ -86,5 +88,6 @@ export const assign_color_varying = `
         vec3 tgridPos = (uTransparencyGridTransform.w * (vModelPosition - uTransparencyGridTransform.xyz)) / uTransparencyGridDim;
         vTransparency = texture3dFrom2dLinear(tTransparencyGrid, tgridPos, uTransparencyGridDim, uTransparencyTexDim).a;
     #endif
+    vTransparency *= uTransparencyStrength;
 #endif
 `;

src/mol-gl/shader/chunks/clip-instance.glsl.ts

@@ -1,12 +1,7 @@
 export const clip_instance = `
 #if defined(dClipVariant_instance) && dClipObjectCount != 0
-    int flag = 0;
-    #if defined(dClipping)
-        flag = int(floor(vClipping * 255.0 + 0.5));
-    #endif
-
     vec4 mCenter = uModel * aTransform * vec4(uInvariantBoundingSphere.xyz, 1.0);
-    if (clipTest(vec4(mCenter.xyz, uInvariantBoundingSphere.w), flag))
+    if (clipTest(vec4(mCenter.xyz, uInvariantBoundingSphere.w)))
         // move out of [ -w, +w ] to 'discard' in vert shader
         gl_Position.z = 2.0 * gl_Position.w;
 #endif