3.31.4

* Fixed degenerate case (1-point) in PCA - now correctly returns identity matrix

* Changelog

.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/pull_request_template.md

@@ -0,0 +1,10 @@
+<!-- Thank you for contributing to Mol* -->
+
+# Description
+
+
+## Actions
+
+- [ ] Added description of changes to the `[Unreleased]` section of `CHANGELOG.md`
+- [ ] Updated headers of modified files
+- [ ] Added my name to `package.json`'s `contributors`

.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

.vscode/extensions.json

@@ -6,7 +6,6 @@
 	"recommendations": [
 		"dbaeumer.vscode-eslint",
 		"firsttris.vscode-jest-runner",
-		"msjsdiag.debugger-for-chrome",
 		"slevesque.shader",
 		"stpn.vscode-graphql",
 		"wayou.vscode-todo-highlight"

CHANGELOG.md

@@ -6,6 +6,293 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.31.4] - 2023-02-24
+
+- Allow link cylinder/line `dashCount` set to '0'
+- Stop animation loop when disposing `PluginContext` (thanks @gfrn for identifying the issue)
+
+## [v3.31.3] - 2023-02-22
+
+- Fix impostor bond visuals not correctly updating on `sizeFactor` changes
+- Fix degenerate case in PCA
+- Fix near clipping avoidance in impostor shaders
+- Update `fs` import in `data-source.ts`
+
+## [v3.31.2] - 2023-02-12
+
+- Fix exit code of volume pack executable (pack.ts). Now exits with non-0 status when an error happens
+- Remove pca transform from components ui focus (too distracting)
+- Fix artefacts with opaque outlines behind transparent objects
+- Fix polymer trace visual not updating
+- Fix use of `WEBGL_provoking_vertex`
+
+## [v3.31.1] - 2023-02-05
+
+- 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 projection
+- 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 `Whole Structure` to `Auto`
+
+## [v3.22.0] - 2022-10-17
+
+- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
+
+## [v3.21.0] - 2022-10-17
+
+- Add `VolumeIsosurfaceParams.pickingGranularity` param
+- Prevent component controls collapsing when option is selected
+
+## [v3.20.0] - 2022-10-16
+
+- [Breaking] Rename the ``model-index`` color theme to ``trajectory-index``
+- Add a new ``model-index`` color theme that uniquely colors each loaded model
+- Add the new ``model-index`` and ``structure-index`` color themes as an option for the carbon color in the ``element-symbol`` and ``ilustrative`` color themes
+- Add ``structure-index`` color theme that uniquely colors each root structure
+- Add ``nearest`` method to ``Lookup3D``
+- Add mipmap-based blur for skybox backgrounds
+
+## [v3.19.0] - 2022-10-01
+
+- Fix "empty textures" error on empty canvas
+- Optimize BinaryCIF integer packing encoder
+- Fix dual depth peeling when post-processing is off or when rendering direct-volumes
+- Add ``cameraClipping.minNear`` parameter
+- Fix black artifacts on specular highlights with transparent background
+
+## [v3.18.0] - 2022-09-17
+
+- Integration of Dual depth peeling - OIT method
+- Stereo camera improvements
+    - Fix param updates not applied
+    - Better param ranges and description
+    - Add timer.mark for left/right camera
+
+## [v3.17.0] - 2022-09-11
+
+- [Fix] Clone ``Canvas3DParams`` when creating a ``Canvas3D`` instance to prevent shared state between multiple instances
+- Add ``includeResidueTest`` option to ``alignAndSuperposeWithSIFTSMapping``
+- Add ``parentDisplay`` param for interactions representation.
+- [Experimental] Add support for PyMOL, VMD, and Jmol atom expressions in selection scripts
+- Support for ``failIfMajorPerformanceCaveat`` webgl attribute. Add ``PluginConfig.General.AllowMajorPerformanceCaveat`` and ``allow-major-performance-caveat`` Viewer GET param.
+- Fix handling of PDB TER records (#549)
+- Add support for getting multiple loci from a representation (``.getAllLoci()``)
+- Add ``key`` property to intra- and inter-bonds for referencing source data
+- Fix click event triggered after move
+
+## [v3.16.0] - 2022-08-25
+
+- Support ``globalColorParams`` and ``globalSymmetryParams`` in common representation params
+- Support ``label`` parameter in ``Viewer.loadStructureFromUrl``
+- Fix ``ViewportHelpContent`` Mouse Controls section
+
+## [v3.15.0] - 2022-08-23
+
+- Fix wboit in Safari >=15 (add missing depth renderbuffer to wboit pass)
+- Add 'Around Camera' option to Volume streaming
+- Avoid queuing more than one update in Volume streaming
+
+## [v3.14.0] - 2022-08-20
+
+- Expose inter-bonds compute params in structure
+- Improve performance of inter/intra-bonds compute
+- Fix defaultAttribs handling in Canvas3DContext.fromCanvas
+- Confal pyramids extension improvements
+    - Add custom labels to Confal pyramids
+    - Improve naming of some internal types in Confal pyramids extension coordinate
+    - Add example mmCIF file with categories necessary to display Confal pyramids
+    - Change the lookup logic of NtC steps from residues
+- Add support for download of gzipped files
+- Don't filter IndexPairBonds by element-based rules in MOL/SDF and MOL2 (without symmetry) models
+- Fix Glycam Saccharide Names used by default
+- Fix GPU surfaces rendering in Safari with WebGL2
+- Add ``fov`` (Field of View) Canvas3D parameter
+- Add ``sceneRadiusFactor`` Canvas3D parameter
+- Add background pass (skybox, image, horizontal/radial gradient)
+    - Set simple-settings presets via ``PluginConfig.Background.Styles``
+    - Example presets in new backgrounds extension
+    - Load skybox/image from URL or File (saved in session)
+    - Opacity, saturation, lightness controls for skybox/image
+    - Coverage (viewport or canvas) controls for image/gradient
+- [Breaking] ``AssetManager`` needs to be passed to various graphics related classes
+- Fix SSAO renderable initialization
+- Reduce number of webgl state changes
+    - Add ``viewport`` and ``scissor`` to state object
+    - Add ``hasOpaque`` to scene object
+- Handle edge cases where some renderables would not get (correctly) rendered
+    - Fix text background rendering for opaque text
+    - Fix helper scenes not shown when rendering directly to draw target
+- Fix ``CustomElementProperty`` coloring not working
+
+## [v3.13.0] - 2022-07-24
+
+- Fix: only update camera state if manualReset is off (#494)
+- Improve handling principal axes of points in a plane
+- Add 'material' annotation support for textures
+- More effort to avoid using ``flat`` qualifier in shaders: add ``dVaryingGroup``
+- Enable ``immediateUpdate`` for iso level in isosurface and volume streaming controls
+- Add support to download CCD from configurable URL
+
+## [v3.12.1] - 2022-07-20
+
+- Fix plugin behavior dispose logic to correctly unsubscribe observables.
+
+## [v3.12.0] - 2022-07-17
+
+- Add ``colorMarker`` option to Renderer. This disables the highlight and select marker at a shader level for faster rendering of large scenes in some cases.
+- Bind shared textures only once per pass, not for each render item
+- Fix missing 'material' annotation for some uniforms, causing unnecessary uniform updates
+- Remove use of ``isnan`` in impostor shaders, not needed and causing slowdown
+- Avoid using ``flat`` qualifier in shaders, causing slowdown
+- Improve CellPack's ``adjustStyle`` option (disable ``colorMarker``, set component options, enable marking w/o ghost)
+- Scan all entities when looking for ``struct_conn`` entries (fixes issue when the same ``label_asym_id`` is used in more than one entity)
+
+## [v3.11.0] - 2022-07-04
+
+- Add ``instanceGranularity`` option for marker, transparency, clipping, overpaint, substance data to save memory
+- CellPack extension tweaks
+    - Use instancing to create DNA/RNA curves to save memory
+    - Enable ``instanceGranularity`` by default
+    - Add ``adjustStyle`` option to LoadCellPackModel action (stylized, no multi-sample, no far clipping, chain picking)
+- Structure Superposition now respects pivot's coordinate system
+
+## [v3.10.2] - 2022-06-26
+
+- Fix superfluous shader varying
+- Improve use of gl_VertexID when possible
+
+## [v3.10.1] - 2022-06-26
+
+- Fix groupCount when updating TextureMesh-based visuals
+
+## [v3.10.0] - 2022-06-24
+
+- Add support for Glycam saccharide names
+- Add ``PluginConfig.Viewport.ShowTrajectoryControls`` config option
+
+## [v3.9.1] - 2022-06-19
+
+- Fix missing ``super.componentWillUnmount()`` calls (@simeonborko)
+- Fix missing ``uGroupCount`` update for visuals
+- Fix missing aromatic bond display
+
+## [v3.9.0] - 2022-05-30
+
+- Improve picking by using drawbuffers (when available) to reduce number of drawcalls
+- GPU timing support
+    - Add ``timing-mode`` Viewer GET param
+    - Add support for webgl timer queries
+    - Add timer marks around GPU render & compute operations
+- Volume Server CIF: Add check that a data block contains volume data before parsing
+- Fix ``Scene.clear`` not clearing primitives & volumes arrays (@JonStargaryen)
+- Fix rendering volumes when wboit is switched off and postprocessing is enabled
+
 ## [v3.8.2] - 2022-05-22
 
 - Fix ``Scene.opacityAverage`` not taking xray shaded into account

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*
@@ -126,7 +126,7 @@ and navigate to `build/viewer`
 
 **GraphQL schemas**
 
-    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
+    node node_modules/@graphql-codegen/cli/cjs/bin -c src/extensions/rcsb/graphql/codegen.yml
 
 ### Other scripts
 **Create chem comp bond table**
@@ -152,7 +152,7 @@ Or
     node lib/commonjs/cli/cif2bcif
 
 E.g.
- 
+
     node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
     node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.8.2",
+  "version": "3.31.4",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -13,14 +13,14 @@
   "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",
     "rebuild": "npm run clean && npm run build",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
     "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
-    "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
+    "build-extra": "cpx \"src/**/*.{scss,html,ico,jpg}\" lib/",
     "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
     "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
     "watch": "concurrently -c \"green,green,gray,gray\" --names \"tsc,srv,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-servers\" \"npm:watch-extra\" \"npm:watch-webpack\"",
@@ -28,7 +28,7 @@
     "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
     "watch-tsc": "tsc --watch --incremental",
     "watch-servers": "tsc --build tsconfig.commonjs.json --watch --incremental",
-    "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
+    "watch-extra": "cpx \"src/**/*.{scss,html,ico,jpg}\" lib/ --watch",
     "watch-webpack": "webpack -w --mode development --stats minimal",
     "watch-webpack-viewer": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.js",
     "watch-webpack-viewer-debug": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.debug.js",
@@ -75,7 +75,9 @@
       "node_modules",
       "lib"
     ],
-    "testURL": "http://localhost/",
+    "testEnvironmentOptions": {
+      "url": "http://localhost/"
+    },
     "testRegex": "\\.spec\\.ts$"
   },
   "author": "Mol* Contributors",
@@ -87,76 +89,90 @@
     "Ludovic Autin <autin@scripps.edu>",
     "Michal Malý <michal.maly@ibt.cas.cz>",
     "Jiří Černý <jiri.cerny@ibt.cas.cz>",
-    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
+    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>",
+    "Adam Midlik <midlik@gmail.com>",
+    "Koya Sakuma <koya.sakuma.work@gmail.com>",
+    "Gianluca Tomasello <giagitom@gmail.com>",
+    "Ke Ma <mark.ma@rcsb.org>",
+    "Jason Pattle <jpattle@exscientia.co.uk>",
+    "David Williams <dwilliams@nobiastx.com>",
+    "Zhenyu Zhang <jump2cn@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.6.2",
-    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.11",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.4.8",
-    "@graphql-codegen/typescript-operations": "^2.4.0",
-    "@types/cors": "^2.8.12",
-    "@types/gl": "^4.1.0",
-    "@types/jest": "^27.5.1",
-    "@types/react": "^18.0.9",
-    "@types/react-dom": "^18.0.4",
-    "@typescript-eslint/eslint-plugin": "^5.25.0",
-    "@typescript-eslint/parser": "^5.25.0",
+    "@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": "^4.5.8",
+    "@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": "^7.2.0",
+    "concurrently": "^7.6.0",
     "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.7.1",
-    "eslint": "^8.16.0",
+    "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",
-    "graphql": "^16.5.0",
-    "http-server": "^14.1.0",
-    "jest": "^28.1.0",
-    "mini-css-extract-plugin": "^2.6.0",
+    "fs-extra": "^11.1.0",
+    "graphql": "^16.6.0",
+    "http-server": "^14.1.1",
+    "jest": "^29.4.1",
+    "mini-css-extract-plugin": "^2.7.2",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "react": "^18.1.0",
-    "react-dom": "^18.1.0",
-    "sass": "^1.52.1",
-    "sass-loader": "^13.0.0",
-    "simple-git": "^3.7.1",
+    "react": "^18.2.0",
+    "react-dom": "^18.2.0",
+    "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": "^28.0.2",
-    "typescript": "^4.6.4",
-    "webpack": "^5.72.1",
-    "webpack-cli": "^4.9.2"
+    "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": "^2.1.1",
+    "@types/benchmark": "^2.1.2",
     "@types/compression": "1.7.2",
-    "@types/express": "^4.17.13",
-    "@types/node": "^16.11.36",
-    "@types/node-fetch": "^2.6.1",
+    "@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",
-    "body-parser": "^1.20.0",
+    "body-parser": "^1.20.1",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.18.1",
+    "express": "^4.18.2",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.14",
-    "immutable": "^4.0.0",
-    "node-fetch": "^2.6.7",
-    "rxjs": "^7.5.5",
-    "swagger-ui-dist": "^4.11.1",
-    "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/index.ts

@@ -58,20 +58,22 @@ class Viewer {
     }
 
     static async create(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
-        const o = { ...DefaultViewerOptions, ...{
-            layoutIsExpanded: false,
-            layoutShowControls: false,
-            layoutShowRemoteState: false,
-            layoutShowSequence: true,
-            layoutShowLog: false,
-            layoutShowLeftPanel: true,
+        const o = {
+            ...DefaultViewerOptions, ...{
+                layoutIsExpanded: false,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
 
-            viewportShowExpand: true,
-            viewportShowControls: false,
-            viewportShowSettings: false,
-            viewportShowSelectionMode: false,
-            viewportShowAnimation: false,
-        } };
+                viewportShowExpand: true,
+                viewportShowControls: false,
+                viewportShowSettings: false,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+            }
+        };
         const defaultSpec = DefaultPluginUISpec();
 
         const spec: PluginUISpec = {
@@ -135,18 +137,16 @@ class Viewer {
             }
         };
 
-        plugin.behaviors.canvas3d.initialized.subscribe(v => {
-            if (v) {
-                PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-                    renderer: {
-                        ...plugin.canvas3d!.props.renderer,
-                        backgroundColor: ColorNames.white,
-                    },
-                    camera: {
-                        ...plugin.canvas3d!.props.camera,
-                        helper: { axes: { name: 'off', params: {} } }
-                    }
-                } });
+        PluginCommands.Canvas3D.SetSettings(plugin, {
+            settings: {
+                renderer: {
+                    ...plugin.canvas3d!.props.renderer,
+                    backgroundColor: ColorNames.white,
+                },
+                camera: {
+                    ...plugin.canvas3d!.props.camera,
+                    helper: { axes: { name: 'off', params: {} } }
+                }
             }
         });
 
@@ -166,7 +166,7 @@ class Viewer {
             structures.push({ ref: structureProperties?.ref || structure.ref });
         }
 
-        // remove current structuresfrom hierarchy as they will be merged
+        // remove current structures from hierarchy as they will be merged
         // TODO only works with using loadStructuresFromUrlsAndMerge once
         //      need some more API metho to work with the hierarchy
         this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');

src/apps/docking-viewer/viewport.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -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: {} },
         }
     } });
 }
@@ -202,14 +205,14 @@ const InteractionsPreset = StructureRepresentationPresetProvider({
         const components = {
             ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
             surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
-            interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
+            interactions: await presetStaticComponent(plugin, structureCell, 'ligand'),
         };
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
             ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
             ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
-            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial, includeParent: true, parentDisplay: 'between' }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
             label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, material: CustomMaterial, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
         };
 

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';
@@ -45,17 +46,21 @@ import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
 import { ObjectKeys } from '../../mol-util/type-helpers';
+import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
+import { Backgrounds } from '../../extensions/backgrounds';
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } 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),
@@ -85,18 +90,24 @@ const DefaultViewerOptions = {
     pickScale: PluginConfig.General.PickScale.defaultValue,
     pickPadding: PluginConfig.General.PickPadding.defaultValue,
     enableWboit: PluginConfig.General.EnableWboit.defaultValue,
+    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,
     viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
     viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
     viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    viewportShowTrajectoryControls: PluginConfig.Viewport.ShowTrajectoryControls.defaultValue,
     pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
     volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
     volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+    saccharideCompIdMapType: 'default' as SaccharideCompIdMapType,
+    volumesAndSegmentationsDefaultServer: VolsegVolumeServerConfig.DefaultServer.defaultValue,
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 
@@ -153,12 +164,16 @@ export class Viewer {
                 [PluginConfig.General.PickScale, o.pickScale],
                 [PluginConfig.General.PickPadding, o.pickPadding],
                 [PluginConfig.General.EnableWboit, o.enableWboit],
+                [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],
                 [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
                 [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.Viewport.ShowTrajectoryControls, o.viewportShowTrajectoryControls],
                 [PluginConfig.State.DefaultServer, o.pluginStateServer],
                 [PluginConfig.State.CurrentServer, o.pluginStateServer],
                 [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
@@ -166,6 +181,8 @@ export class Viewer {
                 [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                 [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
+                [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+                [VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
             ]
         };
 
@@ -192,7 +209,7 @@ export class Viewer {
         return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
     }
 
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions & { label?: string }) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
@@ -201,6 +218,7 @@ export class Viewer {
                     url: Asset.Url(url),
                     format: format as any,
                     isBinary,
+                    label: options?.label,
                     options: { ...params.source.params.options, representationParams: options?.representationParams as any },
                 }
             }
@@ -397,7 +415,7 @@ export class Viewer {
     async loadTrajectory(params: LoadTrajectoryParams) {
         const plugin = this.plugin;
 
-        let model: StateObjectSelector, coords: StateObjectSelector;
+        let model: StateObjectSelector;
 
         if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
             const data = params.model.kind === 'model-data'
@@ -415,14 +433,12 @@ export class Viewer {
             model = await provider!.parse(plugin, data);
         }
 
-        {
-            const data = params.coordinates.kind === 'coordinates-data'
-                ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
-                : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
+        const data = params.coordinates.kind === 'coordinates-data'
+            ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
+            : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
 
-            const provider = plugin.dataFormats.get(params.coordinates.format);
-            coords = await provider!.parse(plugin, data);
-        }
+        const provider = plugin.dataFormats.get(params.coordinates.format);
+        const coords = await provider!.parse(plugin, data);
 
         const trajectory = await plugin.build().toRoot()
             .apply(TrajectoryFromModelAndCoordinates, {
@@ -491,4 +507,4 @@ export const ViewerAutoPreset = StructureRepresentationPresetProvider({
             return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
         }
     }
-});
+});

src/apps/viewer/embedded.html

@@ -38,6 +38,15 @@
                 viewer.loadPdb('7bv2');
                 viewer.loadEmdb('EMD-30210', { detail: 6 });
                 // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
+                //     representationParams: {
+                //         theme: {
+                //             globalName: 'uniform',
+                //             globalColorParams: { value: 0xff0000 }
+                //         }
+                //     },
+                //     label: 'my structure'
+                // });
             });
         </script>
     </body>

src/apps/viewer/index.html

@@ -46,7 +46,10 @@
             }
 
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
+            if (debugMode) molstar.setDebugMode(debugMode);
+
+            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
+            if (timingMode) molstar.setTimingMode(timingMode);
 
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
             var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
@@ -57,7 +60,10 @@
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
+            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,
@@ -71,8 +77,11 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
+                enableWboit: (disableWboit || enableDpoit) ? false : void 0, // use default value if disable-wboit is not set
+                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/chem-comp-dict/create-ions.ts

@@ -15,7 +15,7 @@ const writeFile = util.promisify(fs.writeFile);
 
 import { DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
-import { ensureDataAvailable, readCCD } from './util';
+import { DefaultDataOptions, ensureDataAvailable, readCCD } from './util';
 
 function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
     const ionNames: string[] = [];
@@ -44,8 +44,8 @@ export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").re
     writeFile(filePath, output);
 }
 
-async function run(out: string, forceDownload = false) {
-    await ensureDataAvailable(forceDownload);
+async function run(out: string, options = DefaultDataOptions) {
+    await ensureDataAvailable(options);
     const ccd = await readCCD();
     const ionNames = extractIonNames(ccd);
     if (!fs.existsSync(path.dirname(out))) {
@@ -65,10 +65,15 @@ parser.add_argument('--forceDownload', '-f', {
     action: 'store_true',
     help: 'Force download of CCD and PVCD.'
 });
+parser.add_argument('--ccdUrl', '-c', {
+    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
+    required: false
+});
 interface Args {
     out: string,
     forceDownload?: boolean,
+    ccdUrl?: string
 }
 const args: Args = parser.parse_args();
 
-run(args.out, args.forceDownload);
+run(args.out, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl });

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

@@ -14,7 +14,7 @@ const writeFile = util.promisify(fs.writeFile);
 
 import { DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
-import { ensureDataAvailable, readCCD } from './util';
+import { DefaultDataOptions, ensureDataAvailable, readCCD } from './util';
 
 function extractSaccharideNames(ccd: DatabaseCollection<CCD_Schema>) {
     const saccharideNames: string[] = [];
@@ -47,8 +47,8 @@ export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g,
     writeFile(filePath, output);
 }
 
-async function run(out: string, forceDownload = false) {
-    await ensureDataAvailable(forceDownload);
+async function run(out: string, options = DefaultDataOptions) {
+    await ensureDataAvailable(options);
     const ccd = await readCCD();
     const saccharideNames = extractSaccharideNames(ccd);
     if (!fs.existsSync(path.dirname(out))) {
@@ -68,10 +68,15 @@ parser.add_argument('--forceDownload', '-f', {
     action: 'store_true',
     help: 'Force download of CCD and PVCD.'
 });
+parser.add_argument('--ccdUrl', '-c', {
+    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
+    required: false
+});
 interface Args {
     out: string,
     forceDownload?: boolean,
+    ccdUrl?: string
 }
 const args: Args = parser.parse_args();
 
-run(args.out, args.forceDownload);
+run(args.out, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl });

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

@@ -18,7 +18,7 @@ import { SetUtils } from '../../mol-util/set';
 import { DefaultMap } from '../../mol-util/map';
 import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
 import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
-import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
+import { DefaultDataOptions, ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
 
 type CCB = Table<CCD_Schema['chem_comp_bond']>
 type CCA = Table<CCD_Schema['chem_comp_atom']>
@@ -239,8 +239,8 @@ function createAtoms(ccd: DatabaseCollection<CCD_Schema>, pvcd: DatabaseCollecti
     );
 }
 
-async function run(out: string, binary = false, forceDownload = false, ccaOut?: string) {
-    await ensureDataAvailable(forceDownload);
+async function run(out: string, binary = false, options = DefaultDataOptions, ccaOut?: string) {
+    await ensureDataAvailable(options);
     const ccd = await readCCD();
     const pvcd = await readPVCD();
 
@@ -283,12 +283,22 @@ parser.add_argument('--ccaOut', '-a', {
     help: 'Optional generated file output path for chem_comp_atom data.',
     required: false
 });
+parser.add_argument('--ccdUrl', '-c', {
+    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
+    required: false
+});
+parser.add_argument('--pvcdUrl', '-p', {
+    help: 'Fetch the PVCD from a custom URL. This forces download of the PVCD.',
+    required: false
+});
 interface Args {
     out: string,
     forceDownload?: boolean,
     binary?: boolean,
-    ccaOut?: string
+    ccaOut?: string,
+    ccdUrl?: string,
+    pvcdUrl?: string
 }
 const args: Args = parser.parse_args();
 
-run(args.out, args.binary, args.forceDownload, args.ccaOut);
+run(args.out, args.binary, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl, pvcdUrl: args.pvcdUrl }, args.ccaOut);

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

@@ -35,9 +35,9 @@ export async function ensureAvailable(path: string, url: string, forceDownload =
     }
 }
 
-export async function ensureDataAvailable(forceDownload = false) {
-    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
-    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
+export async function ensureDataAvailable(options: DataOptions) {
+    await ensureAvailable(CCD_PATH, options.ccdUrl || CCD_URL, !!options.ccdUrl || options.forceDownload);
+    await ensureAvailable(PVCD_PATH, options.pvcdUrl || PVCD_URL, !!options.pvcdUrl || options.forceDownload);
 }
 
 export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
@@ -68,6 +68,16 @@ export function getEncodedCif(name: string, database: Database<Database.Schema>,
     return encoder.getData();
 }
 
+export type DataOptions = {
+    ccdUrl?: string,
+    pvcdUrl?: string,
+    forceDownload?: boolean
+}
+
+export const DefaultDataOptions: DataOptions = {
+    forceDownload: false
+};
+
 const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
 const CCD_PATH = path.join(DATA_DIR, 'components.cif');
 const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');

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

@@ -71,6 +71,7 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'ec-type':
         case 'ucode-alphanum-csv':
         case 'id_list':
+        case 'entity_id_list':
             return ListCol('str', ',', description);
         case 'id_list_spc':
             return ListCol('str', ' ', description);
@@ -151,7 +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/controls.tsx

@@ -4,16 +4,16 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as ReactDOM from 'react-dom';
+import { createRoot } from 'react-dom/client';
 import { AlphaOrbitalsExample } from '.';
 import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
 import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
 import { PluginContextContainer } from '../../mol-plugin-ui/plugin';
 
 export function mountControls(orbitals: AlphaOrbitalsExample, parent: Element) {
-    ReactDOM.render(<PluginContextContainer plugin={orbitals.plugin}>
+    createRoot(parent).render(<PluginContextContainer plugin={orbitals.plugin}>
         <Controls orbitals={orbitals} />
-    </PluginContextContainer>, parent);
+    </PluginContextContainer>);
 }
 
 function Controls({ orbitals }: { orbitals: AlphaOrbitalsExample }) {

src/examples/alpha-orbitals/index.html

@@ -55,6 +55,17 @@
             </a>
         </div>
         <script>
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) AlphaOrbitalsExample.setDebugMode(debugMode);
+
+            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
+            if (timingMode) AlphaOrbitalsExample.setTimingMode(timingMode);
+
             AlphaOrbitalsExample.init('app')
         </script>
         <!-- __MOLSTAR_ANALYTICS__ -->

src/examples/alpha-orbitals/index.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -25,6 +25,8 @@ import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
 
+import { setDebugMode, setTimingMode, consoleStats } from '../../mol-util/debug';
+
 interface DemoInput {
     moleculeSdf: string,
     basis: Basis,
@@ -80,24 +82,20 @@ export class AlphaOrbitalsExample {
 
         this.plugin.managers.interactivity.setProps({ granularity: 'element' });
 
-        this.plugin.behaviors.canvas3d.initialized.subscribe(init => {
-            if (!init) return;
-
-            if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
-                PluginCommands.Toast.Show(this.plugin, {
-                    title: 'Error',
-                    message: `Browser/device does not support required WebGL extension (OES_texture_float).`
-                });
-                return;
-            }
-
-            this.load({
-                moleculeSdf: DemoMoleculeSDF,
-                ...DemoOrbitals
+        if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
+            PluginCommands.Toast.Show(this.plugin, {
+                title: 'Error',
+                message: `Browser/device does not support required WebGL extension (OES_texture_float).`
             });
+            return;
+        }
 
-            mountControls(this, document.getElementById('controls')!);
+        this.load({
+            moleculeSdf: DemoMoleculeSDF,
+            ...DemoOrbitals
         });
+
+        mountControls(this, document.getElementById('controls')!);
     }
 
     readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
@@ -222,4 +220,7 @@ export class AlphaOrbitalsExample {
     }
 }
 
-(window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();
+(window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();
+(window as any).AlphaOrbitalsExample.setDebugMode = setDebugMode;
+(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/alpha-orbitals/density.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -8,6 +8,7 @@ import { sortArray } from '../../mol-data/util';
 import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Task } from '../../mol-task';
+import { isTimingMode } from '../../mol-util/debug';
 import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
 import { gpuComputeAlphaOrbitalsDensityGridValues } from './gpu/compute';
 
@@ -19,9 +20,9 @@ export function createSphericalCollocationDensityGrid(
 
         let matrix: Float32Array;
         if (canComputeGrid3dOnGPU(webgl)) {
-            // console.time('gpu');
-            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl!, cubeGrid, orbitals);
-            // console.timeEnd('gpu');
+            if (isTimingMode) webgl.timer.mark('createSphericalCollocationDensityGrid');
+            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl, cubeGrid, orbitals);
+            if (isTimingMode) webgl.timer.markEnd('createSphericalCollocationDensityGrid');
         } else {
             throw new Error('Missing OES_texture_float WebGL extension.');
         }

src/extensions/alpha-orbitals/orbitals.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Inspired by https://github.com/dgasmith/gau2grid.
  *
@@ -10,12 +10,11 @@ import { sortArray } from '../../mol-data/util';
 import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Task } from '../../mol-task';
+import { isTimingMode } from '../../mol-util/debug';
 import { sphericalCollocation } from './collocation';
 import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
 import { gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
 
-// setDebugMode(true);
-
 export function createSphericalCollocationGrid(
     params: CubeGridComputationParams, orbital: AlphaOrbital, webgl?: WebGLContext
 ): Task<CubeGrid> {
@@ -24,9 +23,9 @@ export function createSphericalCollocationGrid(
 
         let matrix: Float32Array;
         if (canComputeGrid3dOnGPU(webgl)) {
-            // console.time('gpu');
-            matrix = await gpuComputeAlphaOrbitalsGridValues(ctx, webgl!, cubeGrid, orbital);
-            // console.timeEnd('gpu');
+            if (isTimingMode) webgl.timer.mark('createSphericalCollocationGrid');
+            matrix = await gpuComputeAlphaOrbitalsGridValues(ctx, webgl, cubeGrid, orbital);
+            if (isTimingMode) webgl.timer.markEnd('createSphericalCollocationGrid');
         } else {
             // console.time('cpu');
             matrix = await sphericalCollocation(cubeGrid, orbital, ctx);

src/extensions/backgrounds/index.ts

@@ -0,0 +1,91 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { PluginConfig } from '../../mol-plugin/config';
+import { Color } from '../../mol-util/color/color';
+
+// from https://visualsonline.cancer.gov/details.cfm?imageid=2304, public domain
+import image_cells from './images/cells.jpg';
+
+// created with http://alexcpeterson.com/spacescape/
+import face_nebula_nx from './skyboxes/nebula/nebula_left2.jpg';
+import face_nebula_ny from './skyboxes/nebula/nebula_bottom4.jpg';
+import face_nebula_nz from './skyboxes/nebula/nebula_back6.jpg';
+import face_nebula_px from './skyboxes/nebula/nebula_right1.jpg';
+import face_nebula_py from './skyboxes/nebula/nebula_top3.jpg';
+import face_nebula_pz from './skyboxes/nebula/nebula_front5.jpg';
+
+export const Backgrounds = PluginBehavior.create<{ }>({
+    name: 'extension-backgrounds',
+    category: 'misc',
+    display: {
+        name: 'Backgrounds'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.config.set(PluginConfig.Background.Styles, [
+                [{
+                    variant: {
+                        name: 'radialGradient',
+                        params: {
+                            centerColor: Color(0xFFFFFF),
+                            edgeColor: Color(0x808080),
+                            ratio: 0.2,
+                            coverage: 'viewport',
+                        }
+                    }
+                }, 'Light Radial Gradient'],
+                [{
+                    variant: {
+                        name: 'image',
+                        params: {
+                            source: {
+                                name: 'url',
+                                params: image_cells
+                            },
+                            lightness: 0,
+                            saturation: 0,
+                            opacity: 1,
+                            coverage: 'viewport',
+                        }
+                    }
+                }, 'Normal Cells Image'],
+                [{
+                    variant: {
+                        name: 'skybox',
+                        params: {
+                            faces: {
+                                name: 'urls',
+                                params: {
+                                    nx: face_nebula_nx,
+                                    ny: face_nebula_ny,
+                                    nz: face_nebula_nz,
+                                    px: face_nebula_px,
+                                    py: face_nebula_py,
+                                    pz: face_nebula_pz,
+                                }
+                            },
+                            lightness: 0,
+                            saturation: 0,
+                            opacity: 1,
+                            blur: 0.3,
+                        }
+                    }
+                }, 'Purple Nebula Skybox'],
+            ]);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.config.set(PluginConfig.Background.Styles, []);
+        }
+    },
+    params: () => ({ })
+});

src/extensions/backgrounds/typings.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+declare module '*.jpg' {
+    const value: string;
+    export = value;
+}

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

@@ -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>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
@@ -12,7 +12,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Ingredient, CellPacking, CompartmentPrimitives } from './data';
 import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
 import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit, Trajectory } from '../../mol-model/structure';
-import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
 import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
 import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
 import { SymmetryOperator } from '../../mol-math/geometry';
@@ -22,17 +22,12 @@ import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, Structure
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { getMatFromResamplePoints } from './curve';
 import { compile } from '../../mol-script/runtime/query/compiler';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
-import { Column } from '../../mol-data/db';
-import { createModels } from '../../mol-model-formats/structure/basic/parser';
 import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
 import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import { objectForEach } from '../../mol-util/object';
 import { readFromFile } from '../../mol-util/data-source';
 import { ColorNames } from '../../mol-util/color/names';
-import { createBasic } from '../../mol-model-formats/structure/basic/schema';
 
 function getCellPackModelUrl(fileName: string, baseUrl: string) {
     return `${baseUrl}/results/${fileName}`;
@@ -142,7 +137,7 @@ async function getStructure(plugin: PluginContext, model: Model, source: Ingredi
 
 function getTransformLegacy(trans: Vec3, rot: Quat) {
     const q: Quat = Quat.create(-rot[3], rot[0], rot[1], rot[2]);
-    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+    const m: Mat4 = Mat4.fromQuat(Mat4(), q);
     Mat4.transpose(m, m);
     Mat4.scale(m, m, Vec3.create(-1.0, 1.0, -1.0));
     Mat4.setTranslation(m, trans);
@@ -151,7 +146,7 @@ function getTransformLegacy(trans: Vec3, rot: Quat) {
 
 function getTransform(trans: Vec3, rot: Quat) {
     const q: Quat = Quat.create(-rot[0], rot[1], rot[2], -rot[3]);
-    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+    const m: Mat4 = Mat4.fromQuat(Mat4(), q);
     const p: Vec3 = Vec3.create(-trans[0], trans[1], trans[2]);
     Mat4.setTranslation(m, p);
     return m;
@@ -214,111 +209,10 @@ function getAssembly(name: string, transforms: Mat4[], structure: Structure) {
     return builder.getStructure();
 }
 
-function getCifCurve(name: string, transforms: Mat4[], model: Model) {
-    if (!MmcifFormat.is(model.sourceData)) throw new Error('mmcif source data needed');
-
-    const { db } = model.sourceData.data;
-    const d = db.atom_site;
-    const n = d._rowCount;
-    const rowCount = n * transforms.length;
-
-    const { offsets, count } = model.atomicHierarchy.chainAtomSegments;
-
-    const x = d.Cartn_x.toArray();
-    const y = d.Cartn_y.toArray();
-    const z = d.Cartn_z.toArray();
-
-    const Cartn_x = new Float32Array(rowCount);
-    const Cartn_y = new Float32Array(rowCount);
-    const Cartn_z = new Float32Array(rowCount);
-    const map = new Uint32Array(rowCount);
-    const seq = new Int32Array(rowCount);
-    let offset = 0;
-    for (let c = 0; c < count; ++c) {
-        const cStart = offsets[c];
-        const cEnd = offsets[c + 1];
-        const cLength = cEnd - cStart;
-        for (let t = 0, tl = transforms.length; t < tl; ++t) {
-            const m = transforms[t];
-            for (let j = cStart; j < cEnd; ++j) {
-                const i = offset + j - cStart;
-                const xj = x[j], yj = y[j], zj = z[j];
-                Cartn_x[i] = m[0] * xj + m[4] * yj + m[8] * zj + m[12];
-                Cartn_y[i] = m[1] * xj + m[5] * yj + m[9] * zj + m[13];
-                Cartn_z[i] = m[2] * xj + m[6] * yj + m[10] * zj + m[14];
-                map[i] = j;
-                seq[i] = t + 1;
-            }
-            offset += cLength;
-        }
-    }
-
-    function multColumn<T>(column: Column<T>) {
-        const array = column.toArray();
-        return Column.ofLambda({
-            value: row => array[map[row]],
-            areValuesEqual: (rowA, rowB) => map[rowA] === map[rowB] || array[map[rowA]] === array[map[rowB]],
-            rowCount, schema: column.schema
-        });
-    }
-
-    const _atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
-        auth_asym_id: CifField.ofColumn(multColumn(d.auth_asym_id)),
-        auth_atom_id: CifField.ofColumn(multColumn(d.auth_atom_id)),
-        auth_comp_id: CifField.ofColumn(multColumn(d.auth_comp_id)),
-        auth_seq_id: CifField.ofNumbers(seq),
-
-        B_iso_or_equiv: CifField.ofColumn(Column.ofConst(0, rowCount, Column.Schema.float)),
-        Cartn_x: CifField.ofNumbers(Cartn_x),
-        Cartn_y: CifField.ofNumbers(Cartn_y),
-        Cartn_z: CifField.ofNumbers(Cartn_z),
-        group_PDB: CifField.ofColumn(Column.ofConst('ATOM', rowCount, Column.Schema.str)),
-        id: CifField.ofColumn(Column.ofLambda({
-            value: row => row,
-            areValuesEqual: (rowA, rowB) => rowA === rowB,
-            rowCount, schema: d.id.schema,
-        })),
-
-        label_alt_id: CifField.ofColumn(multColumn(d.label_alt_id)),
-
-        label_asym_id: CifField.ofColumn(multColumn(d.label_asym_id)),
-        label_atom_id: CifField.ofColumn(multColumn(d.label_atom_id)),
-        label_comp_id: CifField.ofColumn(multColumn(d.label_comp_id)),
-        label_seq_id: CifField.ofNumbers(seq),
-        label_entity_id: CifField.ofColumn(Column.ofConst('1', rowCount, Column.Schema.str)),
-
-        occupancy: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.float)),
-        type_symbol: CifField.ofColumn(multColumn(d.type_symbol)),
-
-        pdbx_PDB_ins_code: CifField.ofColumn(Column.ofConst('', rowCount, Column.Schema.str)),
-        pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.int)),
-    };
-
-    const categories = {
-        entity: CifCategory.ofTable('entity', db.entity),
-        chem_comp: CifCategory.ofTable('chem_comp', db.chem_comp),
-        atom_site: CifCategory.ofFields('atom_site', _atom_site)
-    };
-
-    return {
-        header: name,
-        categoryNames: Object.keys(categories),
-        categories
-    };
-}
-
-async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
-    const cif = getCifCurve(name, transforms, model);
-    const curveModelTask = Task.create('Curve Model', async ctx => {
-        const format = MmcifFormat.fromFrame(cif);
-        const basic = createBasic(format.data.db, true);
-        const models = await createModels(basic, format, ctx);
-        return models.representative;
-    });
-
-    const curveModel = await plugin.runTask(curveModelTask);
-    // ingredient.source.selection = undefined;
-    return getStructure(plugin, curveModel, ingredient);
+async function getCurve(name: string, transforms: Mat4[], model: Model) {
+    const structure = Structure.ofModel(model);
+    const assembly = getAssembly(name, transforms, structure);
+    return assembly;
 }
 
 async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache, location: 'surface' | 'interior' | 'cytoplasme') {
@@ -339,10 +233,10 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
     if (!model) return;
     let structure: Structure;
     if (nbCurve) {
-        structure = await getCurve(plugin, name, ingredient, getCurveTransforms(ingredient), model);
+        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;
@@ -363,7 +257,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
             structure = Structure.transform(structure, m1);
             if (ingredient.offset) {
                 const o: Vec3 = Vec3.create(ingredient.offset[0], ingredient.offset[1], ingredient.offset[2]);
-                if (!Vec3.exactEquals(o, Vec3.zero())) { // -1, 1, 4e-16 ??
+                if (!Vec3.exactEquals(o, Vec3())) { // -1, 1, 4e-16 ??
                     if (location !== 'surface') {
                         Vec3.negate(o, o);
                     }
@@ -377,7 +271,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
                 if (!Vec3.exactEquals(p, Vec3.unitZ)) {
                     const q: Quat = Quat.identity();
                     Quat.rotationTo(q, p, Vec3.unitZ);
-                    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+                    const m: Mat4 = Mat4.fromQuat(Mat4(), q);
                     structure = Structure.transform(structure, m);
                 }
             }
@@ -521,6 +415,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
             .apply(StructureFromAssemblies, undefined, { state: { isGhost: true } })
             .commit({ revertOnError: true });
         const membraneParams = {
+            ignoreLight: params.preset.adjustStyle,
             representation: params.preset.representation,
         };
         await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
@@ -537,6 +432,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
             .apply(StateTransforms.Model.StructureFromModel, props, { state: { isGhost: true } })
             .commit({ revertOnError: true });
         const membraneParams = {
+            ignoreLight: params.preset.adjustStyle,
             representation: params.preset.representation,
         };
         await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
@@ -620,6 +516,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
 
         const packingParams = {
             traceOnly: params.preset.traceOnly,
+            ignoreLight: params.preset.adjustStyle,
             representation: params.preset.representation,
         };
         await CellpackPackingPreset.apply(packing, packingParams, plugin);
@@ -671,7 +568,8 @@ const LoadCellPackModelParams = {
     ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredient files' }),
     preset: PD.Group({
         traceOnly: PD.Boolean(false),
-        representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))
+        adjustStyle: PD.Boolean(true),
+        representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation'] as const))
     }, { isExpanded: true })
 };
 type LoadCellPackModelParams = PD.Values<typeof LoadCellPackModelParams>
@@ -681,5 +579,53 @@ export const LoadCellPackModel = StateAction.build({
     params: LoadCellPackModelParams,
     from: PSO.Root
 })(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
+    if (params.preset.adjustStyle) {
+        ctx.managers.interactivity.setProps({ granularity: 'chain' });
+        ctx.managers.structure.component.setOptions({
+            ... ctx.managers.structure.component.state.options,
+            visualQuality: 'custom',
+            ignoreLight: true,
+            hydrogens: 'hide-all',
+        });
+        ctx.canvas3d?.setProps({
+            multiSample: { mode: 'off' },
+            cameraClipping: { far: false },
+            renderer: { colorMarker: false },
+            marking: {
+                enabled: true,
+                ghostEdgeStrength: 1,
+            },
+            postprocessing: {
+                occlusion: {
+                    name: 'on',
+                    params: {
+                        samples: 32,
+                        radius: 8,
+                        bias: 1,
+                        blurKernelSize: 15,
+                        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,
+                    }
+                }
+            }
+        });
+    }
     await loadPackings(ctx, taskCtx, state, params);
 }));

src/extensions/cellpack/preset.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>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
@@ -13,7 +13,8 @@ import { CellPackGenerateColorThemeProvider } from './color/generate';
 
 export const CellpackPackingPresetParams = {
     traceOnly: PD.Boolean(true),
-    representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
+    ignoreLight: PD.Boolean(false),
+    representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'] as const)),
 };
 export type CellpackPackingPresetParams = PD.ValuesFor<typeof CellpackPackingPresetParams>
 
@@ -27,7 +28,9 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
 
         const reprProps = {
             ignoreHydrogens: true,
-            traceOnly: params.traceOnly
+            traceOnly: params.traceOnly,
+            instanceGranularity: true,
+            ignoreLight: params.ignoreLight,
         };
         const components = {
             polymer: await presetStaticComponent(plugin, structureCell, 'polymer')
@@ -37,8 +40,8 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
             Object.assign(reprProps, {
                 quality: 'custom', resolution: 10, radiusOffset: 2, doubleSided: false
             });
-        } else if (params.representation === 'spacefill' && params.traceOnly) {
-            Object.assign(reprProps, { sizeFactor: 2 });
+        } else if (params.representation === 'spacefill') {
+            Object.assign(reprProps, { sizeFactor: params.traceOnly ? 2 : 1 });
         }
 
         // default is generated
@@ -57,7 +60,8 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
 //
 
 export const CellpackMembranePresetParams = {
-    representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
+    ignoreLight: PD.Boolean(false),
+    representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'] as const)),
 };
 export type CellpackMembranePresetParams = PD.ValuesFor<typeof CellpackMembranePresetParams>
 
@@ -71,6 +75,8 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({
 
         const reprProps = {
             ignoreHydrogens: true,
+            instanceGranularity: true,
+            ignoreLight: params.ignoreLight,
         };
         const components = {
             membrane: await presetStaticComponent(plugin, structureCell, 'all', { label: 'Membrane' })
@@ -84,7 +90,7 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, {});
         const representations = {
-            membrane: builder.buildRepresentation(update, components.membrane, { type: 'gaussian-surface', typeParams: { ...typeParams, ...reprProps }, color: 'uniform', colorParams: { value: ColorNames.lightgrey } }, { tag: 'all' })
+            membrane: builder.buildRepresentation(update, components.membrane, { type: params.representation, typeParams: { ...typeParams, ...reprProps }, color: 'uniform', colorParams: { value: ColorNames.lightgrey } }, { tag: 'all' })
         };
 
         await update.commit({ revertOnError: 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 { Loci } from '../../../mol-model/loci';
-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) {
@@ -48,56 +47,11 @@ 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;
-
-        private labelConfalPyramids = {
-            label: (loci: Loci): string | undefined => {
-                if (!this.params.showToolTip) return void 0;
-
-                /* TODO: Implement this */
-                return void 0;
-            }
-        };
-
-        register(): void {
-            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.managers.lociLabels.addProvider(this.labelConfalPyramids);
-
-            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.managers.lociLabels.removeProvider(this.labelConfalPyramids);
-
-            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(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/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 = {
@@ -247,8 +41,8 @@ export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values
 
     function color(location: Location, isSecondary: boolean): Color {
         if (CPT.isLocation(location)) {
-            const { pyramid, isLower } = location.data;
-            const key = pyramid.NtC + `_${isLower ? 'Lwr' : 'Upr'}` as keyof PyramidsColors;
+            const { step, isLower } = location.data;
+            const key = step.NtC + `_${isLower ? 'Lwr' : 'Upr'}` as keyof PyramidsColors;
             return colorMap[key] ?? ErrorColor;
         }
 
@@ -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.PyramidsData | 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',
@@ -96,75 +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,
-    steps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
-    stepsSummary: StepsSummaryTable): CPT.PyramidsData {
-    const pyramids = new Array<CPT.Pyramid>();
-    const names = new Map<string, number>();
-    const locations = new Array<CPT.Location>();
-    let hasMultipleModels = false;
-
-    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 } = steps;
-
-    if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
-
-    for (let i = 0; i < _rowCount; i++) {
-        const model_num = PDB_model_number.value(i);
-        if (model_num !== model.modelNum)
-            hasMultipleModels = true;
-
-        const { _NtC, _confal_score } = getNtCAndConfalScore(id.value(i), i, stepsSummary);
-
-        const pyramid = {
-            PDB_model_number: model_num,
-            name: name.value(i),
-            auth_asym_id_1: auth_asym_id_1.value(i),
-            auth_seq_id_1: auth_seq_id_1.value(i),
-            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: _confal_score,
-            NtC: _NtC
-        };
-
-        pyramids.push(pyramid);
-        names.set(pyramid.name, pyramids.length - 1);
-
-        locations.push(CPT.Location(pyramid, false));
-        locations.push(CPT.Location(pyramid, true));
-    }
-
-    return { pyramids, names, locations, hasMultipleModels };
-}
-
-function getNtCAndConfalScore(id: number, i: number, stepsSummary: StepsSummaryTable) {
-    const { step_id, confal_score, assigned_NtC } = 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) };
-    }
-    // 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) };
-    }
-    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 { ConfalPyramidsUtil } from './util';
+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';
@@ -16,14 +17,14 @@ import { PrimitiveBuilder } from '../../../mol-geo/primitive/primitive';
 import { LocationIterator } from '../../../mol-geo/util/location-iterator';
 import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Structure, StructureProperties, Unit } from '../../../mol-model/structure';
+import { Structure, Unit } from '../../../mol-model/structure';
 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 { VisualUpdateState } from '../../../mol-repr/util';
 import { VisualContext } from '../../../mol-repr/visual';
-import { getAltResidueLociFromId, StructureGroup } from '../../../mol-repr/structure/visual/util/common';
+import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
 import { NullLocation } from '../../../mol-model/location';
@@ -32,6 +33,12 @@ const t = Mat4.identity();
 const w = Vec3.zero();
 const mp = Vec3.zero();
 
+const posO3 = Vec3();
+const posP = Vec3();
+const posOP1 = Vec3();
+const posOP2 = Vec3();
+const posO5 = Vec3();
+
 function calcMidpoint(mp: Vec3, v: Vec3, w: Vec3) {
     Vec3.sub(mp, v, w);
     Vec3.scale(mp, mp, 0.5);
@@ -53,64 +60,78 @@ function createConfalPyramidsIterator(structureGroup: StructureGroup): LocationI
     const { structure, group } = structureGroup;
     const instanceCount = group.units.length;
 
-    const prop = ConfalPyramidsProvider.get(structure.model).value;
-    if (prop === undefined || prop.data === undefined) {
-        return LocationIterator(0, 1, 1, () => NullLocation);
-    }
+    const data = ConfalPyramidsProvider.get(structure.model)?.value?.data;
+    if (!data) return LocationIterator(0, 1, 1, () => NullLocation);
 
-    const { locations } = prop.data;
+    const halfPyramidsCount = data.steps.length * 2;
 
     const getLocation = (groupIndex: number, instanceIndex: number) => {
-        if (locations.length <= groupIndex) return NullLocation;
-        return locations[groupIndex];
+        if (halfPyramidsCount <= groupIndex) return NullLocation;
+        const idx = Math.floor(groupIndex / 2); // Map groupIndex to a step, see createConfalPyramidsMesh() for full explanation
+        return CPT.Location(data.steps[idx], groupIndex % 2 === 1);
     };
-    return LocationIterator(locations.length, instanceCount, 1, getLocation);
+    return LocationIterator(halfPyramidsCount, instanceCount, 1, getLocation);
 }
 
 function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ConfalPyramidsMeshParams>, mesh?: Mesh) {
     if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
 
-    const prop = ConfalPyramidsProvider.get(structure.model).value;
-    if (prop === undefined || prop.data === undefined) return Mesh.createEmpty(mesh);
+    const data = ConfalPyramidsProvider.get(structure.model)?.value?.data;
+    if (!data) return Mesh.createEmpty(mesh);
 
-    const { pyramids } = prop.data;
-    if (pyramids.length === 0) return Mesh.createEmpty(mesh);
+    const { steps, mapping } = data;
+    if (steps.length === 0) return Mesh.createEmpty(mesh);
+    const vertexCount = (6 * steps.length) / mapping.length;
 
-    const mb = MeshBuilder.createState(512, 512, mesh);
+    const mb = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
 
-    const handler = (pyramid: CPT.Pyramid, first: ConfalPyramidsUtil.FirstResidueAtoms, second: ConfalPyramidsUtil.SecondResidueAtoms, firsLocIndex: number, secondLocIndex: number) => {
-        if (firsLocIndex === -1 || secondLocIndex === -1)
-            throw new Error('Invalid location index');
+    const it = new ConfalPyramidsIterator(structure, unit);
+    while (it.hasNext) {
+        const allPoints = it.move();
+        if (!allPoints)
+            continue;
 
-        const scale = (pyramid.confal_score - 20.0) / 100.0;
-        const O3 = first.O3.pos;
-        const OP1 = second.OP1.pos; const OP2 = second.OP2.pos; const O5 = second.O5.pos; const P = second.P.pos;
+        for (const points of allPoints) {
+            const { O3, P, OP1, OP2, O5, confalScore } = points;
+            const scale = (confalScore - 20.0) / 100.0;
+            // Steps can be drawn in a different order than they are stored.
+            // To make sure that we can get from the drawn pyramid back to the step in represents,
+            // we need to use an appropriate groupId. The stepIdx passed from the iterator
+            // is an index into the array of all steps in the structure.
+            // Since a step is drawn as two "half-pyramids" we need two ids to map to a single step.
+            // To do that, we just multiply the index by 2. idx*2 marks the "upper" half-pyramid,
+            // (idx*2)+1 the "lower" half-pyramid.
+            const groupIdx = points.stepIdx * 2;
 
-        shiftVertex(O3, P, scale);
-        shiftVertex(OP1, P, scale);
-        shiftVertex(OP2, P, scale);
-        shiftVertex(O5, P, scale);
-        calcMidpoint(mp, O3, O5);
+            unit.conformation.invariantPosition(O3, posO3);
+            unit.conformation.invariantPosition(P, posP);
+            unit.conformation.invariantPosition(OP1, posOP1);
+            unit.conformation.invariantPosition(OP2, posOP2);
+            unit.conformation.invariantPosition(O5, posO5);
 
-        mb.currentGroup = firsLocIndex;
-        let pb = PrimitiveBuilder(3);
-        /* Upper part (for first residue in step) */
-        pb.add(O3, OP1, OP2);
-        pb.add(O3, mp, OP1);
-        pb.add(O3, OP2, mp);
-        MeshBuilder.addPrimitive(mb, t, pb.getPrimitive());
+            shiftVertex(posO3, posP, scale);
+            shiftVertex(posOP1, posP, scale);
+            shiftVertex(posOP2, posP, scale);
+            shiftVertex(posO5, posP, scale);
+            calcMidpoint(mp, posO3, posO5);
 
-        /* Lower part (for second residue in step */
-        mb.currentGroup = secondLocIndex;
-        pb = PrimitiveBuilder(3);
-        pb.add(mp, O5, OP1);
-        pb.add(mp, OP2, O5);
-        pb.add(O5, OP2, OP1);
-        MeshBuilder.addPrimitive(mb, t, pb.getPrimitive());
-    };
+            mb.currentGroup = groupIdx;
+            let pb = PrimitiveBuilder(3);
+            /* Upper part (for first residue in step) */
+            pb.add(posO3, posOP1, posOP2);
+            pb.add(posO3, mp, posOP1);
+            pb.add(posO3, posOP2, mp);
+            MeshBuilder.addPrimitive(mb, t, pb.getPrimitive());
 
-    const walker = new ConfalPyramidsUtil.UnitWalker(structure, unit, handler);
-    walker.walk();
+            /* Lower part (for second residue in step) */
+            mb.currentGroup = groupIdx + 1;
+            pb = PrimitiveBuilder(3);
+            pb.add(mp, posO5, posOP1);
+            pb.add(mp, posOP2, posO5);
+            pb.add(posO5, posOP2, posOP1);
+            MeshBuilder.addPrimitive(mb, t, pb.getPrimitive());
+        }
+    }
 
     return MeshBuilder.getMesh(mb);
 }
@@ -124,16 +145,15 @@ function getConfalPyramidLoci(pickingId: PickingId, structureGroup: StructureGro
     const unit = structureGroup.group.units[instanceId];
     if (!Unit.isAtomic(unit)) return EmptyLoci;
 
-    const prop = ConfalPyramidsProvider.get(structure.model).value;
-    if (prop === undefined || prop.data === undefined) return EmptyLoci;
+    const data = ConfalPyramidsProvider.get(structure.model)?.value?.data;
+    if (!data) return EmptyLoci;
 
-    const { locations } = prop.data;
+    const halfPyramidsCount = data.steps.length * 2;
 
-    if (locations.length <= groupId) return EmptyLoci;
-    const altId = StructureProperties.atom.label_alt_id(CPT.toElementLocation(locations[groupId]));
-    const rI = unit.residueIndex[locations[groupId].element.element];
+    if (halfPyramidsCount <= groupId) return EmptyLoci;
 
-    return getAltResidueLociFromId(structure, unit, rI, altId);
+    const idx = Math.floor(groupId / 2); // Map groupIndex to a step, see createConfalPyramidsMesh() for full explanation
+    return CPT.Loci(data.steps, [idx]);
 }
 
 function eachConfalPyramid(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
@@ -178,7 +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

@@ -5,56 +5,29 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 
+import { DnatcoTypes } from '../types';
 import { DataLocation } from '../../../mol-model/location';
-import { ElementIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
+import { DataLoci } from '../../../mol-model/loci';
+import { confalPyramidLabel } from './behavior';
 
 export namespace ConfalPyramidsTypes {
-    export type Pyramid = {
-        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
-    }
+    export interface Location extends DataLocation<DnatcoTypes.HalfStep, {}> {}
 
-    export interface PyramidsData {
-        pyramids: Array<Pyramid>,
-        names: Map<string, number>,
-        locations: Array<Location>,
-        hasMultipleModels: boolean
-    }
-
-    export interface LocationData {
-        readonly pyramid: Pyramid
-        readonly isLower: boolean;
-    }
-
-    export interface Element {
-        structure: Structure;
-        unit: Unit.Atomic;
-        element: ElementIndex;
-    }
-
-    export interface Location extends DataLocation<LocationData, Element> {}
-
-    export function Location(pyramid: Pyramid, isLower: boolean, structure?: Structure, unit?: Unit.Atomic, element?: ElementIndex) {
-        return DataLocation('pyramid', { pyramid, isLower }, { structure: structure as any, unit: unit as any, element: element as any });
+    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 === 'pyramid';
+        return !!x && x.kind === 'data-location' && x.tag === DnatcoTypes.DataTag;
     }
 
-    export function toElementLocation(location: Location) {
-        return StructureElement.Location.create(location.element.structure, location.element.unit, location.element.element);
+    export interface Loci extends DataLoci<DnatcoTypes.Step[], number> {}
+
+    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 === DnatcoTypes.DataTag;
     }
 }

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

@@ -1,295 +1,104 @@
 /**
- * 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 { Vec3 } from '../../../mol-math/linear-algebra';
-import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../../mol-model/structure';
+import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
 
-export namespace ConfalPyramidsUtil {
-    type Residue = Segmentation.Segment<ResidueIndex>;
+export type Pyramid = {
+    O3: ElementIndex,
+    P: ElementIndex,
+    OP1: ElementIndex,
+    OP2: ElementIndex,
+    O5: ElementIndex,
+    confalScore: number,
+    stepIdx: number,
+};
 
-    export type AtomInfo = {
-        pos: Vec3,
-        index: ElementIndex,
-        fakeAltId: string,
-    };
+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);
 
-    export type FirstResidueAtoms = {
-        O3: AtomInfo,
-    };
+    return { O3, P, OP1, OP2, O5, confalScore, stepIdx };
+}
 
-    export type SecondResidueAtoms = {
-        OP1: AtomInfo,
-        OP2: AtomInfo,
-        O5: AtomInfo,
-        P: AtomInfo,
-    };
+export class ConfalPyramidsIterator {
+    private chainIt: Segmentation.SegmentIterator<ChainIndex>;
+    private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
+    private residueOne?: DnatcoUtil.Residue;
+    private residueTwo: DnatcoUtil.Residue;
+    private data?: DnatcoTypes.Steps;
+    private loc: StructureElement.Location;
 
-    type ResidueInfo = {
-        PDB_model_num: number,
-        asym_id: string,
-        auth_asym_id: string,
-        seq_id: number,
-        auth_seq_id: number,
-        comp_id: string,
-        alt_id: string,
-        ins_code: string,
-    };
+    private moveStep() {
+        this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
+        this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
 
-    export type Handler = (pyramid: CPT.Pyramid, first: FirstResidueAtoms, second: SecondResidueAtoms, firstLocIndex: number, secondLocIndex: number) => void;
+        // Check for discontinuity
+        if (this.residueTwo.index !== (this.residueOne!.index + 1))
+            return void 0;
 
-    function residueInfoFromLocation(loc: StructureElement.Location): ResidueInfo {
-        return {
-            PDB_model_num: StructureProperties.unit.model_num(loc),
-            asym_id: StructureProperties.chain.label_asym_id(loc),
-            auth_asym_id: StructureProperties.chain.auth_asym_id(loc),
-            seq_id: StructureProperties.residue.label_seq_id(loc),
-            auth_seq_id: StructureProperties.residue.auth_seq_id(loc),
-            comp_id: StructureProperties.atom.label_comp_id(loc),
-            alt_id: StructureProperties.atom.label_alt_id(loc),
-            ins_code: StructureProperties.residue.pdbx_PDB_ins_code(loc)
-        };
+        return this.toPyramids(this.residueOne!, this.residueTwo);
     }
 
-    export function hasMultipleModels(unit: Unit.Atomic): boolean {
+    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.PDB_ins_code_1, step.PDB_ins_code_2, step.confal_score, idx));
+        }
+
+        return points;
+    }
+
+    constructor(structure: Structure, unit: Unit) {
+        this.chainIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
+        this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+
         const prop = ConfalPyramidsProvider.get(unit.model).value;
-        if (prop === undefined || prop.data === undefined) throw new Error('No custom properties data');
-        return prop.data.hasMultipleModels;
+        this.data = prop?.data;
+
+        if (this.chainIt.hasNext) {
+            this.residueIt.setSegment(this.chainIt.move());
+            if (this.residueIt.hasNext)
+                this.residueTwo = this.residueIt.move();
+        }
+
+        this.loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
     }
 
-    function getPossibleAltIds(residue: Residue, structure: Structure, unit: Unit.Atomic): string[] {
-        const possibleAltIds: string[] = [];
-
-        const loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
-        for (let rI = residue.start; rI <= residue.end - 1; rI++) {
-            loc.element = unit.elements[rI];
-            const altId = StructureProperties.atom.label_alt_id(loc);
-            if (altId !== '' && !possibleAltIds.includes(altId)) possibleAltIds.push(altId);
-        }
-
-        return possibleAltIds;
+    get hasNext() {
+        if (!this.data)
+            return false;
+        return this.residueIt.hasNext
+            ? true
+            : this.chainIt.hasNext;
     }
 
-    class Utility {
-        protected getPyramidByName(name: string): { pyramid: CPT.Pyramid | undefined, index: number } {
-            const index = this.data.names.get(name);
-            if (index === undefined) return { pyramid: undefined, index: -1 };
-
-            return { pyramid: this.data.pyramids[index], index };
+    move() {
+        if (this.residueIt.hasNext) {
+            return this.moveStep();
+        } else {
+            this.residueIt.setSegment(this.chainIt.move());
+            if (this.residueIt.hasNext)
+                this.residueTwo = this.residueIt.move();
+            return this.moveStep();
         }
-
-        protected stepToName(entry_id: string, modelNum: number, locFirst: StructureElement.Location, locSecond: StructureElement.Location, fakeAltId_1: string, fakeAltId_2: string) {
-            const first = residueInfoFromLocation(locFirst);
-            const second = residueInfoFromLocation(locSecond);
-            const model_id = this.hasMultipleModels ? `-m${modelNum}` : '';
-            const alt_id_1 = fakeAltId_1 !== '' ? `.${fakeAltId_1}` : (first.alt_id.length ? `.${first.alt_id}` : '');
-            const alt_id_2 = fakeAltId_2 !== '' ? `.${fakeAltId_2}` : (second.alt_id.length ? `.${second.alt_id}` : '');
-            const ins_code_1 = first.ins_code.length ? `.${first.ins_code}` : '';
-            const ins_code_2 = second.ins_code.length ? `.${second.ins_code}` : '';
-
-            return `${entry_id}${model_id}_${first.auth_asym_id}_${first.comp_id}${alt_id_1}_${first.auth_seq_id}${ins_code_1}_${second.comp_id}${alt_id_2}_${second.auth_seq_id}${ins_code_2}`;
-        }
-
-        constructor(unit: Unit.Atomic) {
-            const prop = ConfalPyramidsProvider.get(unit.model).value;
-            if (prop === undefined || prop.data === undefined) throw new Error('No custom properties data');
-
-            this.data = prop.data;
-            this.hasMultipleModels = hasMultipleModels(unit);
-
-            this.entryId = unit.model.entryId.toLowerCase();
-            this.modelNum = unit.model.modelNum;
-        }
-
-        protected readonly data: CPT.PyramidsData;
-        protected readonly hasMultipleModels: boolean;
-        protected readonly entryId: string;
-        protected readonly modelNum: number;
-    }
-
-    export class UnitWalker extends Utility {
-        private getAtomIndices(names: string[], residue: Residue): ElementIndex[] {
-            const indices: ElementIndex[] = [];
-
-            const loc = StructureElement.Location.create(this.structure, this.unit, -1 as ElementIndex);
-            for (let rI = residue.start; rI <= residue.end - 1; rI++) {
-                loc.element = this.unit.elements[rI];
-                const thisName = StructureProperties.atom.label_atom_id(loc);
-                if (names.includes(thisName)) indices.push(loc.element);
-            }
-
-            if (indices.length === 0) {
-                let namesStr = '';
-                for (const n of names)
-                    namesStr += `${n} `;
-
-                throw new Error(`Element [${namesStr}] not found on residue ${residue.index}`);
-            }
-
-            return indices;
-        }
-
-        private getAtomPositions(indices: ElementIndex[]): Vec3[] {
-            const pos = this.unit.conformation.invariantPosition;
-            const positions: Vec3[] = [];
-
-            for (const eI of indices) {
-                const v = Vec3.zero();
-                pos(eI, v);
-                positions.push(v);
-            }
-
-            return positions;
-        }
-
-        private handleStep(firstAtoms: FirstResidueAtoms[], secondAtoms: SecondResidueAtoms[]) {
-            const modelNum = this.hasMultipleModels ? this.modelNum : -1;
-            let ok = false;
-
-            const firstLoc = StructureElement.Location.create(this.structure, this.unit, -1 as ElementIndex);
-            const secondLoc = StructureElement.Location.create(this.structure, this.unit, -1 as ElementIndex);
-            for (let i = 0; i < firstAtoms.length; i++) {
-                const first = firstAtoms[i];
-                for (let j = 0; j < secondAtoms.length; j++) {
-                    const second = secondAtoms[j];
-                    firstLoc.element = first.O3.index;
-                    secondLoc.element = second.OP1.index;
-
-                    const name = this.stepToName(this.entryId, modelNum, firstLoc, secondLoc, first.O3.fakeAltId, second.OP1.fakeAltId);
-                    const { pyramid, index } = this.getPyramidByName(name);
-                    if (pyramid !== undefined) {
-                        const setLoc = (loc: CPT.Location, eI: ElementIndex) => {
-                            loc.element.structure = this.structure;
-                            loc.element.unit = this.unit;
-                            loc.element.element = eI;
-                        };
-
-                        const locIndex = index * 2;
-                        setLoc(this.data.locations[locIndex], firstLoc.element);
-                        setLoc(this.data.locations[locIndex + 1], secondLoc.element);
-                        this.handler(pyramid, first, second, locIndex, locIndex + 1);
-                        ok = true;
-                    }
-                }
-            }
-
-            if (!ok) throw new Error('Bogus step');
-        }
-
-        private processFirstResidue(residue: Residue, possibleAltIds: string[]) {
-            const indO3 = this.getAtomIndices(['O3\'', 'O3*'], residue);
-            const posO3 = this.getAtomPositions(indO3);
-
-            const altPos: FirstResidueAtoms[] = [
-                { O3: { pos: posO3[0], index: indO3[0], fakeAltId: '' } }
-            ];
-
-            for (let i = 1; i < indO3.length; i++) {
-                altPos.push({ O3: { pos: posO3[i], index: indO3[i], fakeAltId: '' } });
-            }
-
-            if (altPos.length === 1 && possibleAltIds.length > 1) {
-                /* We have some alternate positions on the residue but O3 does not have any - fake them */
-                altPos[0].O3.fakeAltId = possibleAltIds[0];
-
-                for (let i = 1; i < possibleAltIds.length; i++)
-                    altPos.push({ O3: { pos: posO3[0], index: indO3[0], fakeAltId: possibleAltIds[i] } });
-            }
-
-            return altPos;
-        }
-
-        private processSecondResidue(residue: Residue, possibleAltIds: string[]) {
-            const indOP1 = this.getAtomIndices(['OP1'], residue);
-            const indOP2 = this.getAtomIndices(['OP2'], residue);
-            const indO5 = this.getAtomIndices(['O5\'', 'O5*'], residue);
-            const indP = this.getAtomIndices(['P'], residue);
-
-            const posOP1 = this.getAtomPositions(indOP1);
-            const posOP2 = this.getAtomPositions(indOP2);
-            const posO5 = this.getAtomPositions(indO5);
-            const posP = this.getAtomPositions(indP);
-
-            const infoOP1: AtomInfo[] = [];
-            /* We use OP1 as "pivotal" atom. There is no specific reason
-             * to pick OP1, it is as good a choice as any other atom
-             */
-            if (indOP1.length === 1 && possibleAltIds.length > 1) {
-                /* No altIds on OP1, fake them */
-                for (const altId of possibleAltIds)
-                    infoOP1.push({ pos: posOP1[0], index: indOP1[0], fakeAltId: altId });
-            } else {
-                for (let i = 0; i < indOP1.length; i++)
-                    infoOP1.push({ pos: posOP1[i], index: indOP1[i], fakeAltId: '' });
-            }
-
-            const mkInfo = (i: number, indices: ElementIndex[], positions: Vec3[], altId: string) => {
-                if (i >= indices.length) {
-                    const last = indices.length - 1;
-                    return { pos: positions[last], index: indices[last], fakeAltId: altId };
-                }
-
-                return { pos: positions[i], index: indices[i], fakeAltId: altId };
-            };
-
-            const altPos: SecondResidueAtoms[] = [];
-            for (let i = 0; i < infoOP1.length; i++) {
-                const altId = infoOP1[i].fakeAltId;
-
-                const OP2 = mkInfo(i, indOP2, posOP2, altId);
-                const O5 = mkInfo(i, indO5, posO5, altId);
-                const P = mkInfo(i, indP, posP, altId);
-
-                altPos.push({ OP1: infoOP1[i], OP2, O5, P });
-            }
-
-            return altPos;
-        }
-
-        private step(residue: Residue): { firstAtoms: FirstResidueAtoms[], secondAtoms: SecondResidueAtoms[] } {
-            const firstPossibleAltIds = getPossibleAltIds(residue, this.structure, this.unit);
-            const firstAtoms = this.processFirstResidue(residue, firstPossibleAltIds);
-
-            residue = this.residueIt.move();
-
-            const secondPossibleAltIds = getPossibleAltIds(residue, this.structure, this.unit);
-            const secondAtoms = this.processSecondResidue(residue, secondPossibleAltIds);
-
-            return { firstAtoms, secondAtoms };
-        }
-
-        walk() {
-            while (this.chainIt.hasNext) {
-                this.residueIt.setSegment(this.chainIt.move());
-
-                let residue = this.residueIt.move();
-                while (this.residueIt.hasNext) {
-                    try {
-                        const { firstAtoms, secondAtoms } = this.step(residue);
-
-                        this.handleStep(firstAtoms, secondAtoms);
-                    } catch (error) {
-                        /* Skip and move along */
-                        residue = this.residueIt.move();
-                    }
-                }
-            }
-        }
-
-        constructor(private structure: Structure, private unit: Unit.Atomic, private handler: Handler) {
-            super(unit);
-
-            this.chainIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
-            this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-        }
-
-        private chainIt: Segmentation.SegmentIterator<ChainIndex>;
-        private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
     }
 }

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/geo-export/ui.tsx

@@ -60,6 +60,8 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
     }
 
     componentDidMount() {
+        if (!this.plugin.canvas3d) return;
+
         const merged = merge(
             this.controls.behaviors.params,
             this.plugin.canvas3d!.reprCount
@@ -71,6 +73,7 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
     }
 
     componentWillUnmount() {
+        super.componentWillUnmount();
         this._controls?.dispose();
         this._controls = void 0;
     }

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/mp4-export/controls.ts

@@ -118,11 +118,13 @@ export class Mp4Controls extends PluginComponent {
     }
 
     private init() {
+        if (!this.plugin.canvas3d) return;
+
         this.subscribe(this.plugin.managers.animation.events.updated.pipe(debounceTime(16)), () => {
             this.sync();
         });
 
-        this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
+        this.subscribe(this.plugin.canvas3d.resized, () => this.syncInfo());
         this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
 
         this.subscribe(this.plugin.behaviors.state.isBusy, b => this.updateCanApply(b));

src/extensions/mp4-export/encoder.ts

@@ -69,6 +69,7 @@ export async function encodeMp4Animation<A extends PluginStateAnimation>(plugin:
         const dt = durationMs / N;
 
         await ctx.update({ message: 'Rendering...', isIndeterminate: false, current: 0, max: N + 1 });
+        await params.pass.updateBackground();
 
         await plugin.managers.animation.play(params.animation.definition, params.animation.params);
         stoppedAnimation = false;

src/extensions/mp4-export/ui.tsx

@@ -102,6 +102,7 @@ export class Mp4EncoderUI extends CollapsableControls<{}, State> {
     }
 
     componentWillUnmount() {
+        super.componentWillUnmount();
         this._controls?.dispose();
         this._controls = void 0;
     }

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 2022-04-30T15:35:08-07:00
+// Generated on 2023-01-15T10:00:07-08:00
 
 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -13,11 +13,8 @@ export type Scalars = {
   Boolean: boolean;
   Int: number;
   Float: number;
-  /** Built-in scalar representing an instant in time */
   Date: any;
-  /** Built-in scalar for dynamic values */
   ObjectScalar: any;
-  /** Use SPQR's SchemaPrinter to remove this from SDL */
   UNREPRESENTABLE: any;
 };
 
@@ -346,6 +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
@@ -553,6 +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 = {
@@ -664,6 +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>>>;
@@ -704,6 +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;
@@ -716,6 +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>>>;
@@ -789,6 +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 = {
@@ -922,6 +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 = {
@@ -1287,9 +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']>;
@@ -1320,11 +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.
@@ -1485,7 +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
@@ -1561,7 +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
@@ -1571,7 +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
@@ -1617,7 +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
@@ -2001,12 +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']>;
@@ -2031,7 +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']>;
@@ -2218,7 +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.
@@ -2262,7 +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']>;
@@ -2367,6 +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.
    *
@@ -3008,6 +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 = {
@@ -3216,15 +3237,6 @@ export type GroupEntry = {
   readonly rcsb_id: Scalars['String'];
 };
 
-export type GroupMembersAlignmentAlignedRegions = {
-  /** Aligned region length */
-  readonly length: Scalars['Int'];
-  /** Entity seqeunce start position */
-  readonly query_begin: Scalars['Int'];
-  /** NCBI sequence start position */
-  readonly target_begin: Scalars['Int'];
-};
-
 export type GroupMembersAlignmentScores = {
   readonly query_coverage: Scalars['Int'];
   readonly query_length: Scalars['Int'];
@@ -3275,6 +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']>;
@@ -4211,7 +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']>;
@@ -4465,7 +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']>;
@@ -6829,7 +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>;
@@ -6853,9 +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>;
@@ -6863,7 +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>;
@@ -8433,6 +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
@@ -8669,7 +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']>;
@@ -8743,7 +8803,7 @@ export type RcsbEntryContainerIdentifiers = {
    * Entry identifier for the container.
    *
    * Examples:
-   * 1KIP, 4HHB
+   * 4HHB, AF_AFP60325F1, MA_MABAKCEPC0019
    *
    */
   readonly entry_id: Scalars['String'];
@@ -8891,6 +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. */
@@ -8967,6 +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 = {
@@ -9306,6 +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']>;
@@ -10344,7 +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']>;
@@ -10519,7 +10646,7 @@ export type RcsbPolymerEntityGroupMembership = {
 export type RcsbPolymerEntityGroupSequenceAlignment = {
   /** Abstract reference where group members can be aligned to generate a MSA */
   readonly abstract_reference: RcsbPolymerEntityGroupSequenceAlignmentAbstractReference;
-  /** List of alignments with core_entity canonical sequences */
+  /** Alignment with a core_entity canonical sequence */
   readonly group_members_alignment: ReadonlyArray<Maybe<RcsbPolymerEntityGroupSequenceAlignmentGroupMembersAlignment>>;
 };
 
@@ -10531,9 +10658,9 @@ export type RcsbPolymerEntityGroupSequenceAlignmentAbstractReference = {
 };
 
 export type RcsbPolymerEntityGroupSequenceAlignmentGroupMembersAlignment = {
-  /** Aligned region */
-  readonly aligned_regions: ReadonlyArray<Maybe<GroupMembersAlignmentAlignedRegions>>;
-  readonly member_id?: Maybe<Scalars['String']>;
+  /** Alignment region encoded as a triplet [query_begin, target_begin, length] */
+  readonly aligned_regions: ReadonlyArray<Maybe<ReadonlyArray<Maybe<Scalars['Int']>>>>;
+  readonly member_id: Scalars['String'];
   /** Alignment scores */
   readonly scores: GroupMembersAlignmentScores;
 };
@@ -10749,7 +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']>;
@@ -10760,7 +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']>;
@@ -10830,7 +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']>;
@@ -13389,6 +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.
@@ -13539,6 +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) 2018-2021 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 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);
@@ -260,7 +276,8 @@ namespace Camera {
             radius: 0,
             radiusMax: 10,
             fog: 50,
-            clipFar: true
+            clipFar: true,
+            minNear: 5,
         };
     }
 
@@ -276,6 +293,7 @@ namespace Camera {
         radiusMax: number
         fog: number
         clipFar: boolean
+        minNear: number
     }
 
     export function copySnapshot(out: Snapshot, source?: Partial<Snapshot>) {
@@ -292,6 +310,7 @@ namespace Camera {
         if (typeof source.radiusMax !== 'undefined') out.radiusMax = source.radiusMax;
         if (typeof source.fog !== 'undefined') out.fog = source.fog;
         if (typeof source.clipFar !== 'undefined') out.clipFar = source.clipFar;
+        if (typeof source.minNear !== 'undefined') out.minNear = source.minNear;
 
         return out;
     }
@@ -303,6 +322,7 @@ namespace Camera {
             && a.radiusMax === b.radiusMax
             && a.fog === b.fog
             && a.clipFar === b.clipFar
+            && a.minNear === b.minNear
             && Vec3.exactEquals(a.position, b.position)
             && Vec3.exactEquals(a.up, b.up)
             && Vec3.exactEquals(a.target, b.target);
@@ -370,7 +390,7 @@ function updatePers(camera: Camera) {
 }
 
 function updateClip(camera: Camera) {
-    let { radius, radiusMax, mode, fog, clipFar } = camera.state;
+    let { radius, radiusMax, mode, fog, clipFar, minNear } = camera.state;
     if (radius < 0.01) radius = 0.01;
 
     const normalizedFar = clipFar ? radius : radiusMax;
@@ -384,12 +404,12 @@ function updateClip(camera: Camera) {
 
     if (mode === 'perspective') {
         // set at least to 5 to avoid slow sphere impostor rendering
-        near = Math.max(Math.min(radiusMax, 5), near);
-        far = Math.max(5, far);
+        near = Math.max(Math.min(radiusMax, minNear), near);
+        far = Math.max(minNear, far);
     } else {
         // not too close to 0 as it causes issues with outline rendering
-        near = Math.max(Math.min(radiusMax, 5), near);
-        far = Math.max(5, far);
+        near = Math.max(Math.min(radiusMax, minNear), near);
+        far = Math.max(minNear, far);
     }
 
     if (near === far) {

src/mol-canvas3d/camera/stereo.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
@@ -13,8 +13,8 @@ import { Camera, ICamera } from '../camera';
 import { Viewport } from './util';
 
 export const StereoCameraParams = {
-    eyeSeparation: PD.Numeric(0.064, { min: 0.01, max: 0.5, step: 0.001 }),
-    focus: PD.Numeric(10, { min: 1, max: 100, step: 0.01 }),
+    eyeSeparation: PD.Numeric(0.062, { min: 0.02, max: 0.1, step: 0.001 }, { description: 'Distance between left and right camera.' }),
+    focus: PD.Numeric(10, { min: 1, max: 20, step: 0.1 }, { description: 'Apparent object distance.' }),
 };
 export const DefaultStereoCameraProps = PD.getDefaultValues(StereoCameraParams);
 export type StereoCameraProps = PD.Values<typeof StereoCameraParams>

src/mol-canvas3d/canvas3d.ts

@@ -1,8 +1,9 @@
 /**
- * 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>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
 import { BehaviorSubject, Subscription } from 'rxjs';
@@ -30,7 +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 } 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';
@@ -39,7 +40,10 @@ import { Helper } from './helper/helper';
 import { Passes } from './passes/passes';
 import { shallowEqual } from '../mol-util';
 import { MarkingParams } from './passes/marking';
-import { GraphicsRenderVariantsBlended, GraphicsRenderVariantsWboit } from '../mol-gl/webgl/render-item';
+import { GraphicsRenderVariantsBlended, GraphicsRenderVariantsWboit, GraphicsRenderVariantsDpoit } from '../mol-gl/webgl/render-item';
+import { degToRad, radToDeg } from '../mol-math/misc';
+import { AssetManager } from '../mol-util/assets';
+import { deepClone } from '../mol-util/object';
 
 export const Canvas3DParams = {
     camera: PD.Group({
@@ -49,6 +53,7 @@ export const Canvas3DParams = {
             on: PD.Group(StereoCameraParams),
             off: PD.Group({})
         }, { cycle: true, hideIf: p => p?.mode !== 'perspective' }),
+        fov: PD.Numeric(45, { min: 10, max: 130, step: 1 }, { label: 'Field of View' }),
         manualReset: PD.Boolean(false, { isHidden: true }),
     }, { pivot: 'mode' }),
     cameraFog: PD.MappedStatic('on', {
@@ -60,6 +65,7 @@ export const Canvas3DParams = {
     cameraClipping: PD.Group({
         radius: PD.Numeric(100, { min: 0, max: 99, step: 1 }, { label: 'Clipping', description: 'How much of the scene to show.' }),
         far: PD.Boolean(true, { description: 'Hide scene in the distance' }),
+        minNear: PD.Numeric(5, { min: 0.1, max: 100, step: 0.1 }, { description: 'Note, may cause performance issues rendering impostors when set too small and cause issues with outline rendering when too close to 0.' }),
     }, { pivot: 'radius' }),
     viewport: PD.MappedStatic('canvas', {
         canvas: PD.Group({}),
@@ -78,7 +84,9 @@ export const Canvas3DParams = {
     }),
 
     cameraResetDurationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time it takes to reset the camera.' }),
+    sceneRadiusFactor: PD.Numeric(1, { min: 1, max: 10, step: 0.1 }),
     transparentBackground: PD.Boolean(false),
+    dpoitIterations: PD.Numeric(2, { min: 1, max: 10, step: 1 }),
 
     multiSample: PD.Group(MultiSampleParams),
     postprocessing: PD.Group(PostprocessingParams),
@@ -106,11 +114,14 @@ interface Canvas3DContext {
     readonly attribs: Readonly<Canvas3DContext.Attribs>
     readonly contextLost: BehaviorSubject<now.Timestamp>
     readonly contextRestored: BehaviorSubject<now.Timestamp>
+    readonly assetManager: AssetManager
     dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => void
 }
 
 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,
         /** true to support multiple Canvas3D objects with a single context */
@@ -120,14 +131,20 @@ namespace Canvas3DContext {
         /** extra pixels to around target to check in case target is empty */
         pickPadding: 1,
         enableWboit: true,
+        enableDpoit: false,
         preferWebGl1: false
     };
     export type Attribs = typeof DefaultAttribs
 
-    export function fromCanvas(canvas: HTMLCanvasElement, attribs: Partial<Attribs> = {}): Canvas3DContext {
+    export function fromCanvas(canvas: HTMLCanvasElement, assetManager: AssetManager, attribs: Partial<Attribs> = {}): Canvas3DContext {
         const a = { ...DefaultAttribs, ...attribs };
-        const { antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
+
+        if (a.enableWboit && a.enableDpoit) throw new Error('Multiple transparency methods not allowed.');
+
+        const { powerPreference, failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
         const gl = getGLContext(canvas, {
+            powerPreference,
+            failIfMajorPerformanceCaveat,
             antialias,
             preserveDrawingBuffer,
             alpha: true, // the renderer requires an alpha channel
@@ -139,7 +156,7 @@ namespace Canvas3DContext {
 
         const input = InputObserver.fromElement(canvas, { pixelScale, preventGestures: true });
         const webgl = createContext(gl, { pixelScale });
-        const passes = new Passes(webgl, attribs);
+        const passes = new Passes(webgl, assetManager, a);
 
         if (isDebugMode) {
             const loseContextExt = gl.getExtension('WEBGL_lose_context');
@@ -192,6 +209,7 @@ namespace Canvas3DContext {
             attribs: a,
             contextLost,
             contextRestored: webgl.contextRestored,
+            assetManager,
             dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => {
                 input.dispose();
 
@@ -242,6 +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>
 
@@ -278,8 +297,8 @@ namespace Canvas3D {
     export interface DragEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, pageStart: Vec2, pageEnd: Vec2 }
     export interface ClickEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
 
-    export function create({ webgl, input, passes, attribs }: Canvas3DContext, props: Partial<Canvas3DProps> = {}): Canvas3D {
-        const p: Canvas3DProps = { ...DefaultCanvas3DParams, ...props };
+    export function create({ webgl, input, passes, attribs, assetManager }: Canvas3DContext, props: Partial<Canvas3DProps> = {}): Canvas3D {
+        const p: Canvas3DProps = { ...deepClone(DefaultCanvas3DParams), ...deepClone(props) };
 
         const reprRenderObjects = new Map<Representation.Any, Set<GraphicsRenderObject>>();
         const reprUpdatedSubscriptions = new Map<Representation.Any, Subscription>();
@@ -288,6 +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;
 
@@ -296,14 +316,19 @@ namespace Canvas3D {
         let width = 128;
         let height = 128;
         updateViewport();
+        const scene = Scene.create(webgl, passes.draw.dpoitEnabled ? GraphicsRenderVariantsDpoit : (passes.draw.wboitEnabled ? GraphicsRenderVariantsWboit : GraphicsRenderVariantsBlended));
 
-        const scene = Scene.create(webgl, passes.draw.wboitEnabled ? GraphicsRenderVariantsWboit : GraphicsRenderVariantsBlended);
+        function getSceneRadius() {
+            return scene.boundingSphere.radius * p.sceneRadiusFactor;
+        }
 
         const camera = new Camera({
             position: Vec3.create(0, 0, 100),
             mode: p.camera.mode,
             fog: p.cameraFog.name === 'on' ? p.cameraFog.params.intensity : 0,
-            clipFar: p.cameraClipping.far
+            clipFar: p.cameraClipping.far,
+            minNear: p.cameraClipping.minNear,
+            fov: degToRad(p.camera.fov),
         }, { x, y, width, height }, { pixelScale: attribs.pixelScale });
         const stereoCamera = new StereoCamera(camera, p.camera.stereo.params);
 
@@ -315,6 +340,10 @@ namespace Canvas3D {
         const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera, p.interaction);
         const multiSampleHelper = new MultiSampleHelper(passes.multiSample);
 
+        passes.draw.postprocessing.background.update(camera, p.postprocessing.background, changed => {
+            if (changed) requestDraw();
+        });
+
         let cameraResetRequested = false;
         let nextCameraResetDuration: number | undefined = void 0;
         let nextCameraResetSnapshot: Camera.SnapshotProvider | undefined = void 0;
@@ -395,7 +424,7 @@ namespace Canvas3D {
                 y > gl.drawingBufferHeight || y + height < 0
             ) return false;
 
-            const markingUpdated = resolveMarking();
+            const markingUpdated = resolveMarking() && (renderer.props.colorMarker || p.marking.enabled);
 
             let didRender = false;
             controls.update(currentTime);
@@ -413,6 +442,7 @@ namespace Canvas3D {
                     cam = stereoCamera;
                 }
 
+                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;
@@ -420,6 +450,8 @@ namespace Canvas3D {
                 } else {
                     passes.draw.render(ctx, p, true);
                 }
+                if (isTimingMode) webgl.timer.markEnd('Canvas3D.render');
+
                 // if only marking has updated, do not set the flag to dirty
                 pickHelper.dirty = pickHelper.dirty || shouldRender;
                 didRender = true;
@@ -520,7 +552,7 @@ namespace Canvas3D {
                 const focus = camera.getFocus(center, radius);
                 const next = typeof nextCameraResetSnapshot === 'function' ? nextCameraResetSnapshot(scene, camera) : nextCameraResetSnapshot;
                 const snapshot = next ? { ...focus, ...next } : focus;
-                camera.setState({ ...snapshot, radiusMax: scene.boundingSphere.radius }, duration);
+                camera.setState({ ...snapshot, radiusMax: getSceneRadius() }, duration);
             }
 
             nextCameraResetDuration = void 0;
@@ -563,7 +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())) {
@@ -571,7 +607,7 @@ namespace Canvas3D {
             }
             if (oldBoundingSphereVisible.radius === 0) nextCameraResetDuration = 0;
 
-            camera.setState({ radiusMax: scene.boundingSphere.radius }, 0);
+            if (!p.camera.manualReset) camera.setState({ radiusMax: getSceneRadius() }, 0);
             reprCount.next(reprRenderObjects.size);
             if (isDebugMode) consoleStats();
 
@@ -593,6 +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) {
@@ -647,7 +685,7 @@ namespace Canvas3D {
 
         function getProps(): Canvas3DProps {
             const radius = scene.boundingSphere.radius > 0
-                ? 100 - Math.round((camera.transition.target.radius / scene.boundingSphere.radius) * 100)
+                ? 100 - Math.round((camera.transition.target.radius / getSceneRadius()) * 100)
                 : 0;
 
             return {
@@ -655,14 +693,17 @@ namespace Canvas3D {
                     mode: camera.state.mode,
                     helper: { ...helper.camera.props },
                     stereo: { ...p.camera.stereo },
+                    fov: Math.round(radToDeg(camera.state.fov)),
                     manualReset: !!p.camera.manualReset
                 },
                 cameraFog: camera.state.fog > 0
                     ? { name: 'on' as const, params: { intensity: camera.state.fog } }
                     : { name: 'off' as const, params: {} },
-                cameraClipping: { far: camera.state.clipFar, radius },
+                cameraClipping: { far: camera.state.clipFar, radius, minNear: camera.state.minNear },
                 cameraResetDurationMs: p.cameraResetDurationMs,
+                sceneRadiusFactor: p.sceneRadiusFactor,
                 transparentBackground: p.transparentBackground,
+                dpoitIterations: p.dpoitIterations,
                 viewport: p.viewport,
 
                 postprocessing: { ...p.postprocessing },
@@ -695,6 +736,8 @@ namespace Canvas3D {
             resized.next(+new Date());
         }
 
+        addConsoleStatsProvider(consoleStats);
+
         return {
             webgl,
 
@@ -757,6 +800,7 @@ namespace Canvas3D {
             set notifyDidDraw(v: boolean) { notifyDidDraw = v; },
             didDraw,
             commited,
+            commitQueueSize,
             reprCount,
             resized,
             setProps: (properties, doNotRequestDraw = false) => {
@@ -764,10 +808,19 @@ namespace Canvas3D {
                     ? produce(getProps(), properties as any)
                     : properties;
 
+                if (props.sceneRadiusFactor !== undefined) {
+                    p.sceneRadiusFactor = props.sceneRadiusFactor;
+                    camera.setState({ radiusMax: getSceneRadius() }, 0);
+                }
+
                 const cameraState: Partial<Camera.Snapshot> = Object.create(null);
                 if (props.camera && props.camera.mode !== undefined && props.camera.mode !== camera.state.mode) {
                     cameraState.mode = props.camera.mode;
                 }
+                const oldFov = Math.round(radToDeg(camera.state.fov));
+                if (props.camera && props.camera.fov !== undefined && props.camera.fov !== oldFov) {
+                    cameraState.fov = degToRad(props.camera.fov);
+                }
                 if (props.cameraFog !== undefined && props.cameraFog.params) {
                     const newFog = props.cameraFog.name === 'on' ? props.cameraFog.params.intensity : 0;
                     if (newFog !== camera.state.fog) cameraState.fog = newFog;
@@ -776,8 +829,11 @@ namespace Canvas3D {
                     if (props.cameraClipping.far !== undefined && props.cameraClipping.far !== camera.state.clipFar) {
                         cameraState.clipFar = props.cameraClipping.far;
                     }
+                    if (props.cameraClipping.minNear !== undefined && props.cameraClipping.minNear !== camera.state.minNear) {
+                        cameraState.minNear = props.cameraClipping.minNear;
+                    }
                     if (props.cameraClipping.radius !== undefined) {
-                        const radius = (scene.boundingSphere.radius / 100) * (100 - props.cameraClipping.radius);
+                        const radius = (getSceneRadius() / 100) * (100 - props.cameraClipping.radius);
                         if (radius > 0 && radius !== cameraState.radius) {
                             // if radius = 0, NaNs happen
                             cameraState.radius = Math.max(radius, 0.01);
@@ -788,9 +844,13 @@ namespace Canvas3D {
 
                 if (props.camera?.helper) helper.camera.setProps(props.camera.helper);
                 if (props.camera?.manualReset !== undefined) p.camera.manualReset = props.camera.manualReset;
-                if (props.camera?.stereo !== undefined) Object.assign(p.camera.stereo, props.camera.stereo);
+                if (props.camera?.stereo !== undefined) {
+                    Object.assign(p.camera.stereo, props.camera.stereo);
+                    stereoCamera.setProps(p.camera.stereo.params);
+                }
                 if (props.cameraResetDurationMs !== undefined) p.cameraResetDurationMs = props.cameraResetDurationMs;
                 if (props.transparentBackground !== undefined) p.transparentBackground = props.transparentBackground;
+                if (props.dpoitIterations !== undefined) p.dpoitIterations = props.dpoitIterations;
                 if (props.viewport !== undefined) {
                     const doNotUpdate = p.viewport === props.viewport ||
                         (p.viewport.name === props.viewport.name && shallowEqual(p.viewport.params, props.viewport.params));
@@ -802,6 +862,12 @@ namespace Canvas3D {
                     }
                 }
 
+                if (props.postprocessing?.background) {
+                    Object.assign(p.postprocessing.background, props.postprocessing.background);
+                    passes.draw.postprocessing.background.update(camera, p.postprocessing.background, changed => {
+                        if (changed && !doNotRequestDraw) requestDraw();
+                    });
+                }
                 if (props.postprocessing) Object.assign(p.postprocessing, props.postprocessing);
                 if (props.marking) Object.assign(p.marking, props.marking);
                 if (props.multiSample) Object.assign(p.multiSample, props.multiSample);
@@ -820,7 +886,7 @@ namespace Canvas3D {
                 }
             },
             getImagePass: (props: Partial<ImageProps> = {}) => {
-                return new ImagePass(webgl, renderer, scene, camera, helper, passes.draw.wboitEnabled, props);
+                return new ImagePass(webgl, assetManager, renderer, scene, camera, helper, passes.draw.wboitEnabled, passes.draw.dpoitEnabled, props);
             },
             getRenderObjects(): GraphicsRenderObject[] {
                 const renderObjects: GraphicsRenderObject[] = [];
@@ -842,6 +908,7 @@ namespace Canvas3D {
             },
             dispose: () => {
                 contextRestoredSub.unsubscribe();
+                cancelAnimationFrame(animationFrameHandle);
 
                 markBuffer = [];
 
@@ -850,6 +917,8 @@ namespace Canvas3D {
                 controls.dispose();
                 renderer.dispose();
                 interactionHelper.dispose();
+
+                removeConsoleStatsProvider(consoleStats);
             }
         };
 
@@ -885,4 +954,4 @@ namespace Canvas3D {
             Viewport.set(controls.viewport, x, y, width, height);
         }
     }
-}
+}

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/background.ts

@@ -0,0 +1,467 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QuadPositions, } from '../../mol-gl/compute/util';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { AttributeSpec, DefineSpec, TextureSpec, UniformSpec, Values, ValueSpec } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { background_frag } from '../../mol-gl/shader/background.frag';
+import { background_vert } from '../../mol-gl/shader/background.vert';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { createNullTexture, CubeFaces, Texture } from '../../mol-gl/webgl/texture';
+import { Mat4 } from '../../mol-math/linear-algebra/3d/mat4';
+import { ValueCell } from '../../mol-util/value-cell';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { isTimingMode } from '../../mol-util/debug';
+import { Camera, ICamera } from '../camera';
+import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
+import { Vec2 } from '../../mol-math/linear-algebra/3d/vec2';
+import { Color } from '../../mol-util/color';
+import { Asset, AssetManager } from '../../mol-util/assets';
+import { Vec4 } from '../../mol-math/linear-algebra/3d/vec4';
+
+const SharedParams = {
+    opacity: PD.Numeric(1, { min: 0.0, max: 1.0, step: 0.01 }),
+    saturation: PD.Numeric(0, { min: -1, max: 1, step: 0.01 }),
+    lightness: PD.Numeric(0, { min: -1, max: 1, step: 0.01 }),
+};
+
+const SkyboxParams = {
+    faces: PD.MappedStatic('urls', {
+        urls: PD.Group({
+            nx: PD.Text('', { label: 'Negative X / Left' }),
+            ny: PD.Text('', { label: 'Negative Y / Bottom' }),
+            nz: PD.Text('', { label: 'Negative Z / Back' }),
+            px: PD.Text('', { label: 'Positive X / Right' }),
+            py: PD.Text('', { label: 'Positive Y / Top' }),
+            pz: PD.Text('', { label: 'Positive Z / Front' }),
+        }, { isExpanded: true, label: 'URLs' }),
+        files: PD.Group({
+            nx: PD.File({ label: 'Negative X / Left', accept: 'image/*' }),
+            ny: PD.File({ label: 'Negative Y / Bottom', accept: 'image/*' }),
+            nz: PD.File({ label: 'Negative Z / Back', accept: 'image/*' }),
+            px: PD.File({ label: 'Positive X / Right', accept: 'image/*' }),
+            py: PD.File({ label: 'Positive Y / Top', accept: 'image/*' }),
+            pz: PD.File({ label: 'Positive Z / Front', accept: 'image/*' }),
+        }, { isExpanded: true, label: 'Files' }),
+    }),
+    blur: PD.Numeric(0, { min: 0.0, max: 1.0, step: 0.01 }, { description: 'Note, this only works in WebGL2 or when "EXT_shader_texture_lod" is available.' }),
+    ...SharedParams,
+};
+type SkyboxProps = PD.Values<typeof SkyboxParams>
+
+const ImageParams = {
+    source: PD.MappedStatic('url', {
+        url: PD.Text(''),
+        file: PD.File({ accept: 'image/*' }),
+    }),
+    ...SharedParams,
+    coverage: PD.Select('viewport', PD.arrayToOptions(['viewport', 'canvas'])),
+};
+type ImageProps = PD.Values<typeof ImageParams>
+
+const HorizontalGradientParams = {
+    topColor: PD.Color(Color(0xDDDDDD)),
+    bottomColor: PD.Color(Color(0xEEEEEE)),
+    ratio: PD.Numeric(0.5, { min: 0.0, max: 1.0, step: 0.01 }),
+    coverage: PD.Select('viewport', PD.arrayToOptions(['viewport', 'canvas'])),
+};
+
+const RadialGradientParams = {
+    centerColor: PD.Color(Color(0xDDDDDD)),
+    edgeColor: PD.Color(Color(0xEEEEEE)),
+    ratio: PD.Numeric(0.5, { min: 0.0, max: 1.0, step: 0.01 }),
+    coverage: PD.Select('viewport', PD.arrayToOptions(['viewport', 'canvas'])),
+};
+
+export const BackgroundParams = {
+    variant: PD.MappedStatic('off', {
+        off: PD.EmptyGroup(),
+        skybox: PD.Group(SkyboxParams, { isExpanded: true }),
+        image: PD.Group(ImageParams, { isExpanded: true }),
+        horizontalGradient: PD.Group(HorizontalGradientParams, { isExpanded: true }),
+        radialGradient: PD.Group(RadialGradientParams, { isExpanded: true }),
+    }, { label: 'Environment' }),
+};
+export type BackgroundProps = PD.Values<typeof BackgroundParams>
+
+export class BackgroundPass {
+    private renderable: BackgroundRenderable;
+
+    private skybox: {
+        texture: Texture
+        props: SkyboxProps
+        assets: Asset[]
+        loaded: boolean
+    } | undefined;
+
+    private image: {
+        texture: Texture
+        props: ImageProps
+        asset: Asset
+        loaded: boolean
+    } | undefined;
+
+    private readonly camera = new Camera();
+    private readonly target = Vec3();
+    private readonly position = Vec3();
+    private readonly dir = Vec3();
+
+    readonly texture: Texture;
+
+    constructor(private readonly webgl: WebGLContext, private readonly assetManager: AssetManager, width: number, height: number) {
+        this.renderable = getBackgroundRenderable(webgl, width, height);
+    }
+
+    setSize(width: number, height: number) {
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+
+        if (width !== w || height !== h) {
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    private clearSkybox() {
+        if (this.skybox !== undefined) {
+            this.skybox.texture.destroy();
+            this.skybox.assets.forEach(a => this.assetManager.release(a));
+            this.skybox = undefined;
+        }
+    }
+
+    private updateSkybox(camera: ICamera, props: SkyboxProps, onload?: (changed: boolean) => void) {
+        const tf = this.skybox?.props.faces;
+        const f = props.faces.params;
+        if (!f.nx || !f.ny || !f.nz || !f.px || !f.py || !f.pz) {
+            this.clearSkybox();
+            onload?.(false);
+            return;
+        }
+        if (!this.skybox || !tf || !areSkyboxTexturePropsEqual(props.faces, this.skybox.props.faces)) {
+            this.clearSkybox();
+            const { texture, assets } = getSkyboxTexture(this.webgl, this.assetManager, props.faces, errored => {
+                if (this.skybox) this.skybox.loaded = !errored;
+                onload?.(true);
+            });
+            this.skybox = { texture, props: { ...props }, assets, loaded: false };
+            ValueCell.update(this.renderable.values.tSkybox, texture);
+            this.renderable.update();
+        } else {
+            onload?.(false);
+        }
+        if (!this.skybox) return;
+
+        let cam = camera;
+        if (camera.state.mode === 'orthographic') {
+            this.camera.setState({ ...camera.state, mode: 'perspective' });
+            this.camera.update();
+            cam = this.camera;
+        }
+
+        const m = this.renderable.values.uViewDirectionProjectionInverse.ref.value;
+        Vec3.sub(this.dir, cam.state.position, cam.state.target);
+        Vec3.setMagnitude(this.dir, this.dir, 0.1);
+        Vec3.copy(this.position, this.dir);
+        Mat4.lookAt(m, this.position, this.target, cam.state.up);
+        Mat4.mul(m, cam.projection, m);
+        Mat4.invert(m, m);
+        ValueCell.update(this.renderable.values.uViewDirectionProjectionInverse, m);
+
+        ValueCell.updateIfChanged(this.renderable.values.uBlur, props.blur);
+        ValueCell.updateIfChanged(this.renderable.values.uOpacity, props.opacity);
+        ValueCell.updateIfChanged(this.renderable.values.uSaturation, props.saturation);
+        ValueCell.updateIfChanged(this.renderable.values.uLightness, props.lightness);
+        ValueCell.updateIfChanged(this.renderable.values.dVariant, 'skybox');
+        this.renderable.update();
+    }
+
+    private clearImage() {
+        if (this.image !== undefined) {
+            this.image.texture.destroy();
+            this.assetManager.release(this.image.asset);
+            this.image = undefined;
+        }
+    }
+
+    private updateImage(props: ImageProps, onload?: (loaded: boolean) => void) {
+        if (!props.source.params) {
+            this.clearImage();
+            onload?.(false);
+            return;
+        }
+        if (!this.image || !this.image.props.source.params || !areImageTexturePropsEqual(props.source, this.image.props.source)) {
+            this.clearImage();
+            const { texture, asset } = getImageTexture(this.webgl, this.assetManager, props.source, errored => {
+                if (this.image) this.image.loaded = !errored;
+                onload?.(true);
+            });
+            this.image = { texture, props: { ...props }, asset, loaded: false };
+            ValueCell.update(this.renderable.values.tImage, texture);
+            this.renderable.update();
+        } else {
+            onload?.(false);
+        }
+        if (!this.image) return;
+
+        ValueCell.updateIfChanged(this.renderable.values.uOpacity, props.opacity);
+        ValueCell.updateIfChanged(this.renderable.values.uSaturation, props.saturation);
+        ValueCell.updateIfChanged(this.renderable.values.uLightness, props.lightness);
+        ValueCell.updateIfChanged(this.renderable.values.uViewportAdjusted, props.coverage === 'viewport' ? true : false);
+        ValueCell.updateIfChanged(this.renderable.values.dVariant, 'image');
+        this.renderable.update();
+    }
+
+    private updateImageScaling() {
+        const v = this.renderable.values;
+        const [w, h] = v.uTexSize.ref.value;
+        const iw = this.image?.texture.getWidth() || 0;
+        const ih = this.image?.texture.getHeight() || 0;
+        const r = w / h;
+        const ir = iw / ih;
+        // responsive scaling with offset
+        if (r < ir) {
+            ValueCell.update(v.uImageScale, Vec2.set(v.uImageScale.ref.value, iw * h / ih, h));
+        } else {
+            ValueCell.update(v.uImageScale, Vec2.set(v.uImageScale.ref.value, w, ih * w / iw));
+        }
+        const [rw, rh] = v.uImageScale.ref.value;
+        const sr = rw / rh;
+        if (sr > r) {
+            ValueCell.update(v.uImageOffset, Vec2.set(v.uImageOffset.ref.value, (1 - r / sr) / 2, 0));
+        } else {
+            ValueCell.update(v.uImageOffset, Vec2.set(v.uImageOffset.ref.value, 0, (1 - sr / r) / 2));
+        }
+    }
+
+    private updateGradient(colorA: Color, colorB: Color, ratio: number, variant: 'horizontalGradient' | 'radialGradient', viewportAdjusted: boolean) {
+        ValueCell.update(this.renderable.values.uGradientColorA, Color.toVec3Normalized(this.renderable.values.uGradientColorA.ref.value, colorA));
+        ValueCell.update(this.renderable.values.uGradientColorB, Color.toVec3Normalized(this.renderable.values.uGradientColorB.ref.value, colorB));
+        ValueCell.updateIfChanged(this.renderable.values.uGradientRatio, ratio);
+        ValueCell.updateIfChanged(this.renderable.values.uViewportAdjusted, viewportAdjusted);
+        ValueCell.updateIfChanged(this.renderable.values.dVariant, variant);
+        this.renderable.update();
+    }
+
+    update(camera: ICamera, props: BackgroundProps, onload?: (changed: boolean) => void) {
+        if (props.variant.name === 'off') {
+            this.clearSkybox();
+            this.clearImage();
+            onload?.(false);
+            return;
+        } else if (props.variant.name === 'skybox') {
+            this.clearImage();
+            this.updateSkybox(camera, props.variant.params, onload);
+        } else if (props.variant.name === 'image') {
+            this.clearSkybox();
+            this.updateImage(props.variant.params, onload);
+        } else if (props.variant.name === 'horizontalGradient') {
+            this.clearSkybox();
+            this.clearImage();
+            this.updateGradient(props.variant.params.topColor, props.variant.params.bottomColor, props.variant.params.ratio, props.variant.name, props.variant.params.coverage === 'viewport' ? true : false);
+            onload?.(false);
+        } else if (props.variant.name === 'radialGradient') {
+            this.clearSkybox();
+            this.clearImage();
+            this.updateGradient(props.variant.params.centerColor, props.variant.params.edgeColor, props.variant.params.ratio, props.variant.name, props.variant.params.coverage === 'viewport' ? true : false);
+            onload?.(false);
+        }
+
+        const { x, y, width, height } = camera.viewport;
+        ValueCell.update(this.renderable.values.uViewport, Vec4.set(this.renderable.values.uViewport.ref.value, x, y, width, height));
+    }
+
+    isEnabled(props: BackgroundProps) {
+        return !!(
+            (this.skybox && this.skybox.loaded) ||
+            (this.image && this.image.loaded) ||
+            props.variant.name === 'horizontalGradient' ||
+            props.variant.name === 'radialGradient'
+        );
+    }
+
+    private isReady() {
+        return !!(
+            (this.skybox && this.skybox.loaded) ||
+            (this.image && this.image.loaded) ||
+            this.renderable.values.dVariant.ref.value === 'horizontalGradient' ||
+            this.renderable.values.dVariant.ref.value === 'radialGradient'
+        );
+    }
+
+    render() {
+        if (!this.isReady()) return;
+
+        if (this.renderable.values.dVariant.ref.value === 'image') {
+            this.updateImageScaling();
+        }
+
+        if (isTimingMode) this.webgl.timer.mark('BackgroundPass.render');
+        this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('BackgroundPass.render');
+    }
+
+    dispose() {
+        this.clearSkybox();
+        this.clearImage();
+    }
+}
+
+//
+
+const SkyboxName = 'background-skybox';
+
+type CubeAssets = { [k in keyof CubeFaces]: Asset };
+
+function getCubeAssets(assetManager: AssetManager, faces: SkyboxProps['faces']): CubeAssets {
+    if (faces.name === 'urls') {
+        return {
+            nx: Asset.getUrlAsset(assetManager, faces.params.nx),
+            ny: Asset.getUrlAsset(assetManager, faces.params.ny),
+            nz: Asset.getUrlAsset(assetManager, faces.params.nz),
+            px: Asset.getUrlAsset(assetManager, faces.params.px),
+            py: Asset.getUrlAsset(assetManager, faces.params.py),
+            pz: Asset.getUrlAsset(assetManager, faces.params.pz),
+        };
+    } else {
+        return {
+            nx: faces.params.nx!,
+            ny: faces.params.ny!,
+            nz: faces.params.nz!,
+            px: faces.params.px!,
+            py: faces.params.py!,
+            pz: faces.params.pz!,
+        };
+    }
+}
+
+function getCubeFaces(assetManager: AssetManager, cubeAssets: CubeAssets): CubeFaces {
+    const resolve = (asset: Asset) => {
+        return assetManager.resolve(asset, 'binary').run().then(a => new Blob([a.data]));
+    };
+
+    return {
+        nx: resolve(cubeAssets.nx),
+        ny: resolve(cubeAssets.ny),
+        nz: resolve(cubeAssets.nz),
+        px: resolve(cubeAssets.px),
+        py: resolve(cubeAssets.py),
+        pz: resolve(cubeAssets.pz),
+    };
+}
+
+function getSkyboxHash(faces: SkyboxProps['faces']) {
+    if (faces.name === 'urls') {
+        return `${SkyboxName}_${faces.params.nx}|${faces.params.ny}|${faces.params.nz}|${faces.params.px}|${faces.params.py}|${faces.params.pz}`;
+    } else {
+        return `${SkyboxName}_${faces.params.nx?.id}|${faces.params.ny?.id}|${faces.params.nz?.id}|${faces.params.px?.id}|${faces.params.py?.id}|${faces.params.pz?.id}`;
+    }
+}
+
+function areSkyboxTexturePropsEqual(facesA: SkyboxProps['faces'], facesB: SkyboxProps['faces']) {
+    return getSkyboxHash(facesA) === getSkyboxHash(facesB);
+}
+
+function getSkyboxTexture(ctx: WebGLContext, assetManager: AssetManager, faces: SkyboxProps['faces'], onload?: (errored?: boolean) => void): { texture: Texture, assets: Asset[] } {
+    const cubeAssets = getCubeAssets(assetManager, faces);
+    const cubeFaces = getCubeFaces(assetManager, cubeAssets);
+    const assets = [cubeAssets.nx, cubeAssets.ny, cubeAssets.nz, cubeAssets.px, cubeAssets.py, cubeAssets.pz];
+    const texture = ctx.resources.cubeTexture(cubeFaces, true, onload);
+    return { texture, assets };
+}
+
+//
+
+const ImageName = 'background-image';
+
+function getImageHash(source: ImageProps['source']) {
+    if (source.name === 'url') {
+        return `${ImageName}_${source.params}`;
+    } else {
+        return `${ImageName}_${source.params?.id}`;
+    }
+}
+
+function areImageTexturePropsEqual(sourceA: ImageProps['source'], sourceB: ImageProps['source']) {
+    return getImageHash(sourceA) === getImageHash(sourceB);
+}
+
+function getImageTexture(ctx: WebGLContext, assetManager: AssetManager, source: ImageProps['source'], onload?: (errored?: boolean) => void): { texture: Texture, asset: Asset } {
+    const texture = ctx.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+    const img = new Image();
+    img.onload = () => {
+        texture.load(img);
+        onload?.();
+    };
+    img.onerror = () => {
+        onload?.(true);
+    };
+    const asset = source.name === 'url'
+        ? Asset.getUrlAsset(assetManager, source.params)
+        : source.params!;
+    assetManager.resolve(asset, 'binary').run().then(a => {
+        const blob = new Blob([a.data]);
+        img.src = URL.createObjectURL(blob);
+    });
+    return { texture, asset };
+}
+
+//
+
+const BackgroundSchema = {
+    drawCount: ValueSpec('number'),
+    instanceCount: ValueSpec('number'),
+    aPosition: AttributeSpec('float32', 2, 0),
+    tSkybox: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    tImage: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    uImageScale: UniformSpec('v2'),
+    uImageOffset: UniformSpec('v2'),
+    uTexSize: UniformSpec('v2'),
+    uViewport: UniformSpec('v4'),
+    uViewportAdjusted: UniformSpec('b'),
+    uViewDirectionProjectionInverse: UniformSpec('m4'),
+    uGradientColorA: UniformSpec('v3'),
+    uGradientColorB: UniformSpec('v3'),
+    uGradientRatio: UniformSpec('f'),
+    uBlur: UniformSpec('f'),
+    uOpacity: UniformSpec('f'),
+    uSaturation: UniformSpec('f'),
+    uLightness: UniformSpec('f'),
+    dVariant: DefineSpec('string', ['skybox', 'image', 'verticalGradient', 'horizontalGradient', 'radialGradient']),
+};
+const SkyboxShaderCode = ShaderCode('background', background_vert, background_frag, {
+    shaderTextureLod: 'optional'
+});
+type BackgroundRenderable = ComputeRenderable<Values<typeof BackgroundSchema>>
+
+function getBackgroundRenderable(ctx: WebGLContext, width: number, height: number): BackgroundRenderable {
+    const values: Values<typeof BackgroundSchema> = {
+        drawCount: ValueCell.create(6),
+        instanceCount: ValueCell.create(1),
+        aPosition: ValueCell.create(QuadPositions),
+        tSkybox: ValueCell.create(createNullTexture()),
+        tImage: ValueCell.create(createNullTexture()),
+        uImageScale: ValueCell.create(Vec2()),
+        uImageOffset: ValueCell.create(Vec2()),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
+        uViewport: ValueCell.create(Vec4()),
+        uViewportAdjusted: ValueCell.create(true),
+        uViewDirectionProjectionInverse: ValueCell.create(Mat4()),
+        uGradientColorA: ValueCell.create(Vec3()),
+        uGradientColorB: ValueCell.create(Vec3()),
+        uGradientRatio: ValueCell.create(0.5),
+        uBlur: ValueCell.create(0),
+        uOpacity: ValueCell.create(1),
+        uSaturation: ValueCell.create(0),
+        uLightness: ValueCell.create(0),
+        dVariant: ValueCell.create('skybox'),
+    };
+
+    const schema = { ...BackgroundSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', SkyboxShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-canvas3d/passes/dpoit.ts

@@ -0,0 +1,309 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Gianluca Tomasello <giagitom@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
+ * Adapted from https://github.com/tsherif/webgl2examples, The MIT License, Copyright © 2017 Tarek Sherif, Shuai Shao
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { ValueCell } from '../../mol-util';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { evaluateDpoit_frag } from '../../mol-gl/shader/evaluate-dpoit.frag';
+import { blendBackDpoit_frag } from '../../mol-gl/shader/blend-back-dpoit.frag';
+import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
+import { Vec2 } from '../../mol-math/linear-algebra';
+import { isDebugMode, isTimingMode } from '../../mol-util/debug';
+import { isWebGL2 } from '../../mol-gl/webgl/compat';
+
+const BlendBackDpoitSchema = {
+    ...QuadSchema,
+    tDpoitBackColor: TextureSpec('texture', 'rgba', 'float', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+};
+const BlendBackDpoitShaderCode = ShaderCode('blend-back-dpoit', quad_vert, blendBackDpoit_frag);
+type BlendBackDpoitRenderable = ComputeRenderable<Values<typeof BlendBackDpoitSchema>>
+
+function getBlendBackDpoitRenderable(ctx: WebGLContext, dopitBlendBackTexture: Texture): BlendBackDpoitRenderable {
+    const values: Values<typeof BlendBackDpoitSchema> = {
+        ...QuadValues,
+        tDpoitBackColor: ValueCell.create(dopitBlendBackTexture),
+        uTexSize: ValueCell.create(Vec2.create(dopitBlendBackTexture.getWidth(), dopitBlendBackTexture.getHeight())),
+    };
+
+    const schema = { ...BlendBackDpoitSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', BlendBackDpoitShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+const EvaluateDpoitSchema = {
+    ...QuadSchema,
+    tDpoitFrontColor: TextureSpec('texture', 'rgba', 'float', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+};
+const EvaluateDpoitShaderCode = ShaderCode('evaluate-dpoit', quad_vert, evaluateDpoit_frag);
+type EvaluateDpoitRenderable = ComputeRenderable<Values<typeof EvaluateDpoitSchema>>
+
+function getEvaluateDpoitRenderable(ctx: WebGLContext, dpoitFrontColorTexture: Texture): EvaluateDpoitRenderable {
+    const values: Values<typeof EvaluateDpoitSchema> = {
+        ...QuadValues,
+        tDpoitFrontColor: ValueCell.create(dpoitFrontColorTexture),
+        uTexSize: ValueCell.create(Vec2.create(dpoitFrontColorTexture.getWidth(), dpoitFrontColorTexture.getHeight())),
+    };
+
+    const schema = { ...EvaluateDpoitSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', EvaluateDpoitShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+export class DpoitPass {
+    private readonly DEPTH_CLEAR_VALUE = -99999.0; // NOTE same constant is set in shaders
+    private readonly MAX_DEPTH = 1.0;
+    private readonly MIN_DEPTH = 0.0;
+
+    private passCount = 0;
+    private writeId: number;
+    private readId: number;
+
+    private readonly blendBackRenderable: BlendBackDpoitRenderable;
+    private readonly renderable: EvaluateDpoitRenderable;
+
+    private readonly depthFramebuffers: Framebuffer[];
+    private readonly colorFramebuffers: Framebuffer[];
+
+    private readonly depthTextures: Texture[];
+    private readonly colorFrontTextures: Texture[];
+    private readonly colorBackTextures: Texture[];
+
+    private _supported = false;
+    get supported() {
+        return this._supported;
+    }
+
+    bind() {
+        const { state, gl, extensions: { blendMinMax } } = this.webgl;
+
+        // initialize
+        this.passCount = 0;
+
+        this.depthFramebuffers[0].bind();
+        state.clearColor(this.DEPTH_CLEAR_VALUE, this.DEPTH_CLEAR_VALUE, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.depthFramebuffers[1].bind();
+        state.clearColor(-this.MIN_DEPTH, this.MAX_DEPTH, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.colorFramebuffers[0].bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.colorFramebuffers[1].bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.depthFramebuffers[0].bind();
+        state.blendEquation(blendMinMax!.MAX);
+        state.depthMask(false);
+
+        return {
+            depth: this.depthTextures[1],
+            frontColor: this.colorFrontTextures[1],
+            backColor: this.colorBackTextures[1]
+        };
+    }
+
+    bindDualDepthPeeling() {
+        const { state, gl, extensions: { blendMinMax } } = this.webgl;
+
+        this.readId = this.passCount % 2;
+        this.writeId = 1 - this.readId; // ping-pong: 0 or 1
+
+        this.passCount += 1; // increment for next pass
+
+        this.depthFramebuffers[this.writeId].bind();
+        state.clearColor(this.DEPTH_CLEAR_VALUE, this.DEPTH_CLEAR_VALUE, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.colorFramebuffers[this.writeId].bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.depthFramebuffers[this.writeId].bind();
+        state.blendEquation(blendMinMax!.MAX);
+        state.depthMask(false);
+
+        return {
+            depth: this.depthTextures[this.readId],
+            frontColor: this.colorFrontTextures[this.readId],
+            backColor: this.colorBackTextures[this.readId]
+        };
+    }
+
+    renderBlendBack() {
+        if (isTimingMode) this.webgl.timer.mark('DpoitPass.renderBlendBack');
+        const { state, gl } = this.webgl;
+
+        state.blendEquation(gl.FUNC_ADD);
+        state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
+
+        ValueCell.update(this.blendBackRenderable.values.tDpoitBackColor, this.colorBackTextures[this.writeId]);
+
+        this.blendBackRenderable.update();
+        this.blendBackRenderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.renderBlendBack');
+    }
+
+    render() {
+        if (isTimingMode) this.webgl.timer.mark('DpoitPass.render');
+        const { state, gl } = this.webgl;
+
+        state.blendFunc(gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
+
+        ValueCell.update(this.renderable.values.tDpoitFrontColor, this.colorFrontTextures[this.writeId]);
+
+        this.renderable.update();
+        this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.render');
+    }
+
+    setSize(width: number, height: number) {
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        if (width !== w || height !== h) {
+            for (let i = 0; i < 2; i++) {
+                this.depthTextures[i].define(width, height);
+                this.colorFrontTextures[i].define(width, height);
+                this.colorBackTextures[i].define(width, height);
+            }
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.blendBackRenderable.values.uTexSize, Vec2.set(this.blendBackRenderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    reset() {
+        if (this._supported) this._init();
+    }
+
+    private _init() {
+        const { extensions: { drawBuffers } } = this.webgl;
+        for (let i = 0; i < 2; i++) {
+            // depth
+            this.depthFramebuffers[i].bind();
+            drawBuffers!.drawBuffers([
+                drawBuffers!.COLOR_ATTACHMENT0,
+                drawBuffers!.COLOR_ATTACHMENT1,
+                drawBuffers!.COLOR_ATTACHMENT2
+            ]);
+
+            this.colorFrontTextures[i].attachFramebuffer(this.depthFramebuffers[i], 'color0');
+            this.colorBackTextures[i].attachFramebuffer(this.depthFramebuffers[i], 'color1');
+            this.depthTextures[i].attachFramebuffer(this.depthFramebuffers[i], 'color2');
+
+            // color
+            this.colorFramebuffers[i].bind();
+            drawBuffers!.drawBuffers([
+                drawBuffers!.COLOR_ATTACHMENT0,
+                drawBuffers!.COLOR_ATTACHMENT1
+            ]);
+
+            this.colorFrontTextures[i].attachFramebuffer(this.colorFramebuffers[i], 'color0');
+            this.colorBackTextures[i].attachFramebuffer(this.colorFramebuffers[i], 'color1');
+        }
+    }
+
+    static isSupported(webgl: WebGLContext) {
+        const { extensions: { drawBuffers, textureFloat, colorBufferFloat, blendMinMax } } = webgl;
+        if (!textureFloat || !colorBufferFloat || !drawBuffers || !blendMinMax) {
+            if (isDebugMode) {
+                const missing: string[] = [];
+                if (!textureFloat) missing.push('textureFloat');
+                if (!colorBufferFloat) missing.push('colorBufferFloat');
+                if (!drawBuffers) missing.push('drawBuffers');
+                if (!blendMinMax) missing.push('blendMinMax');
+                console.log(`Missing "${missing.join('", "')}" extensions required for "dpoit"`);
+            }
+            return false;
+        } else {
+            return true;
+        }
+    }
+
+    constructor(private webgl: WebGLContext, width: number, height: number) {
+        if (!DpoitPass.isSupported(webgl)) return;
+
+        const { resources, extensions: { colorBufferHalfFloat, textureHalfFloat } } = webgl;
+
+        // textures
+
+        if (isWebGL2(webgl.gl)) {
+            this.depthTextures = [
+                resources.texture('image-float32', 'rg', 'float', 'nearest'),
+                resources.texture('image-float32', 'rg', 'float', 'nearest')
+            ];
+
+            this.colorFrontTextures = colorBufferHalfFloat && textureHalfFloat ? [
+                resources.texture('image-float16', 'rgba', 'fp16', 'nearest'),
+                resources.texture('image-float16', 'rgba', 'fp16', 'nearest')
+            ] : [
+                resources.texture('image-float32', 'rgba', 'float', 'nearest'),
+                resources.texture('image-float32', 'rgba', 'float', 'nearest')
+            ];
+
+            this.colorBackTextures = colorBufferHalfFloat && textureHalfFloat ? [
+                resources.texture('image-float16', 'rgba', 'fp16', 'nearest'),
+                resources.texture('image-float16', 'rgba', 'fp16', 'nearest')
+            ] : [
+                resources.texture('image-float32', 'rgba', 'float', 'nearest'),
+                resources.texture('image-float32', 'rgba', 'float', 'nearest')
+            ];
+        } else {
+            // in webgl1 drawbuffers must be in the same format for some reason
+
+            this.depthTextures = [
+                resources.texture('image-float32', 'rgba', 'float', 'nearest'),
+                resources.texture('image-float32', 'rgba', 'float', 'nearest')
+            ];
+
+            this.colorFrontTextures = [
+                resources.texture('image-float32', 'rgba', 'float', 'nearest'),
+                resources.texture('image-float32', 'rgba', 'float', 'nearest')
+            ];
+
+            this.colorBackTextures = [
+                resources.texture('image-float32', 'rgba', 'float', 'nearest'),
+                resources.texture('image-float32', 'rgba', 'float', 'nearest')
+            ];
+        }
+
+        this.depthTextures[0].define(width, height);
+        this.depthTextures[1].define(width, height);
+
+        this.colorFrontTextures[0].define(width, height);
+        this.colorFrontTextures[1].define(width, height);
+
+        this.colorBackTextures[0].define(width, height);
+        this.colorBackTextures[1].define(width, height);
+
+        // framebuffers
+
+        this.depthFramebuffers = [resources.framebuffer(), resources.framebuffer()];
+        this.colorFramebuffers = [resources.framebuffer(), resources.framebuffer()];
+
+        // renderables
+
+        this.blendBackRenderable = getBlendBackDpoitRenderable(webgl, this.colorBackTextures[0]);
+        this.renderable = getEvaluateDpoitRenderable(webgl, this.colorFrontTextures[0]);
+
+        this._supported = true;
+        this._init();
+    }
+}

src/mol-canvas3d/passes/draw.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 Gianluca Tomasello <giagitom@gmail.com>
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
@@ -17,14 +18,18 @@ import { Helper } from '../helper/helper';
 
 import { StereoCamera } from '../camera/stereo';
 import { WboitPass } from './wboit';
+import { DpoitPass } from './dpoit';
 import { AntialiasingPass, PostprocessingPass, PostprocessingProps } from './postprocessing';
 import { MarkingPass, MarkingProps } from './marking';
 import { CopyRenderable, createCopyRenderable } from '../../mol-gl/compute/util';
+import { isTimingMode } from '../../mol-util/debug';
+import { AssetManager } from '../../mol-util/assets';
 
 type Props = {
-    postprocessing: PostprocessingProps
-    marking: MarkingProps
+    postprocessing: PostprocessingProps;
+    marking: MarkingProps;
     transparentBackground: boolean;
+    dpoitIterations: number;
 }
 
 type RenderContext = {
@@ -49,7 +54,8 @@ export class DrawPass {
     private copyFboTarget: CopyRenderable;
     private copyFboPostprocessing: CopyRenderable;
 
-    private wboit: WboitPass | undefined;
+    private readonly wboit: WboitPass | undefined;
+    private readonly dpoit: DpoitPass | undefined;
     private readonly marking: MarkingPass;
     readonly postprocessing: PostprocessingPass;
     private readonly antialiasing: AntialiasingPass;
@@ -58,11 +64,13 @@ export class DrawPass {
         return !!this.wboit?.supported;
     }
 
-    constructor(private webgl: WebGLContext, width: number, height: number, enableWboit: boolean) {
+    get dpoitEnabled() {
+        return !!this.dpoit?.supported;
+    }
+
+    constructor(private webgl: WebGLContext, assetManager: AssetManager, width: number, height: number, enableWboit: boolean, enableDpoit: boolean) {
         const { extensions, resources, isWebGL2 } = webgl;
-
         this.drawTarget = createNullRenderTarget(webgl.gl);
-
         this.colorTarget = webgl.createRenderTarget(width, height, true, 'uint8', 'linear');
         this.packedDepth = !extensions.depthTexture;
 
@@ -77,8 +85,9 @@ export class DrawPass {
         }
 
         this.wboit = enableWboit ? new WboitPass(webgl, width, height) : undefined;
+        this.dpoit = enableDpoit ? new DpoitPass(webgl, width, height) : undefined;
         this.marking = new MarkingPass(webgl, width, height);
-        this.postprocessing = new PostprocessingPass(webgl, this);
+        this.postprocessing = new PostprocessingPass(webgl, assetManager, this);
         this.antialiasing = new AntialiasingPass(webgl, this);
 
         this.copyFboTarget = createCopyRenderable(webgl, this.colorTarget.texture);
@@ -87,6 +96,7 @@ export class DrawPass {
 
     reset() {
         this.wboit?.reset();
+        this.dpoit?.reset();
     }
 
     setSize(width: number, height: number) {
@@ -110,26 +120,29 @@ export class DrawPass {
                 this.wboit.setSize(width, height);
             }
 
+            if (this.dpoit?.supported) {
+                this.dpoit.setSize(width, height);
+            }
+
             this.marking.setSize(width, height);
             this.postprocessing.setSize(width, height);
             this.antialiasing.setSize(width, height);
         }
     }
 
-    private _renderWboit(renderer: Renderer, camera: ICamera, scene: Scene, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
-        if (!this.wboit?.supported) throw new Error('expected wboit to be supported');
+    private _renderDpoit(renderer: Renderer, camera: ICamera, scene: Scene, iterations: number, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+        if (!this.dpoit?.supported) throw new Error('expected dpoit to be supported');
 
-        this.colorTarget.bind();
+        this.depthTextureOpaque.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
         renderer.clear(true);
 
         // render opaque primitives
-        this.depthTextureOpaque.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-        this.colorTarget.bind();
-        renderer.clearDepth();
-        renderer.renderWboitOpaque(scene.primitives, camera, null);
+        if (scene.hasOpaque) {
+            renderer.renderDpoitOpaque(scene.primitives, camera, null);
+        }
 
         if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
                 this.depthTargetTransparent.bind();
                 renderer.clearDepth(true);
                 if (scene.opacityAverage < 1) {
@@ -137,14 +150,72 @@ 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');
+
+        // render transparent primitives
+        if (scene.opacityAverage < 1) {
+            const target = PostprocessingPass.isEnabled(postprocessingProps)
+                ? this.postprocessing.target : this.colorTarget;
+
+            const dpoitTextures = this.dpoit.bind();
+            renderer.renderDpoitTransparent(scene.primitives, camera, this.depthTextureOpaque, dpoitTextures);
+
+            for (let i = 0; i < iterations; i++) {
+                if (isTimingMode) this.webgl.timer.mark('DpoitPass.layer');
+                const dpoitTextures = this.dpoit.bindDualDepthPeeling();
+                renderer.renderDpoitTransparent(scene.primitives, camera, this.depthTextureOpaque, dpoitTextures);
+
+                target.bind();
+                this.dpoit.renderBlendBack();
+                if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.layer');
+            }
+
+            // evaluate dpoit
+            target.bind();
+            this.dpoit.render();
+        }
+
+        // render transparent volumes
+        if (scene.volumes.renderables.length > 0) {
+            renderer.renderDpoitVolume(scene.volumes, camera, this.depthTextureOpaque);
+        }
+    }
+
+    private _renderWboit(renderer: Renderer, camera: ICamera, scene: Scene, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+        if (!this.wboit?.supported) throw new Error('expected wboit to be supported');
+
+        this.depthTextureOpaque.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+        renderer.clear(true);
+
+        // render opaque primitives
+        if (scene.hasOpaque) {
+            renderer.renderWboitOpaque(scene.primitives, camera, null);
+        }
+
+        if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
+                this.depthTargetTransparent.bind();
+                renderer.clearDepth(true);
+                if (scene.opacityAverage < 1) {
+                    renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
+                }
+            }
+
+            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
         }
 
         // render transparent primitives and volumes
         if (scene.opacityAverage < 1 || scene.volumes.renderables.length > 0) {
             this.wboit.bind();
-            renderer.renderWboitTransparent(scene.primitives, camera, this.depthTextureOpaque);
-            renderer.renderWboitTransparent(scene.volumes, camera, this.depthTextureOpaque);
+            if (scene.opacityAverage < 1) {
+                renderer.renderWboitTransparent(scene.primitives, camera, this.depthTextureOpaque);
+            }
+            if (scene.volumes.renderables.length > 0) {
+                renderer.renderWboitTransparent(scene.volumes, camera, this.depthTextureOpaque);
+            }
 
             // evaluate wboit
             if (PostprocessingPass.isEnabled(postprocessingProps)) {
@@ -160,14 +231,17 @@ export class DrawPass {
         if (toDrawingBuffer) {
             this.drawTarget.bind();
         } else {
-            this.colorTarget.bind();
             if (!this.packedDepth) {
                 this.depthTextureOpaque.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+            } else {
+                this.colorTarget.bind();
             }
         }
 
         renderer.clear(true);
-        renderer.renderBlendedOpaque(scene.primitives, camera, null);
+        if (scene.hasOpaque) {
+            renderer.renderBlendedOpaque(scene.primitives, camera, null);
+        }
 
         if (!toDrawingBuffer) {
             // do a depth pass if not rendering to drawing buffer and
@@ -186,7 +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) {
@@ -194,7 +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');
@@ -203,13 +277,34 @@ export class DrawPass {
                 }
             }
 
-            renderer.renderBlendedVolume(scene.volumes, camera, this.depthTextureOpaque);
+            if (scene.volumes.renderables.length > 0) {
+                const target = PostprocessingPass.isEnabled(postprocessingProps)
+                    ? this.postprocessing.target : this.colorTarget;
+
+                if (!this.packedDepth) {
+                    this.depthTextureOpaque.detachFramebuffer(target.framebuffer, 'depth');
+                } else {
+                    this.colorTarget.depthRenderbuffer?.detachFramebuffer(target.framebuffer);
+                }
+                target.bind();
+
+                renderer.renderBlendedVolume(scene.volumes, camera, this.depthTextureOpaque);
+
+                if (!this.packedDepth) {
+                    this.depthTextureOpaque.attachFramebuffer(target.framebuffer, 'depth');
+                } else {
+                    this.colorTarget.depthRenderbuffer?.attachFramebuffer(target.framebuffer);
+                }
+                target.bind();
+            }
         }
 
-        renderer.renderBlendedTransparent(scene.primitives, camera, null);
+        if (scene.opacityAverage < 1) {
+            renderer.renderBlendedTransparent(scene.primitives, camera, null);
+        }
     }
 
-    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, props: Props) {
+    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
         const volumeRendering = scene.volumes.renderables.length > 0;
         const postprocessingEnabled = PostprocessingPass.isEnabled(props.postprocessing);
         const antialiasingEnabled = AntialiasingPass.isEnabled(props.postprocessing);
@@ -217,56 +312,56 @@ export class DrawPass {
 
         const { x, y, width, height } = camera.viewport;
         renderer.setViewport(x, y, width, height);
-        renderer.update(camera);
+        renderer.update(camera, scene);
 
-        if (props.transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
+        if (transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
             this.drawTarget.bind();
             renderer.clear(false);
         }
 
         if (this.wboitEnabled) {
-            this._renderWboit(renderer, camera, scene, props.transparentBackground, props.postprocessing);
+            this._renderWboit(renderer, camera, scene, transparentBackground, props.postprocessing);
+        } else if (this.dpoitEnabled) {
+            this._renderDpoit(renderer, camera, scene, props.dpoitIterations, transparentBackground, props.postprocessing);
         } else {
-            this._renderBlended(renderer, camera, scene, !volumeRendering && !postprocessingEnabled && !antialiasingEnabled && toDrawingBuffer, props.transparentBackground, props.postprocessing);
+            this._renderBlended(renderer, camera, scene, !volumeRendering && !postprocessingEnabled && !antialiasingEnabled && toDrawingBuffer, transparentBackground, props.postprocessing);
         }
 
-        if (postprocessingEnabled) {
-            this.postprocessing.target.bind();
-        } else if (!toDrawingBuffer || volumeRendering || this.wboitEnabled) {
-            this.colorTarget.bind();
-        } else {
-            this.drawTarget.bind();
-        }
+        const target = postprocessingEnabled
+            ? this.postprocessing.target
+            : !toDrawingBuffer || volumeRendering || this.wboitEnabled || this.dpoitEnabled
+                ? this.colorTarget
+                : this.drawTarget;
 
-        if (markingEnabled) {
-            if (scene.markerAverage > 0) {
-                const markingDepthTest = props.marking.ghostEdgeStrength < 1;
-                if (markingDepthTest && scene.markerAverage !== 1) {
-                    this.marking.depthTarget.bind();
-                    renderer.clear(false, true);
-                    renderer.renderMarkingDepth(scene.primitives, camera, null);
-                }
-
-                this.marking.maskTarget.bind();
+        if (markingEnabled && scene.markerAverage > 0) {
+            const markingDepthTest = props.marking.ghostEdgeStrength < 1;
+            if (markingDepthTest && scene.markerAverage !== 1) {
+                this.marking.depthTarget.bind();
                 renderer.clear(false, true);
-                renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
-
-                this.marking.update(props.marking);
-                this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
+                renderer.renderMarkingDepth(scene.primitives, camera, null);
             }
+
+            this.marking.maskTarget.bind();
+            renderer.clear(false, true);
+            renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
+
+            this.marking.update(props.marking);
+            this.marking.render(camera.viewport, target);
+        } else {
+            target.bind();
         }
 
         if (helper.debug.isEnabled) {
             helper.debug.syncVisibility();
-            renderer.renderBlended(helper.debug.scene, camera, null);
+            renderer.renderBlended(helper.debug.scene, camera);
         }
         if (helper.handle.isEnabled) {
-            renderer.renderBlended(helper.handle.scene, camera, null);
+            renderer.renderBlended(helper.handle.scene, camera);
         }
         if (helper.camera.isEnabled) {
             helper.camera.update(camera);
-            renderer.update(helper.camera.camera);
-            renderer.renderBlended(helper.camera.scene, helper.camera.camera, null);
+            renderer.update(helper.camera.camera, helper.camera.scene);
+            renderer.renderBlended(helper.camera.scene, helper.camera.camera);
         }
 
         if (antialiasingEnabled) {
@@ -277,7 +372,7 @@ export class DrawPass {
             this.webgl.state.disable(this.webgl.gl.DEPTH_TEST);
             if (postprocessingEnabled) {
                 this.copyFboPostprocessing.render();
-            } else if (volumeRendering || this.wboitEnabled) {
+            } else if (volumeRendering || this.wboitEnabled || this.dpoitEnabled) {
                 this.copyFboTarget.render();
             }
         }
@@ -286,17 +381,27 @@ export class DrawPass {
     }
 
     render(ctx: RenderContext, props: Props, toDrawingBuffer: boolean) {
+        if (isTimingMode) this.webgl.timer.mark('DrawPass.render');
         const { renderer, camera, scene, helper } = ctx;
-        renderer.setTransparentBackground(props.transparentBackground);
+
+        this.postprocessing.setTransparentBackground(props.transparentBackground);
+        const transparentBackground = props.transparentBackground || this.postprocessing.background.isEnabled(props.postprocessing.background);
+
+        renderer.setTransparentBackground(transparentBackground);
         renderer.setDrawingBufferSize(this.colorTarget.getWidth(), this.colorTarget.getHeight());
         renderer.setPixelRatio(this.webgl.pixelRatio);
 
         if (StereoCamera.is(camera)) {
-            this._render(renderer, camera.left, scene, helper, toDrawingBuffer, props);
-            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, props);
+            if (isTimingMode) this.webgl.timer.mark('StereoCamera.left');
+            this._render(renderer, camera.left, scene, helper, toDrawingBuffer, transparentBackground, props);
+            if (isTimingMode) this.webgl.timer.markEnd('StereoCamera.left');
+            if (isTimingMode) this.webgl.timer.mark('StereoCamera.right');
+            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, transparentBackground, props);
+            if (isTimingMode) this.webgl.timer.markEnd('StereoCamera.right');
         } else {
-            this._render(renderer, camera, scene, helper, toDrawingBuffer, props);
+            this._render(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
         }
+        if (isTimingMode) this.webgl.timer.markEnd('DrawPass.render');
     }
 
     getColorTarget(postprocessingProps: PostprocessingProps): RenderTarget {
@@ -307,4 +412,4 @@ export class DrawPass {
         }
         return this.colorTarget;
     }
-}
+}

src/mol-canvas3d/passes/fxaa.ts

@@ -18,6 +18,7 @@ import { quad_vert } from '../../mol-gl/shader/quad.vert';
 import { fxaa_frag } from '../../mol-gl/shader/fxaa.frag';
 import { Viewport } from '../camera/util';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { isTimingMode } from '../../mol-util/debug';
 
 export const FxaaParams = {
     edgeThresholdMin: PD.Numeric(0.0312, { min: 0.0312, max: 0.0833, step: 0.0001 }, { description: 'Trims the algorithm from processing darks.' }),
@@ -43,8 +44,8 @@ export class FxaaPass {
         state.depthMask(false);
 
         const { x, y, width, height } = viewport;
-        gl.viewport(x, y, width, height);
-        gl.scissor(x, y, width, height);
+        state.viewport(x, y, width, height);
+        state.scissor(x, y, width, height);
 
         state.clearColor(0, 0, 0, 1);
         gl.clear(gl.COLOR_BUFFER_BIT);
@@ -83,6 +84,7 @@ export class FxaaPass {
     }
 
     render(viewport: Viewport, target: RenderTarget | undefined) {
+        if (isTimingMode) this.webgl.timer.mark('FxaaPass.render');
         if (target) {
             target.bind();
         } else {
@@ -90,6 +92,7 @@ export class FxaaPass {
         }
         this.updateState(viewport);
         this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('FxaaPass.render');
     }
 }
 

src/mol-canvas3d/passes/image.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>
  */
@@ -18,9 +18,11 @@ import { PixelData } from '../../mol-util/image';
 import { Helper } from '../helper/helper';
 import { CameraHelper, CameraHelperParams } from '../helper/camera-helper';
 import { MarkingParams } from './marking';
+import { AssetManager } from '../../mol-util/assets';
 
 export const ImageParams = {
     transparentBackground: PD.Boolean(false),
+    dpoitIterations: PD.Numeric(2, { min: 1, max: 10, step: 1 }),
     multiSample: PD.Group(MultiSampleParams),
     postprocessing: PD.Group(PostprocessingParams),
     marking: PD.Group(MarkingParams),
@@ -47,10 +49,10 @@ export class ImagePass {
     get width() { return this._width; }
     get height() { return this._height; }
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, helper: Helper, enableWboit: boolean, props: Partial<ImageProps>) {
+    constructor(private webgl: WebGLContext, assetManager: AssetManager, private renderer: Renderer, private scene: Scene, private camera: Camera, helper: Helper, enableWboit: boolean, enableDpoit: boolean, props: Partial<ImageProps>) {
         this.props = { ...PD.getDefaultValues(ImageParams), ...props };
 
-        this.drawPass = new DrawPass(webgl, 128, 128, enableWboit);
+        this.drawPass = new DrawPass(webgl, assetManager, 128, 128, enableWboit, enableDpoit);
         this.multiSamplePass = new MultiSamplePass(webgl, this.drawPass);
         this.multiSampleHelper = new MultiSampleHelper(this.multiSamplePass);
 
@@ -63,6 +65,14 @@ export class ImagePass {
         this.setSize(1024, 768);
     }
 
+    updateBackground() {
+        return new Promise<void>(resolve => {
+            this.drawPass.postprocessing.background.update(this.camera, this.props.postprocessing.background, () => {
+                resolve();
+            });
+        });
+    }
+
     setSize(width: number, height: number) {
         if (width === this._width && height === this._height) return;