3.25.0

Fix Handling of Gzipped Assets by Reverting #615

.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

@@ -9,12 +9,12 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-node@v2
       with:
-        node-version: 17
+        node-version: 16
     - run: npm ci
     - run: sudo apt-get install xvfb
     - name: Lint
       run: npm run lint
     - name: Test
-      run: xvfb-run --auto-servernum npm run jest
+      run: npm install --no-save "gl@^5.0.0" && xvfb-run --auto-servernum npm run jest
     - name: Build
       run: npm run build

.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 +6,337 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [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
+
+## [v3.8.1] - 2022-05-14
+
+- Fix issues with marking camera/handle helper (#433)
+- Fix issues with array uniforms when running with headless-gl
+- Fix Polymer Chain Instance coloring
+- Improve performance of scene marker/opacity average calculation
+
+## [v3.8.0] - 2022-04-30
+
+- Add support for outlines around transparent objects
+- Improve per-group transparency when wboit is switched off
+- Improve ``ColorTheme`` typing with ``ColorType`` generic.
+    - Defaults to ``ColorTypeLocation``
+    - Set when using ``ColorTypeDirect`` or ``ColorTypeGrid``
+- Fix case handling of ``struct_conf`` mmCIF enumeration field (#425)
+- Fix ``allowTransparentBackfaces`` for per-group transparency
+- Fix ``FormatRegistry.isApplicable`` returning true for unregistered formats
+- Fix: handle building of ``GridLookup3D`` with zero cell size
+- Fix ``ignoreLight`` for direct-volume rendering with webgl1
+- Fix (non-black) outlines when using transparent background
+
+## [v3.7.0] - 2022-04-13
+
+- Fix ``xrayShaded`` for texture-mesh geometries
+- [Breaking] Change ``allowTransparentBackfaces`` to ``transparentBackfaces`` with options ``off``, ``on``, ``opaque``. This was only added in 3.6.0, so allowing a breaking change here.
+    - ``off``: don't show (default)
+    - ``on``: show with transparency
+    - ``opaque``: show fully opaque
+- Add option to disable file drop overlay.
+
+## [v3.6.2] - 2022-04-05
+
+- ModelServer ligand queries: fixes for alternate locations, additional atoms & UNL ligand
+- React 18 friendly ``useBehavior`` hook.
+
+## [v3.6.1] - 2022-04-03
+
+- Fix React18 related UI regressions.
+
+## [v3.6.0] - 2022-04-03
+
+- Check that model and coordinates have same element count when creating a trajectory
+- Fix aromatic rings assignment: do not mix flags and planarity test
+- Improve bonds assignment of coarse grained models: check for IndexPairBonds and exhaustive StructConn
+- Fix unit mapping in bondedAtomicPairs MolScript query
+- Improve pdb parsing: handle non unique atom and chain names (fixes #156)
+- Fix volume streaming for entries with multiple contour lists
+- Add ``allowTransparentBackfaces`` parameter to support double-sided rendering of transparent geometries
+- Fix handling of case insensitive mmCIF enumeration fields (including entity.type)
+- Fix ``disable-wboit`` Viewer GET param
+- Add support for React 18.
+    - Used by importing ``createPluginUI`` from ``mol-plugin-ui/react18``;
+    - In Mol* 4.0, React 18 will become the default option.
+
+## [v3.5.0] - 2022-03-25
+
+- Fix issues with bounding-sphere & color-smoothing (mostly for small geometries)
+- Support BCIF => CIF conversion in ``cif2bcif`` CLI tool
+
+## [v3.4.0] - 2022-03-13
+
+- Fix handling of mmcif with empty ``label_*`` fields
+- Improve saccharide detection (compare against list from CCD)
+- Fix legend label of hydrophobicity color theme
+- Add ``LoadTrajectory`` action
+- Add ``CustomImportControls`` to left panel
+- Add Zenodo import extension (load structures, trajectories, volumes, and zip files)
+- Fix loading of some compressed files within sessions
+- Fix wrong element assignment for atoms with Charmm ion names
+- Fix handling of empty symmetry cell data
+- Add support for ``trr`` and ``nctraj`` coordinates files
+- Add support for ``prmtop`` and ``top`` topology files
+
+## [v3.3.1] - 2022-02-27
+
+- Fix issue with unit boundary reuse (do at visual level instead)
+- Add option to ignore ions for inter-unit bond computation
+
+## [v3.3.0] - 2022-02-27
+
+- Fix parsing contour-level from emdb v3 header files
+- Fix invalid CSS (#376)
+- Fix "texture not renderable" & "texture not bound" warnings (#319)
+- Fix visual for bonds between two aromatic rings
+- Fix visual for delocalized bonds (parsed from mmcif and mol2)
+- Fix ring computation algorithm
+- Add ``UnitResonance`` property with info about delocalized triplets
+- Resolve marking in main renderer loop to improve overall performance
+- Use ``throttleTime`` instead of ``debounceTime`` in sequence viewer for better responsiveness
+- Change line geometry default ``scaleFactor`` to 2 (3 is too big after fixing line rendering)
+- Trajectory animation performance improvements
+    - Reuse ``Model.CoarseGrained`` for coordinate trajectories
+    - Avoid calculating ``InterUnitBonds`` when ``Structure.parent`` ones are empty
+    - Reuse unit boundary if sphere has not changed too much
+    - Don't show 'inter-bond' and 'element-cross' visuals in line representations of polymerAndLigand preset
+- Fix additional mononucleotides detected as polymer components
+- Fix and improve ``canRemap`` handling in ``IntraUnitBonds``
+- Reuse occlusion for secondary passes during multi-sampling
+- Check if marking passes are needed before doing them
+- Add ``resolutionScale`` parameter to allow trading quality of occlusion for performance
+
+## [v3.2.0] - 2022-02-17
+
+- Rename "best database mapping" to "SIFTS Mapping"
+- Add schema and export support for ``atom_site.pdbx_sifts_xref_*`` fields
+- Add schema export support for ``atom_site.pdbx_label_index`` field
+- Add `traceOnly` parameter to chain/UniProt-based structure alignment
+- Store ``IndexPairBonds`` as a dynamic property.
+
+## [v3.1.0] - 2022-02-06
+
+- Fix ``xrayShaded`` & ``ignoreLight`` params not working at the same time
+- Add ``ignoreLight`` to component params
+- Tweaks for cleaner default representation style
+    - Cartoon: use ``nucleotide-ring`` instead of ``nucleotide-block``
+    - Focus: use ``xrayShaded`` instead of opacity; adjust target size; don't show non-covalent interactions twice
+- Fix representation preset side effects (changing post-processing parameters, see #363)
+- Add Quick Styles panel (default, illustrative, stylized)
+- Fix exported structure missing secondary-structure categories (#364)
+- Fix volume streaming error message: distinguish between missing data and server error (#364)
+
+## [v3.0.2] - 2022-01-30
+
+- Fix color smoothing of elongated structures (by fixing ``Sphere.expand`` for spheres with highly directional extrema)
+- Fix entity label not displayed when multiple instances of the same entity are highlighted
+- Fix empty elements created in ``StructureElement.Loci.extendToAllInstances``
+- Measurement options tweaks (allow larger ``textSize``; make ``customText`` essential)
+- Fix visual visibility sync edge case when changing state snapshots
+
+## [v3.0.1] - 2022-01-27
+
+- Fix marking pass not working with ``transparentBackground``
+- Fix pdbe xray maps url not https
+- Fix entity-id color theme broken for non-IHM models
+- Improve/fix marking of ``InteractionsInterUnitVisual`` (mark when all contact-feature members are given)
+- Add missing "entity-id" and "enity-source" options for carbon coloring to "element-symbol" color theme
+- Fix VolumeServer/query CLI
+- Support automatic iso-value adjustment for VolumeServer data in ``Viewer.loadVolumeFromUrl``
+- Emit drag event whenever started within viewport (not only for non-empty loci)
+
+## [v3.0.0] - 2022-01-23
+
+- Assembly handling tweaks:
+    - Do not include suffix for "identity assembly operators"
+    - Do not include assembly-related categories to export if the structure was composed from an assembly
+    - Special case for ``structAsymMap`` if Mol* asym id operator mapping is present
+- Support for opening ZIP files with multiple entries
+- Add Model Export extension
+- Bugfix: Automatically treat empty string as "non-present" value in BinaryCIF writer.
+- Fix coarse model support in entity-id color theme
+- Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
+- Add custom colors to "element-symbol", "molecule-type", "residue-name", and "secondary-structure" themes
+- Support/bugfixes for ``atom_site.pdbx_sifts_xref`` categories
+- Improve/fix marking of ``InteractionsIntraUnitVisual`` (mark when all contact-feature members are given)
+
 ## [v3.0.0-dev.10] - 2022-01-17
 
 - Fix ``getOperatorsForIndex``
@@ -19,7 +350,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add "camera rock" state animation
 - Add support for custom colors to "molecule-type" theme
 - [Breaking] Add style parameter to "illustrative" color theme
-    - Defaults to "entity-id" style instad of "chain-id"
+    - Defaults to "entity-id" style instead of "chain-id"
 - Add "illustrative" representation preset
 
 ## [v3.0.0-dev.9] - 2022-01-09

CITATION.cff

@@ -0,0 +1,72 @@
+cff-version: 1.2.0
+title: >-
+  Mol* library
+message: >-
+  Please cite this software using the metadata from
+  'preferred-citation'.
+authors:
+  - given-names: Alexander S
+    family-names: Rose
+    orcid: 'https://orcid.org/0000-0002-0893-5551'
+  - given-names: David
+    family-names: Sehnal
+    orcid: 'https://orcid.org/0000-0002-0682-3089'
+  - given-names: Sebastian
+    family-names: Bittrich
+    orcid: 'https://orcid.org/0000-0003-3576-0387'
+  - given-names: Áron Samuel
+    family-names: Kovács
+  - given-names: Ludovic
+    family-names: Autin
+    orcid: 'https://orcid.org/0000-0002-2197-191X'
+  - given-names: Michal
+    family-names: Malý
+  - given-names: Jiří
+    family-names: Černý
+  - given-names: Panagiotis
+    family-names: Tourlas
+type: software
+doi: 10.5281/zenodo.3947306
+preferred-citation:
+  authors:
+    - given-names: David
+      family-names: Sehnal
+      orcid: 'https://orcid.org/0000-0002-0682-3089'
+    - given-names: Sebastian
+      family-names: Bittrich
+      orcid: 'https://orcid.org/0000-0003-3576-0387'
+    - given-names: Mandar
+      family-names: Deshpande
+      orcid: 'https://orcid.org/0000-0002-9043-7665'
+    - given-names: Radka
+      family-names: Svobodová
+      orcid: 'https://orcid.org/0000-0002-3840-8760'
+    - given-names: Karel
+      family-names: Berka
+      orcid: 'https://orcid.org/0000-0001-9472-2589'
+    - given-names: Václav
+      family-names: Bazgier
+      orcid: 'https://orcid.org/0000-0003-3393-3010'
+    - given-names: Sameer
+      family-names: Velankar
+      orcid: 'https://orcid.org/0000-0002-8439-5964'
+    - given-names: Stephen K
+      family-names: Burley
+      orcid: 'https://orcid.org/0000-0002-2487-9713'
+    - given-names: Jaroslav
+      family-names: Koča
+      orcid: 'https://orcid.org/0000-0002-2780-4901'
+    - given-names: Alexander S
+      family-names: Rose
+      orcid: 'https://orcid.org/0000-0002-0893-5551'
+  title: >-
+    Mol* Viewer: modern web app for 3D visualization
+    and analysis of large biomolecular structures
+  type: article
+  doi: 10.1093/nar/gkab314
+  journal: "Nucleic Acids Research"
+  issue: W1
+  volume: 49
+  year: 2021
+  month: 7
+  pages: "W431–W437"

README.md

@@ -120,10 +120,13 @@ and navigate to `build/viewer`
 
     node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
 
+**Saccharide names**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts
 
 **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**
@@ -138,7 +141,7 @@ and navigate to `build/viewer`
 
     export NODE_PATH="lib"; node build/state-docs
 
-**Convert any CIF to BinaryCIF**
+**Convert any CIF to BinaryCIF (or vice versa)**
 
     node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
 
@@ -148,6 +151,11 @@ 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
+
 ## Development
 
 ### Installation

data/cif-field-names/mmcif-field-names.csv

@@ -24,6 +24,11 @@ atom_site.auth_asym_id
 atom_site.auth_seq_id
 atom_site.pdbx_PDB_model_num
 atom_site.ihm_model_id
+atom_site.pdbx_label_index
+atom_site.pdbx_sifts_xref_db_name
+atom_site.pdbx_sifts_xref_db_acc
+atom_site.pdbx_sifts_xref_db_num
+atom_site.pdbx_sifts_xref_db_res
 
 atom_site_anisotrop.id
 atom_site_anisotrop.U

docs/file-formats.md

@@ -0,0 +1,44 @@
+
+Support file formats and their extensions.
+
+## Structure
+
+- MMCIF and CIFCORE (mmCIF and coreCIF schemas): cif, bcif, mmcif, mcif
+- GRO: gro
+- MOL: mol
+- MOL2: mol2
+- PDB/PDBQT: pdb, ent, pdbqt
+- SDF: sdf, sd
+- XYZ: xyz
+
+
+## Topology
+
+Need to be loaded together with Coordinates.
+
+- PRMTOP: prmtop, parm7
+- PSF: psf
+- TOP: top
+
+## Coordinates
+
+Need to be loaded together with a Structure or Topology.
+
+- DCD: dcd
+- NCTRAJ: nc, nctraj
+- TRR: trr
+- XTC: xtc
+
+
+## Volume
+
+- CCP4/MRC/MAP: ccp4, mrc, map
+- CUBE (may include a Structure): cub, cube
+- DSN6/BRIX: dsn6, brix
+- DX and DXBIN: dx, dxbin
+- DSCIF (DensityServer CIF schema): cif, bcif
+
+
+## Shape
+
+- PLY

docs/interesting-pdb-entries.md

@@ -13,6 +13,7 @@
     * DZ has C1 instead of N1 (e.g. 6I4N)
     * DP has N5 instead of C5 and C7 instead of N7 (e.g. 6I4N)
 * Beta & Gamma peptides (e.g. 1GAC, 6PQF)
+* Helices of D-amino acids (e.g. 7QDI)
 * Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
 * Polymers with residues with missing trace atoms (e.g. 2QFJ)
 * Modified RNA bases (1y26, 5L4O)
@@ -34,6 +35,14 @@
     * ACE (many, e.g. 5AGU, 1E1X)
     * ACY in 7ABY
     * NH2 (many, e.g. 6Y13)
+* Ligands with many rings
+    * STU (e.g. 1U59) - many fused rings
+    * HT (e.g. 127D) - rings connected by a single bond
+    * J2C (e.g. 7EFJ) - rings connected by a single atom
+    * RBF (e.g. 7QF2) - three linearly fused rings
+    * TA1 (e.g. 1JFF) - many fused rings (incl. a 8-member rings)
+    * BPA (e.g. 1JDG) - many fused rings
+    * CLR (e.g. 3GKI) - four fused rings
 
 Assembly symmetries
 * 5M30 (Assembly 1, C3 local and pseudo)

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.0-dev.10",
+  "version": "3.25.0",
   "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 run lint && jest",
+    "test": "npm install --no-save \"gl@^5.0.0\" && 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",
@@ -87,77 +89,79 @@
     "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>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.3.1",
-    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.2",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.3",
-    "@graphql-codegen/typescript-operations": "^2.2.2",
+    "@graphql-codegen/add": "^3.2.1",
+    "@graphql-codegen/cli": "^2.13.11",
+    "@graphql-codegen/time": "^3.2.1",
+    "@graphql-codegen/typescript": "^2.8.1",
+    "@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
+    "@graphql-codegen/typescript-graphql-request": "^4.5.8",
+    "@graphql-codegen/typescript-operations": "^2.5.6",
     "@types/cors": "^2.8.12",
-    "@types/gl": "^4.1.0",
-    "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.9.1",
-    "@typescript-eslint/parser": "^5.9.1",
+    "@types/gl": "^6.0.1",
+    "@types/jest": "^29.2.2",
+    "@types/react": "^18.0.25",
+    "@types/react-dom": "^18.0.8",
+    "@typescript-eslint/eslint-plugin": "^5.42.1",
+    "@typescript-eslint/parser": "^5.42.1",
     "benchmark": "^2.1.4",
-    "concurrently": "^7.0.0",
-    "cpx2": "^4.1.2",
+    "concurrently": "^7.5.0",
+    "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.5.1",
-    "eslint": "^8.7.0",
+    "css-loader": "^6.7.2",
+    "eslint": "^8.27.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
-    "fs-extra": "^10.0.0",
-    "graphql": "^16.2.0",
-    "http-server": "^14.1.0",
-    "jest": "^27.4.7",
-    "mini-css-extract-plugin": "~2.4.7",
+    "fs-extra": "^10.1.0",
+    "graphql": "^16.6.0",
+    "http-server": "^14.1.1",
+    "jest": "^29.3.1",
+    "mini-css-extract-plugin": "^2.6.1",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass": "^1.48.0",
-    "sass-loader": "^12.4.0",
-    "simple-git": "^2.48.0",
+    "react": "^18.2.0",
+    "react-dom": "^18.2.0",
+    "sass": "^1.56.1",
+    "sass-loader": "^13.2.0",
+    "simple-git": "^3.15.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.4",
-    "webpack": "^5.66.0",
-    "webpack-cli": "^4.9.1"
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.8.4",
+    "webpack": "^5.75.0",
+    "webpack-cli": "^4.10.0"
   },
   "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": "^16.11.19",
-    "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.38",
-    "@types/react-dom": "^17.0.11",
+    "@types/express": "^4.17.14",
+    "@types/node": "^16.18.3",
+    "@types/node-fetch": "^2.6.2",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
-    "body-parser": "^1.19.1",
+    "body-parser": "^1.20.1",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.17.2",
+    "express": "^4.18.2",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.12",
-    "immutable": "^4.0.0",
-    "node-fetch": "^2.6.2",
-    "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.1.3",
-    "tslib": "^2.3.1",
+    "immer": "^9.0.16",
+    "immutable": "^4.1.0",
+    "node-fetch": "^2.6.7",
+    "rxjs": "^7.5.7",
+    "swagger-ui-dist": "^4.15.5",
+    "tslib": "^2.4.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"
   },
   "peerDependencies": {
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2"
-  },
-  "optionalDependencies": {
-    "gl": "^5.0.0"
+    "react": "^18.1.0 || ^17.0.2 || ^16.14.0",
+    "react-dom": "^18.1.0 || ^17.0.2 || ^16.14.0"
   }
 }

src/apps/docking-viewer/index.ts

@@ -8,7 +8,7 @@
 import { Structure } from '../../mol-model/structure';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
@@ -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>
  */
@@ -44,10 +44,11 @@ function occlusionStyle(plugin: PluginContext) {
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'on', params: {
-                samples: 64,
-                radius: 8,
-                bias: 1.0,
-                blurKernelSize: 13
+                bias: 0.8,
+                blurKernelSize: 15,
+                radius: 5,
+                samples: 32,
+                resolutionScale: 1
             } },
             outline: { name: 'on', params: {
                 scale: 1.0,
@@ -201,14 +202,14 @@ 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

@@ -13,22 +13,26 @@ 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';
 import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { ZenodoImport } from '../../extensions/zenodo';
+import { Volume } from '../../mol-model/volume';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
 import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -41,15 +45,18 @@ 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 } from '../../mol-util/debug';
 
 const CustomFormats = [
     ['g3d', G3dProvider] as const
 ];
 
 const Extensions = {
+    'backgrounds': PluginSpec.Behavior(Backgrounds),
     'cellpack': PluginSpec.Behavior(CellPack),
     'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
     'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
@@ -57,9 +64,11 @@ const Extensions = {
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
     'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
     'g3d': PluginSpec.Behavior(G3DFormat),
+    'model-export': PluginSpec.Behavior(ModelExport),
     'mp4-export': PluginSpec.Behavior(Mp4Export),
     'geo-export': PluginSpec.Behavior(GeometryExport),
     'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+    'zenodo-import': PluginSpec.Behavior(ZenodoImport),
 };
 
 const DefaultViewerOptions = {
@@ -79,18 +88,22 @@ 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,
 
     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,
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 
@@ -99,7 +112,14 @@ export class Viewer {
     }
 
     static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
+        const definedOptions = {} as any;
+        // filter for defined properies only so the default values
+        // are property applied
+        for (const p of Object.keys(options) as (keyof ViewerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
         const defaultSpec = DefaultPluginUISpec();
 
         const spec: PluginUISpec = {
@@ -140,12 +160,15 @@ 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.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],
@@ -153,6 +176,7 @@ export class Viewer {
                 [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                 [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
+                [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
             ]
         };
 
@@ -179,7 +203,7 @@ 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: {
@@ -188,6 +212,7 @@ 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 },
                 }
             }
@@ -357,11 +382,13 @@ export class Viewer {
 
             const repr = plugin.build();
             for (const iso of isovalues) {
+                const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume;
+                const volumeData = volume.cell!.obj!.data;
                 repr
-                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                    .to(volume)
                     .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
                         type: 'isosurface',
-                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
                         color: 'uniform',
                         colorParams: { value: iso.color }
                     }));
@@ -382,7 +409,7 @@ 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'
@@ -400,14 +427,12 @@ 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, {
@@ -441,11 +466,11 @@ export interface VolumeIsovalueInfo {
 export interface LoadTrajectoryParams {
     model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
     | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
-    | { kind: 'topology-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    | { kind: 'topology-url', url: string, format: BuiltInTopologyFormat, isBinary?: boolean }
+    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInTopologyFormat },
     modelLabel?: string,
-    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    coordinates: { kind: 'coordinates-url', url: string, format: BuiltInCoordinatesFormat, isBinary?: boolean }
+    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInCoordinatesFormat },
     coordinatesLabel?: string,
     preset?: keyof PresetTrajectoryHierarchy
 }
@@ -476,4 +501,4 @@ 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 +60,9 @@
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').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';
 
             molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
@@ -71,8 +76,10 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: !disableWboit,
+                enableWboit: (disableWboit || enableDpoit) ? false : void 0, // use default value if disable-wboit is not set
+                enableDpoit: enableDpoit ? true : void 0,
                 preferWebgl1: preferWebgl1,
+                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();
                 if (snapshotId) viewer.setRemoteSnapshot(snapshotId);

src/apps/viewer/index.ts

@@ -9,4 +9,4 @@ import './embedded.html';
 import './favicon.ico';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
-export * from './app';
+export * from './app';

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

@@ -1,8 +1,9 @@
 #!/usr/bin/env node
 /**
- * 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 Josh McMenemy <josh.mcmenemy@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import * as argparse from 'argparse';
@@ -14,7 +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[] = [];
@@ -31,11 +32,11 @@ function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
 
 function writeIonNamesFile(filePath: string, ionNames: string[]) {
     const output = `/**
- * 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.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
- * @author molstar/chem-comp-dict/create-table cli
+ * @author molstar/chem-comp-dict/create-ions cli
  */
 
 export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
@@ -43,8 +44,8 @@ export const IonNames = new Set(${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))) {
@@ -64,10 +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

@@ -0,0 +1,82 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+const writeFile = util.promisify(fs.writeFile);
+
+import { DatabaseCollection } from '../../mol-data/db';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { DefaultDataOptions, ensureDataAvailable, readCCD } from './util';
+
+function extractSaccharideNames(ccd: DatabaseCollection<CCD_Schema>) {
+    const saccharideNames: string[] = [];
+    for (const k in ccd) {
+        const { chem_comp } = ccd[k];
+        const type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push(
+        'UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+        'SQD', // SULFOQUINOVOSYLDIACYLGLYCEROL, via GlyFinder
+    );
+    return saccharideNames;
+}
+
+function writeSaccharideNamesFile(filePath: string, ionNames: string[]) {
+    const output = `/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+
+export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+    writeFile(filePath, output);
+}
+
+async function run(out: string, options = DefaultDataOptions) {
+    await ensureDataAvailable(options);
+    const ccd = await readCCD();
+    const saccharideNames = extractSaccharideNames(ccd);
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeSaccharideNamesFile(out, saccharideNames);
+}
+
+const parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+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, { 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/cif2bcif/converter.ts

@@ -71,7 +71,7 @@ function classify(name: string, field: CifField): CifWriter.Field {
 }
 
 export function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
-    return Task.create<Uint8Array>('BinaryCIF', async ctx => {
+    return Task.create<Uint8Array>('Convert CIF', async ctx => {
         const encodingProvider: BinaryEncodingProvider = hints
             ? CifWriter.createEncodingProviderFromJsonConfig(hints)
             : { get: (c, f) => void 0 };

src/cli/cif2bcif/index.ts

@@ -18,7 +18,7 @@ async function process(srcPath: string, outPath: string, configPath?: string, fi
     const config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
     const filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
 
-    const res = await convert(srcPath, false, config, filter);
+    const res = await convert(srcPath, srcPath.toLowerCase().indexOf('.bcif') > 0, config, filter);
     await write(outPath, res);
 }
 
@@ -38,13 +38,13 @@ function run(args: Args) {
 
 const parser = new argparse.ArgumentParser({
     add_help: true,
-    description: 'Convert any CIF file to a BCIF file'
+    description: 'Convert any BCIF file to a CIF file or vice versa'
 });
 parser.add_argument('src', {
-    help: 'Source CIF path'
+    help: 'Source file path'
 });
 parser.add_argument('out', {
-    help: 'Output BCIF path'
+    help: 'Output file path'
 });
 parser.add_argument('-c', '--config', {
     help: 'Optional encoding strategy/precision config path',

src/cli/cifschema/index.ts

@@ -161,7 +161,7 @@ const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.
 const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`;
 const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
 const MA_DIC_PATH = `${DIC_DIR}/ma-extension.dic`;
-const MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/MA-dictionary/master/mmcif_ma.dic';
+const MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic';
 
 const CIF_CORE_DIC_PATH = `${DIC_DIR}/cif_core.dic`;
 const CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -13,15 +13,17 @@ export function getFieldType(type: string, description: string, values?: string[
     switch (type) {
         // mmCIF
         case 'code':
-        case 'ucode':
         case 'line':
-        case 'uline':
         case 'text':
         case 'char':
-        case 'uchar3':
-        case 'uchar1':
         case 'boolean':
             return values && values.length ? EnumCol(values, 'str', description) : StrCol(description);
+        case 'ucode':
+        case 'uline':
+        case 'uchar3':
+        case 'uchar1':
+            // only force lower-case for enums
+            return values && values.length ? EnumCol(values.map(x => x.toLowerCase()), 'lstr', description) : StrCol(description);
         case 'aliasname':
         case 'name':
         case 'idname':
@@ -49,6 +51,7 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'operation_expression':
         case 'point_symmetry':
         case '4x3_matrix':
+        case '3x4_matrix':
         case '3x4_matrices':
         case 'point_group':
         case 'point_group_helical':
@@ -68,6 +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);

src/cli/cifschema/util/generate.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,7 +10,7 @@ import { FieldPath } from '../../../mol-io/reader/cif/schema';
 
 function header(name: string, info: string, moldataImportPath: string) {
     return `/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated '${name}' schema file. ${info}
  *
@@ -35,13 +35,17 @@ function getTypeShorthands(schema: Database, fields?: Filter) {
         const { columns } = schema.tables[table];
         Object.keys(columns).forEach(columnName => {
             if (fields && !fields[table][columnName]) return;
-            types.add(schema.tables[table].columns[columnName].type);
+            const col = schema.tables[table].columns[columnName];
+            if (col.type === 'enum') types.add(col.subType);
+            types.add(col.type);
         });
     });
     const shorthands: string[] = [];
     types.forEach(type => {
         switch (type) {
             case 'str': shorthands.push('const str = Schema.str;'); break;
+            case 'ustr': shorthands.push('const ustr = Schema.ustr;'); break;
+            case 'lstr': shorthands.push('const lstr = Schema.lstr;'); break;
             case 'int': shorthands.push('const int = Schema.int;'); break;
             case 'float': shorthands.push('const float = Schema.float;'); break;
             case 'coord': shorthands.push('const coord = Schema.coord;'); break;

src/cli/cifschema/util/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -29,8 +29,8 @@ export function FloatCol(description: string): FloatCol { return { type: 'float'
 export type CoordCol = { type: 'coord' } & BaseCol
 export function CoordCol(description: string): CoordCol { return { type: 'coord', description }; }
 
-export type EnumCol = { type: 'enum', subType: 'int' | 'str', values: string[] } & BaseCol
-export function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol {
+export type EnumCol = { type: 'enum', subType: 'int' | 'str' | 'ustr' | 'lstr', values: string[] } & BaseCol
+export function EnumCol(values: string[], subType: 'int' | 'str' | 'ustr' | 'lstr', description: string): EnumCol {
     return { type: 'enum', description, values, subType };
 }
 

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>
  */
@@ -11,7 +11,7 @@ import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-f
 import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
 import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -25,6 +25,8 @@ import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
 
+import { setDebugMode, setTimingMode } from '../../mol-util/debug';
+
 interface DemoInput {
     moleculeSdf: string,
     basis: Basis,
@@ -218,4 +220,6 @@ 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;

src/examples/basic-wrapper/index.ts

@@ -9,7 +9,7 @@ import { EmptyLoci } from '../../mol-model/loci';
 import { StructureSelection } from '../../mol-model/structure';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';

src/examples/lighting/index.ts

@@ -6,7 +6,7 @@
 
 import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -24,7 +24,7 @@ const Canvas3DPresets = {
     illustrative: {
         canvas3d: <Preset>{
             postprocessing: {
-                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                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) } }
             },
             renderer: {
@@ -36,7 +36,7 @@ const Canvas3DPresets = {
     occlusion: {
         canvas3d: <Preset>{
             postprocessing: {
-                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
                 outline: { name: 'off', params: {} }
             },
             renderer: {

src/examples/proteopedia-wrapper/index.ts

@@ -10,7 +10,7 @@ import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/mod
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';

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/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';
@@ -22,10 +22,6 @@ 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';
@@ -141,7 +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);
@@ -150,7 +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;
@@ -213,110 +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 models = await createModels(format.data.db, 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') {
@@ -337,7 +233,7 @@ 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;
@@ -361,7 +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);
                     }
@@ -375,7 +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);
                 }
             }
@@ -519,6 +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);
@@ -535,6 +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);
@@ -618,6 +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);
@@ -669,7 +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>
@@ -679,5 +579,43 @@ 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,
+            showHydrogens: false,
+        });
+        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,
+                    }
+                },
+                outline: {
+                    name: 'on',
+                    params: {
+                        scale: 1,
+                        threshold: 0.33,
+                        color: ColorNames.black,
+                    }
+                }
+            }
+        });
+    }
     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/confal-pyramids/behavior.ts

@@ -8,7 +8,7 @@
 import { ConfalPyramidsColorThemeProvider } from './color';
 import { ConfalPyramids, ConfalPyramidsProvider } from './property';
 import { ConfalPyramidsRepresentationProvider } from './representation';
-import { Loci } from '../../../mol-model/loci';
+import { ConfalPyramidsTypes } from './types';
 import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
 import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
 import { StateObjectRef } from '../../../mol-state';
@@ -56,21 +56,10 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
         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);
@@ -88,7 +77,6 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
 
         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);
@@ -101,3 +89,13 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
         showToolTip: PD.Boolean(true)
     })
 });
+
+export function confalPyramidLabel(halfPyramid: ConfalPyramidsTypes.HalfPyramid) {
+    const { step } = halfPyramid;
+    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

@@ -11,149 +11,248 @@ 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 } from '../../../mol-util/color';
+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 { iterableToArray } from '../../../mol-data/util';
+import { ObjectKeys } from '../../../mol-util/type-helpers';
 
-const DefaultColor = Color(0xCCCCCC);
 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);
 
-type ConformerClasses = 'A' | 'B' | 'BII' | 'miB' | 'Z' | 'IC' | 'OPN' | 'SYN' | 'N';
+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,
+});
+type PyramidsColors = typeof PyramidsColors;
 
-const ColorMapping: ReadonlyMap<ConformerClasses, Color> = new Map([
-    ['A', Color(0xFFC1C1)],
-    ['B', Color(0xC8CFFF)],
-    ['BII', Color(0x0059DA)],
-    ['miB', Color(0x3BE8FB)],
-    ['Z', Color(0x01F60E)],
-    ['IC', Color(0xFA5CFB)],
-    ['OPN', Color(0xE90000)],
-    ['SYN', Color(0xFFFF01)],
-    ['N', Color(0xF2F2F2)],
-]);
+export const ConfalPyramidsColorThemeParams = {
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(PyramidsColors))
+    }),
+};
+export type ConfalPyramidsColorThemeParams = typeof ConfalPyramidsColorThemeParams;
 
-const NtCToClasses: ReadonlyMap<string, [ConformerClasses, ConformerClasses]> = new Map([
-    ['NANT', ['N', 'N']],
-    ['AA00', ['A', 'A']],
-    ['AA02', ['A', 'A']],
-    ['AA03', ['A', 'A']],
-    ['AA04', ['A', 'A']],
-    ['AA08', ['A', 'A']],
-    ['AA09', ['A', 'A']],
-    ['AA01', ['A', 'A']],
-    ['AA05', ['A', 'A']],
-    ['AA06', ['A', 'A']],
-    ['AA10', ['A', 'A']],
-    ['AA11', ['A', 'A']],
-    ['AA07', ['A', 'A']],
-    ['AA12', ['A', 'A']],
-    ['AA13', ['A', 'A']],
-    ['AB01', ['A', 'B']],
-    ['AB02', ['A', 'B']],
-    ['AB03', ['A', 'B']],
-    ['AB04', ['A', 'B']],
-    ['AB05', ['A', 'B']],
-    ['BA01', ['B', 'A']],
-    ['BA05', ['B', 'A']],
-    ['BA09', ['B', 'A']],
-    ['BA08', ['BII', 'A']],
-    ['BA10', ['B', 'A']],
-    ['BA13', ['BII', 'A']],
-    ['BA16', ['BII', 'A']],
-    ['BA17', ['BII', 'A']],
-    ['BB00', ['B', 'B']],
-    ['BB01', ['B', 'B']],
-    ['BB17', ['B', 'B']],
-    ['BB02', ['B', 'B']],
-    ['BB03', ['B', 'B']],
-    ['BB11', ['B', 'B']],
-    ['BB16', ['B', 'B']],
-    ['BB04', ['B', 'BII']],
-    ['BB05', ['B', 'BII']],
-    ['BB07', ['BII', 'BII']],
-    ['BB08', ['BII', 'BII']],
-    ['BB10', ['miB', 'miB']],
-    ['BB12', ['miB', 'miB']],
-    ['BB13', ['miB', 'miB']],
-    ['BB14', ['miB', 'miB']],
-    ['BB15', ['miB', 'miB']],
-    ['BB20', ['miB', 'miB']],
-    ['IC01', ['IC', 'IC']],
-    ['IC02', ['IC', 'IC']],
-    ['IC03', ['IC', 'IC']],
-    ['IC04', ['IC', 'IC']],
-    ['IC05', ['IC', 'IC']],
-    ['IC06', ['IC', 'IC']],
-    ['IC07', ['IC', 'IC']],
-    ['OP01', ['OPN', 'OPN']],
-    ['OP02', ['OPN', 'OPN']],
-    ['OP03', ['OPN', 'OPN']],
-    ['OP04', ['OPN', 'OPN']],
-    ['OP05', ['OPN', 'OPN']],
-    ['OP06', ['OPN', 'OPN']],
-    ['OP07', ['OPN', 'OPN']],
-    ['OP08', ['OPN', 'OPN']],
-    ['OP09', ['OPN', 'OPN']],
-    ['OP10', ['OPN', 'OPN']],
-    ['OP11', ['OPN', 'OPN']],
-    ['OP12', ['OPN', 'OPN']],
-    ['OP13', ['OPN', 'OPN']],
-    ['OP14', ['OPN', 'OPN']],
-    ['OP15', ['OPN', 'OPN']],
-    ['OP16', ['OPN', 'OPN']],
-    ['OP17', ['OPN', 'OPN']],
-    ['OP18', ['OPN', 'OPN']],
-    ['OP19', ['OPN', 'OPN']],
-    ['OP20', ['OPN', 'OPN']],
-    ['OP21', ['OPN', 'OPN']],
-    ['OP22', ['OPN', 'OPN']],
-    ['OP23', ['OPN', 'OPN']],
-    ['OP24', ['OPN', 'OPN']],
-    ['OP25', ['OPN', 'OPN']],
-    ['OP26', ['OPN', 'OPN']],
-    ['OP27', ['OPN', 'OPN']],
-    ['OP28', ['OPN', 'OPN']],
-    ['OP29', ['OPN', 'OPN']],
-    ['OP30', ['OPN', 'OPN']],
-    ['OP31', ['OPN', 'OPN']],
-    ['OPS1', ['OPN', 'OPN']],
-    ['OP1S', ['OPN', 'SYN']],
-    ['AAS1', ['SYN', 'A']],
-    ['AB1S', ['A', 'SYN']],
-    ['AB2S', ['A', 'SYN']],
-    ['BB1S', ['B', 'SYN']],
-    ['BB2S', ['B', 'SYN']],
-    ['BBS1', ['SYN', 'B']],
-    ['ZZ01', ['Z', 'Z']],
-    ['ZZ02', ['Z', 'Z']],
-    ['ZZ1S', ['Z', 'SYN']],
-    ['ZZ2S', ['Z', 'SYN']],
-    ['ZZS1', ['SYN', 'Z']],
-    ['ZZS2', ['SYN', 'Z']],
-]);
-
-function getConformerColor(ntc: string, useLower: boolean): Color {
-    const item = NtCToClasses.get(ntc);
-    if (!item) return ErrorColor;
-    return ColorMapping.get(useLower ? item[1] : item[0]) ?? ErrorColor;
-}
-
-export const ConfalPyramidsColorThemeParams = {};
-export type ConfalPyramidsColorThemeParams = typeof ConfalPyramidsColorThemeParams
 export function getConfalPyramidsColorThemeParams(ctx: ThemeDataContext) {
-    return ConfalPyramidsColorThemeParams; // TODO return copy
+    return PD.clone(ConfalPyramidsColorThemeParams);
 }
 
 export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values<ConfalPyramidsColorThemeParams>): ColorTheme<ConfalPyramidsColorThemeParams> {
+    const colorMap = props.colors.name === 'default' ? PyramidsColors : props.colors.params;
+
     function color(location: Location, isSecondary: boolean): Color {
         if (CPT.isLocation(location)) {
-            const { pyramid, isLower } = location.data;
-            return getConformerColor(pyramid.NtC, isLower);
+            const { step, isLower } = location.data;
+            const key = step.NtC + `_${isLower ? 'Lwr' : 'Upr'}` as keyof PyramidsColors;
+            return colorMap[key] ?? ErrorColor;
         }
 
-        return DefaultColor;
+        return ErrorColor;
     }
 
     return {
@@ -162,12 +261,7 @@ export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values
         color,
         props,
         description: Description,
-        legend: TableLegend(iterableToArray(ColorMapping.entries()).map(([conformer, color]) => {
-            return [conformer, color] as [string, Color];
-        }).concat([
-            ['Error', ErrorColor],
-            ['Unknown', DefaultColor]
-        ]))
+        legend: TableLegend(ObjectKeys(colorMap).map(k => [k.replace('_', ' '), colorMap[k]] as [string, Color]).concat([['Error', ErrorColor]])),
     };
 }
 

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

@@ -16,7 +16,7 @@ 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 type ConfalPyramids = PropertyWrapper<CPT.Steps | undefined>;
 
 export namespace ConfalPyramids {
     export const Schema = {
@@ -105,36 +105,42 @@ export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramids
 
 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;
+function createPyramidsFromCif(
+    model: Model,
+    cifSteps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
+    stepsSummary: StepsSummaryTable
+): CPT.Steps {
+    const steps = new Array<CPT.Step>();
+    const mapping = new Array<CPT.MappedChains>();
 
     const {
         id, PDB_model_number, name,
         auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
         auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
-        _rowCount } = steps;
+        _rowCount
+    } = cifSteps;
 
     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;
-            continue; // We are only interested in data for the current model
-        }
+        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;
 
-        const { _NtC, _confal_score } = getNtCAndConfalScore(id.value(i), i, stepsSummary);
+        if (mapping.length <= modelIdx || !mapping[modelIdx])
+            mapping[modelIdx] = new Map<string, CPT.MappedResidues>();
 
-        const pyramid = {
-            PDB_model_number: model_num,
+        const step = {
+            PDB_model_number: modelNum,
             name: name.value(i),
-            auth_asym_id_1: auth_asym_id_1.value(i),
-            auth_seq_id_1: auth_seq_id_1.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),
@@ -143,30 +149,41 @@ function createPyramidsFromCif(model: Model,
             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
+            confal_score,
+            NtC,
+            rmsd,
         };
 
-        pyramids.push(pyramid);
-        names.set(pyramid.name, pyramids.length - 1);
+        steps.push(step);
 
-        locations.push(CPT.Location(pyramid, false));
-        locations.push(CPT.Location(pyramid, true));
+        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 { pyramids, names, locations, hasMultipleModels };
+    return { steps, mapping };
 }
 
-function getNtCAndConfalScore(id: number, i: number, stepsSummary: StepsSummaryTable) {
-    const { step_id, confal_score, assigned_NtC } = stepsSummary;
+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) };
+        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) };
+        if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
     }
     throw new Error('Inconsistent mmCIF data');
 }

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

@@ -6,7 +6,7 @@
  */
 
 import { ConfalPyramids, ConfalPyramidsProvider } from './property';
-import { ConfalPyramidsUtil } from './util';
+import { ConfalPyramidsIterator } from './util';
 import { ConfalPyramidsTypes as CPT } from './types';
 import { Interval } from '../../../mol-data/int';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
@@ -16,14 +16,14 @@ 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 +32,12 @@ 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 +59,76 @@ 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();
 
-        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 +142,17 @@ 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
+    const step = data.steps[idx];
+
+    return CPT.Loci({ step, isLower: groupId % 2 === 1 }, [{}]);
 }
 
 function eachConfalPyramid(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {

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

@@ -6,10 +6,13 @@
  */
 
 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 = {
+    export const DataTag = 'dnatco-confal-half-pyramid';
+
+    export type Step = {
         PDB_model_number: number,
         name: string,
         auth_asym_id_1: string,
@@ -23,38 +26,40 @@ export namespace ConfalPyramidsTypes {
         label_alt_id_2: string,
         PDB_ins_code_2: string,
         confal_score: number,
-        NtC: string
+        NtC: string,
+        rmsd: number,
     }
 
-    export interface PyramidsData {
-        pyramids: Array<Pyramid>,
-        names: Map<string, number>,
-        locations: Array<Location>,
-        hasMultipleModels: boolean
+    export type MappedChains = Map<string, MappedResidues>;
+    export type MappedResidues = Map<number, number[]>;
+
+    export interface Steps {
+        steps: Array<Step>,
+        mapping: MappedChains[],
     }
 
-    export interface LocationData {
-        readonly pyramid: Pyramid
-        readonly isLower: boolean;
+    export interface HalfPyramid {
+        step: Step,
+        isLower: boolean,
     }
 
-    export interface Element {
-        structure: Structure;
-        unit: Unit.Atomic;
-        element: ElementIndex;
-    }
+    export interface Location extends DataLocation<HalfPyramid, {}> {}
 
-    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: Step, isLower: boolean) {
+        return DataLocation(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 === DataTag;
     }
 
-    export function toElementLocation(location: Location) {
-        return StructureElement.Location.create(location.element.structure, location.element.unit, location.element.element);
+    export interface Loci extends DataLoci<HalfPyramid, {}> {}
+
+    export function Loci(data: HalfPyramid, elements: ReadonlyArray<{}>): Loci {
+        return DataLoci(DataTag, data, elements, undefined, () => confalPyramidLabel(data));
+    }
+
+    export function isLoci(x: any): x is Loci {
+        return !!x && x.kind === 'data-loci' && x.tag === DataTag;
     }
 }

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

@@ -7,293 +7,121 @@
 
 import { ConfalPyramidsProvider } from './property';
 import { ConfalPyramidsTypes as CPT } from './types';
-import { OrderedSet, Segmentation } from '../../../mol-data/int';
-import { Vec3 } from '../../../mol-math/linear-algebra';
+import { Segmentation } from '../../../mol-data/int';
 import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../../mol-model/structure';
 
-export namespace ConfalPyramidsUtil {
-    type Residue = Segmentation.Segment<ResidueIndex>;
+type Residue = Segmentation.Segment<ResidueIndex>;
 
-    export type AtomInfo = {
-        pos: Vec3,
-        index: ElementIndex,
-        fakeAltId: string,
-    };
+export type Pyramid = {
+    O3: ElementIndex,
+    P: ElementIndex,
+    OP1: ElementIndex,
+    OP2: ElementIndex,
+    O5: ElementIndex,
+    confalScore: number,
+    stepIdx: number,
+};
 
-    export type FirstResidueAtoms = {
-        O3: AtomInfo,
-    };
+const EmptyStepIndices = new Array<number>();
 
-    export type SecondResidueAtoms = {
-        OP1: AtomInfo,
-        OP2: AtomInfo,
-        O5: AtomInfo,
-        P: AtomInfo,
-    };
+function copyResidue(r?: Residue) {
+    return r ? { index: r.index, start: r.start, end: r.end } : void 0;
+}
 
-    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,
-    };
+function getAtomIndex(loc: StructureElement.Location, residue: Residue, names: string[], altId: string): ElementIndex {
+    for (let eI = residue.start; eI < residue.end; eI++) {
+        loc.element = loc.unit.elements[eI];
+        const elName = StructureProperties.atom.label_atom_id(loc);
+        const elAltId = StructureProperties.atom.label_alt_id(loc);
 
-    export type Handler = (pyramid: CPT.Pyramid, first: FirstResidueAtoms, second: SecondResidueAtoms, firstLocIndex: number, secondLocIndex: number) => void;
-
-    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)
-        };
+        if (names.includes(elName) && (elAltId === altId || elAltId.length === 0))
+            return loc.element;
     }
 
-    export function hasMultipleModels(unit: Unit.Atomic): boolean {
+    return -1 as ElementIndex;
+}
+
+function getPyramid(loc: StructureElement.Location, one: Residue, two: Residue, altIdOne: string, altIdTwo: string, confalScore: number, stepIdx: number): Pyramid {
+    const O3 = getAtomIndex(loc, one, ['O3\'', 'O3*'], altIdOne);
+    const P = getAtomIndex(loc, two, ['P'], altIdTwo);
+    const OP1 = getAtomIndex(loc, two, ['OP1'], altIdTwo);
+    const OP2 = getAtomIndex(loc, two, ['OP2'], altIdTwo);
+    const O5 = getAtomIndex(loc, two, ['O5\'', 'O5*'], altIdTwo);
+
+    return { O3, P, OP1, OP2, O5, confalScore, stepIdx };
+}
+
+export class ConfalPyramidsIterator {
+    private chainIt: Segmentation.SegmentIterator<ChainIndex>;
+    private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
+    private residueOne?: Residue;
+    private residueTwo: Residue;
+    private data?: CPT.Steps;
+    private loc: StructureElement.Location;
+
+    private getStepIndices(r: Residue) {
+        this.loc.element = this.loc.unit.elements[r.start];
+
+        const modelIdx = StructureProperties.unit.model_num(this.loc) - 1;
+        const chainId = StructureProperties.chain.auth_asym_id(this.loc);
+        const seqId = StructureProperties.residue.auth_seq_id(this.loc);
+
+        const chains = this.data!.mapping[modelIdx];
+        if (!chains) return EmptyStepIndices;
+        const residues = chains.get(chainId);
+        if (!residues) return EmptyStepIndices;
+        return residues.get(seqId) ?? EmptyStepIndices;
+    }
+
+    private moveStep() {
+        this.residueOne = copyResidue(this.residueTwo);
+        this.residueTwo = copyResidue(this.residueIt.move())!;
+
+        return this.toPyramids(this.residueOne!, this.residueTwo);
+    }
+
+    private toPyramids(one: Residue, two: Residue) {
+        const indices = this.getStepIndices(one);
+
+        const points = [];
+        for (const idx of indices) {
+            const step = this.data!.steps[idx];
+            points.push(getPyramid(this.loc, one, two, step.label_alt_id_1, step.label_alt_id_2, step.confal_score, idx));
+        }
+
+        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 getPossibleAltIdsIndices(eIFirst: ElementIndex, eILast: ElementIndex, structure: Structure, unit: Unit.Atomic): string[] {
-        const loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
-
-        const uIFirst = OrderedSet.indexOf(unit.elements, eIFirst);
-        const uILast = OrderedSet.indexOf(unit.elements, eILast);
-
-        const possibleAltIds: string[] = [];
-        for (let uI = uIFirst; uI <= uILast; uI++) {
-            loc.element = unit.elements[uI];
-            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;
     }
 
-    function getPossibleAltIdsResidue(residue: Residue, structure: Structure, unit: Unit.Atomic): string[] {
-        return getPossibleAltIdsIndices(unit.elements[residue.start], unit.elements[residue.end - 1], structure, unit);
-    }
-
-    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());
+            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[] {
-            let rI = residue.start;
-            const rILast = residue.end - 1;
-            const indices: ElementIndex[] = [];
-
-            for (; rI !== rILast; rI++) {
-                const eI = this.unit.elements[rI];
-                const loc = StructureElement.Location.create(this.structure, this.unit, eI);
-                const thisName = StructureProperties.atom.label_atom_id(loc);
-                if (names.includes(thisName)) indices.push(eI);
-            }
-
-            if (indices.length === 0)
-                throw new Error(`Element ${name} 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 = getPossibleAltIdsResidue(residue, this.structure, this.unit);
-            const firstAtoms = this.processFirstResidue(residue, firstPossibleAltIds);
-
-            residue = this.residueIt.move();
-
-            const secondPossibleAltIds = getPossibleAltIdsResidue(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/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/model-export/export.ts

@@ -0,0 +1,87 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { utf8ByteCount, utf8Write } from '../../mol-io/common/utf8';
+import { to_mmCIF, Unit } from '../../mol-model/structure';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { getFormattedTime } from '../../mol-util/date';
+import { download } from '../../mol-util/download';
+import { zip } from '../../mol-util/zip/zip';
+
+export async function exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
+    try {
+        await plugin.runTask(_exportHierarchy(plugin, options), { useOverlay: true });
+    } catch (e) {
+        console.error(e);
+        plugin.log.error(`Model export failed. See console for details.`);
+    }
+}
+
+function _exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
+    return Task.create('Export', async ctx => {
+        await ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false });
+
+        const format = options?.format ?? 'cif';
+        const { structures } = plugin.managers.structure.hierarchy.current;
+
+        const files: [name: string, data: string | Uint8Array][] = [];
+        const entryMap = new Map<string, number>();
+
+        for (const _s of structures) {
+            const s = _s.transform?.cell.obj?.data ?? _s.cell.obj?.data;
+            if (!s) continue;
+            if (s.models.length > 1) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`);
+                continue;
+            }
+            if (s.units.some(u => !Unit.isAtomic(u))) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`);
+                continue;
+            }
+
+            const name = entryMap.has(s.model.entryId)
+                ? `${s.model.entryId}_${entryMap.get(s.model.entryId)! + 1}.${format}`
+                : `${s.model.entryId}.${format}`;
+            entryMap.set(s.model.entryId, (entryMap.get(s.model.entryId) ?? 0) + 1);
+
+            await ctx.update({ message: `Exporting ${s.model.entryId}...`, isIndeterminate: true, canAbort: false });
+            if (s.elementCount > 100000) {
+                // Give UI chance to update, only needed for larger structures.
+                await new Promise(res => setTimeout(res, 50));
+            }
+
+            try {
+                files.push([name, to_mmCIF(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+            } catch (e) {
+                if (format === 'cif' && s.elementCount > 2000000) {
+                    plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
+                }
+                throw e;
+            }
+        }
+
+        if (files.length === 1) {
+            download(new Blob([files[0][1]]), files[0][0]);
+        } else if (files.length > 1) {
+            const zipData: Record<string, Uint8Array> = {};
+            for (const [fn, data] of files) {
+                if (data instanceof Uint8Array) {
+                    zipData[fn] = data;
+                } else {
+                    const bytes = new Uint8Array(utf8ByteCount(data));
+                    utf8Write(bytes, 0, data);
+                    zipData[fn] = bytes;
+                }
+            }
+            await ctx.update({ message: `Compressing Data...`, isIndeterminate: true, canAbort: false });
+            const buffer = await zip(ctx, zipData);
+            download(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), `structures_${getFormattedTime()}.zip`);
+        }
+
+        plugin.log.info(`[Export] Done.`);
+    });
+}

src/extensions/model-export/index.ts

@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { ModelExportUI } from './ui';
+
+export const ModelExport = PluginBehavior.create<{}>({
+    name: 'extension-model-export',
+    category: 'misc',
+    display: {
+        name: 'Model Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{}> {
+        register(): void {
+            this.ctx.customStructureControls.set('model-export', ModelExportUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customStructureControls.delete('model-export');
+        }
+    },
+    params: () => ({})
+});

src/extensions/model-export/ui.tsx

@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { useState } from 'react';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { GetAppSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { PluginContext } from '../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { exportHierarchy } from './export';
+
+export class ModelExportUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState {
+        return {
+            header: 'Export Models',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: GetAppSvg }
+        };
+    }
+    protected renderControls(): JSX.Element | null {
+        return <ExportControls plugin={this.plugin} />;
+    }
+}
+
+const Params = {
+    format: PD.Select<'cif' | 'bcif'>('cif', [['cif', 'mmCIF'], ['bcif', 'Binary mmCIF']])
+};
+const DefaultParams = PD.getDefaultValues(Params);
+
+function ExportControls({ plugin }: { plugin: PluginContext }) {
+    const [params, setParams] = useState(DefaultParams);
+    const [exporting, setExporting] = useState(false);
+    useBehavior(plugin.managers.structure.hierarchy.behaviors.selection); // triggers UI update
+    const isBusy = useBehavior(plugin.behaviors.state.isBusy);
+    const hierarchy = plugin.managers.structure.hierarchy.current;
+
+    let label: string = 'Nothing to Export';
+    if (hierarchy.structures.length === 1) {
+        label = 'Export';
+    } if (hierarchy.structures.length > 1) {
+        label = 'Export (as ZIP)';
+    }
+
+    const onExport = async () => {
+        setExporting(true);
+        try {
+            await exportHierarchy(plugin, { format: params.format });
+        } finally {
+            setExporting(false);
+        }
+    };
+
+    return <>
+        <ParameterControls params={Params} values={params} onChangeValues={setParams} isDisabled={isBusy || exporting} />
+        <Button
+            onClick={onExport}
+            style={{ marginTop: 1 }}
+            disabled={isBusy || hierarchy.structures.length === 0 || exporting}
+            commit={hierarchy.structures.length ? 'on' : 'off'}
+        >
+            {label}
+        </Button>
+    </>;
+}

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/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 2022-01-15T19:52:34-08:00
+// Generated on 2022-08-20T16:36:05-07:00
 
 /** 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;
 };
 
@@ -477,6 +474,8 @@ export type ClustersMembers = {
 export type CoreAssembly = {
   /** Get PDB entry that includes this assembly. */
   readonly entry?: Maybe<CoreEntry>;
+  /** Get all pairwise polymer interfaces for this PDB assembly. */
+  readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
   readonly pdbx_struct_assembly?: Maybe<PdbxStructAssembly>;
   readonly pdbx_struct_assembly_auth_evidence?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyAuthEvidence>>>;
   readonly pdbx_struct_assembly_gen?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyGen>>>;
@@ -657,6 +656,8 @@ export type CoreEntry = {
   readonly em_staining?: Maybe<ReadonlyArray<Maybe<EmStaining>>>;
   readonly em_vitrification?: Maybe<ReadonlyArray<Maybe<EmVitrification>>>;
   readonly entry?: Maybe<Entry>;
+  /** Get all groups for this PDB entry. */
+  readonly entry_groups?: Maybe<ReadonlyArray<Maybe<GroupEntry>>>;
   readonly exptl?: Maybe<ReadonlyArray<Maybe<Exptl>>>;
   readonly exptl_crystal?: Maybe<ReadonlyArray<Maybe<ExptlCrystal>>>;
   readonly exptl_crystal_grow?: Maybe<ReadonlyArray<Maybe<ExptlCrystalGrow>>>;
@@ -701,6 +702,7 @@ export type CoreEntry = {
   readonly rcsb_associated_holdings?: Maybe<CurrentEntry>;
   readonly rcsb_binding_affinity?: Maybe<ReadonlyArray<Maybe<RcsbBindingAffinity>>>;
   readonly rcsb_entry_container_identifiers: RcsbEntryContainerIdentifiers;
+  readonly rcsb_entry_group_membership?: Maybe<ReadonlyArray<Maybe<RcsbEntryGroupMembership>>>;
   readonly rcsb_entry_info: RcsbEntryInfo;
   readonly rcsb_external_references?: Maybe<ReadonlyArray<Maybe<RcsbExternalReferences>>>;
   /**
@@ -724,6 +726,16 @@ export type CoreEntry = {
   readonly symmetry?: Maybe<Symmetry>;
 };
 
+export type CoreInterface = {
+  readonly rcsb_id: Scalars['String'];
+  readonly rcsb_interface_container_identifiers: RcsbInterfaceContainerIdentifiers;
+  readonly rcsb_interface_info?: Maybe<RcsbInterfaceInfo>;
+  /** List of operations for each interface partner. */
+  readonly rcsb_interface_operator: ReadonlyArray<Maybe<ReadonlyArray<Maybe<ReadonlyArray<Maybe<Scalars['String']>>>>>>;
+  readonly rcsb_interface_partner: ReadonlyArray<Maybe<RcsbInterfacePartner>>;
+  readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+};
+
 export type CoreNonpolymerEntity = {
   /** Get PDB entry that contains this non-polymer entity. */
   readonly entry?: Maybe<CoreEntry>;
@@ -839,6 +851,8 @@ export type CorePolymerEntity = {
   readonly pdbx_entity_src_syn?: Maybe<ReadonlyArray<Maybe<PdbxEntitySrcSyn>>>;
   /** Get all unique Pfam annotations associated with this molecular entity. */
   readonly pfams?: Maybe<ReadonlyArray<Maybe<CorePfam>>>;
+  /** Get all groups for this PDB entity. */
+  readonly polymer_entity_groups?: Maybe<ReadonlyArray<Maybe<GroupPolymerEntity>>>;
   /** Get all unique polymer instances (chains) for this molecular entity. */
   readonly polymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CorePolymerEntityInstance>>>;
   /** Get a BIRD chemical components described in this molecular entity. */
@@ -875,6 +889,7 @@ export type CorePolymerEntity = {
   readonly rcsb_polymer_entity_container_identifiers: RcsbPolymerEntityContainerIdentifiers;
   readonly rcsb_polymer_entity_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeature>>>;
   readonly rcsb_polymer_entity_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityFeatureSummary>>>;
+  readonly rcsb_polymer_entity_group_membership?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityGroupMembership>>>;
   readonly rcsb_polymer_entity_keywords?: Maybe<RcsbPolymerEntityKeywords>;
   readonly rcsb_polymer_entity_name_com?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityNameCom>>>;
   readonly rcsb_polymer_entity_name_sys?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityNameSys>>>;
@@ -3186,6 +3201,79 @@ export type GeneName = {
   readonly value?: Maybe<Scalars['String']>;
 };
 
+export type GroupEntry = {
+  /** Get provenance associated with this group. */
+  readonly group_provenance?: Maybe<GroupProvenance>;
+  readonly rcsb_group_accession_info?: Maybe<RcsbGroupAccessionInfo>;
+  readonly rcsb_group_container_identifiers: RcsbGroupContainerIdentifiers;
+  readonly rcsb_group_info: RcsbGroupInfo;
+  readonly rcsb_group_related?: Maybe<ReadonlyArray<Maybe<RcsbGroupRelated>>>;
+  readonly rcsb_group_statistics?: Maybe<RcsbGroupStatistics>;
+  /** A unique textual identifier for a group */
+  readonly rcsb_id: Scalars['String'];
+};
+
+export type GroupMembersAlignmentScores = {
+  readonly query_coverage: Scalars['Int'];
+  readonly query_length: Scalars['Int'];
+  readonly target_coverage: Scalars['Int'];
+  readonly target_length: Scalars['Int'];
+};
+
+export type GroupPolymerEntity = {
+  /** Get provenance associated with this group. */
+  readonly group_provenance?: Maybe<GroupProvenance>;
+  readonly rcsb_group_accession_info?: Maybe<RcsbGroupAccessionInfo>;
+  readonly rcsb_group_container_identifiers: RcsbGroupContainerIdentifiers;
+  readonly rcsb_group_info: RcsbGroupInfo;
+  readonly rcsb_group_related?: Maybe<ReadonlyArray<Maybe<RcsbGroupRelated>>>;
+  readonly rcsb_group_statistics?: Maybe<RcsbGroupStatistics>;
+  /** A unique textual identifier for a group */
+  readonly rcsb_id: Scalars['String'];
+  readonly rcsb_polymer_entity_group_members_rankings?: Maybe<ReadonlyArray<Maybe<RcsbPolymerEntityGroupMembersRankings>>>;
+  readonly rcsb_polymer_entity_group_sequence_alignment?: Maybe<RcsbPolymerEntityGroupSequenceAlignment>;
+};
+
+export type GroupProvenance = {
+  readonly rcsb_group_aggregation_method?: Maybe<RcsbGroupAggregationMethod>;
+  readonly rcsb_group_provenance_container_identifiers?: Maybe<RcsbGroupProvenanceContainerIdentifiers>;
+  /** A unique textual identifier for a group provenance */
+  readonly rcsb_id?: Maybe<Scalars['String']>;
+};
+
+export type InterfacePartnerFeatureAdditionalProperties = {
+  /**
+   * The additional property name.
+   *
+   * Allowable values:
+   * TO_BE_DEFINED
+   *
+   */
+  readonly name?: Maybe<Scalars['String']>;
+  /** The value(s) of the additional property. */
+  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
+};
+
+export type InterfacePartnerFeatureFeaturePositions = {
+  /** An identifier for the monomer at which this segment of the feature begins. */
+  readonly beg_seq_id: Scalars['Int'];
+  /** An identifier for the monomer at which this segment of the feature ends. */
+  readonly end_seq_id?: Maybe<Scalars['Int']>;
+  /** The value(s) of the feature over the monomer segment. */
+  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
+};
+
+export type MethodDetails = {
+  /** A description of special aspects of the clustering process */
+  readonly description?: Maybe<Scalars['String']>;
+  /** Defines the name of the description associated with the clustering process */
+  readonly name?: Maybe<Scalars['String']>;
+  /** Defines the type of the description associated with the clustering process */
+  readonly type?: Maybe<Scalars['String']>;
+  /** Defines the value associated with the clustering process */
+  readonly value?: Maybe<Scalars['Float']>;
+};
+
 export type PdbxAuditRevisionCategory = {
   /**
    * The category updated in the pdbx_audit_revision_category record.
@@ -6745,6 +6833,16 @@ export type Query = {
   readonly entries?: Maybe<ReadonlyArray<Maybe<CoreEntry>>>;
   /** Get PDB entry given the PDB id. */
   readonly entry?: Maybe<CoreEntry>;
+  /** Given a group ID get a group object formed by aggregating individual structures that share a degree of similarity */
+  readonly entry_group?: Maybe<GroupEntry>;
+  /** Given a list of group IDs get a list of group objects formed by aggregating structures that share a degree of similarity */
+  readonly entry_groups?: Maybe<ReadonlyArray<Maybe<GroupEntry>>>;
+  /** Given a group provenance ID get an object that describes aggregation method used to create groups */
+  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. */
+  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. */
   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. */
@@ -6757,6 +6855,10 @@ export type Query = {
   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>;
+  /** Given a group ID get a group object formed by aggregating polymer entities that share a degree of similarity */
+  readonly polymer_entity_group?: Maybe<GroupPolymerEntity>;
+  /** Given a list of group IDs get a list of group objects formed by aggregating polymer entities that share a degree of similarity */
+  readonly polymer_entity_groups?: Maybe<ReadonlyArray<Maybe<GroupPolymerEntity>>>;
   /** Get a PDB polymer entity instance (chain), given the PDB ID and ENTITY INSTANCE ID. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
   readonly polymer_entity_instance?: Maybe<CorePolymerEntityInstance>;
   /** Get a list of PDB 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. */
@@ -6831,6 +6933,38 @@ export type QueryEntryArgs = {
 };
 
 
+/** Query root */
+export type QueryEntry_GroupArgs = {
+  group_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryEntry_GroupsArgs = {
+  group_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
+};
+
+
+/** Query root */
+export type QueryGroup_ProvenanceArgs = {
+  group_provenance_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryInterfaceArgs = {
+  assembly_id: Scalars['String'];
+  entry_id: Scalars['String'];
+  interface_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryInterfacesArgs = {
+  interface_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
 /** Query root */
 export type QueryNonpolymer_EntitiesArgs = {
   entity_ids: ReadonlyArray<Scalars['String']>;
@@ -6870,6 +7004,18 @@ export type QueryPolymer_EntityArgs = {
 };
 
 
+/** Query root */
+export type QueryPolymer_Entity_GroupArgs = {
+  group_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryPolymer_Entity_GroupsArgs = {
+  group_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
+};
+
+
 /** Query root */
 export type QueryPolymer_Entity_InstanceArgs = {
   asym_id: Scalars['String'];
@@ -6952,6 +7098,8 @@ export type RcsbAssemblyContainerIdentifiers = {
   readonly assembly_id: Scalars['String'];
   /** Entry identifier for the container. */
   readonly entry_id: Scalars['String'];
+  /** List of binary interface Ids within the assembly (it points to interface id collection). */
+  readonly interface_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
   /**
    * A unique identifier for each object in this assembly container formed by
    *  a dash separated concatenation of entry and assembly identifiers.
@@ -7010,6 +7158,24 @@ export type RcsbAssemblyInfo = {
    *  This is the total count of non-polymer entity instances generated in the assembly coordinate data.
    */
   readonly nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
+  /** Number of heterologous (both binding sites are different) interface entities */
+  readonly num_heterologous_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of heteromeric (both partners are different polymeric entities) interface entities */
+  readonly num_heteromeric_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of homomeric (both partners are the same polymeric entity) interface entities */
+  readonly num_homomeric_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of polymer-polymer interface entities, grouping equivalent interfaces at the entity level (i.e. same entity_ids on either side, with similar but not identical binding sites) */
+  readonly num_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of geometrically equivalent (i.e. same asym_ids on either side) polymer-polymer interfaces in the assembly */
+  readonly num_interfaces?: Maybe<Scalars['Int']>;
+  /** Number of isologous (both binding sites are same, i.e. interface is symmetric) interface entities */
+  readonly num_isologous_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of nucleic acid-nucleic acid interface entities */
+  readonly num_na_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of protein-nucleic acid interface entities */
+  readonly num_prot_na_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of protein-protein interface entities */
+  readonly num_protein_interface_entities?: Maybe<Scalars['Int']>;
   /** The assembly non-hydrogen polymer entity atomic coordinate count. */
   readonly polymer_atom_count?: Maybe<Scalars['Int']>;
   /**
@@ -7085,6 +7251,10 @@ export type RcsbAssemblyInfo = {
    *  This is the total count of solvent entity instances generated in the assembly coordinate data.
    */
   readonly solvent_entity_instance_count?: Maybe<Scalars['Int']>;
+  /** Total buried surface area calculated as the sum of buried surface areas over all interfaces */
+  readonly total_assembly_buried_surface_area?: Maybe<Scalars['Float']>;
+  /** Total number of interfacing residues in the assembly, calculated as the sum of interfacing residues over all interfaces */
+  readonly total_number_interface_residues?: Maybe<Scalars['Int']>;
   /**
    * The number of unmodeled polymer monomers in the assembly coordinate data. This is
    *  the total count of monomers with unreported coordinate data for all polymer
@@ -8590,6 +8760,25 @@ export type RcsbEntryContainerIdentifiers = {
   readonly water_entity_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
 };
 
+export type RcsbEntryGroupMembership = {
+  /**
+   * Method used to establish group membership
+   *
+   * Allowable values:
+   * matching_deposit_group_id
+   *
+   */
+  readonly aggregation_method: Scalars['String'];
+  /**
+   * A unique identifier for a group of entries
+   *
+   * Examples:
+   * G_1001001
+   *
+   */
+  readonly group_id: Scalars['String'];
+};
+
 export type RcsbEntryInfo = {
   /** The number of assemblies defined for this entry including the deposited assembly. */
   readonly assembly_count?: Maybe<Scalars['Int']>;
@@ -8817,6 +9006,220 @@ export type RcsbGenomicLineage = {
   readonly name?: Maybe<Scalars['String']>;
 };
 
+export type RcsbGroupAccessionInfo = {
+  /** Identifies the version of the groups solution */
+  readonly version: Scalars['Int'];
+};
+
+export type RcsbGroupAggregationMethod = {
+  /** The details on a method used to calculate cluster solutions */
+  readonly method: RcsbGroupAggregationMethodMethod;
+  readonly similarity_criteria?: Maybe<RcsbGroupAggregationMethodSimilarityCriteria>;
+  /**
+   * Specifies the type of similarity criteria used to aggregate members into higher levels in the hierarchy
+   *
+   * Allowable values:
+   * sequence_identity, matching_uniprot_accession, matching_deposit_group_id
+   *
+   */
+  readonly type: Scalars['String'];
+};
+
+export type RcsbGroupAggregationMethodMethod = {
+  /** Additional details describing the clustering process */
+  readonly details?: Maybe<ReadonlyArray<Maybe<MethodDetails>>>;
+  /**
+   * The name of the software or the method used to calculate cluster solutions
+   *
+   * Allowable values:
+   * mmseqs2, matching_reference_identity
+   *
+   */
+  readonly name: Scalars['String'];
+  /**
+   * The version of the software.
+   *
+   * Examples:
+   * v1.0, 3.1-2, unknown
+   *
+   */
+  readonly version?: Maybe<Scalars['String']>;
+};
+
+export type RcsbGroupAggregationMethodSimilarityCriteria = {
+  /**
+   * A function or similarity measure that quantifies the similarity between two members
+   *
+   * Allowable values:
+   * rmsd, sequence_identity
+   *
+   */
+  readonly similarity_function?: Maybe<Scalars['String']>;
+};
+
+export type RcsbGroupContainerIdentifiers = {
+  /** A unique textual identifier for a group */
+  readonly group_id: Scalars['String'];
+  /** Member identifiers representing a group */
+  readonly group_member_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+  /**
+   * A unique group provenance identifier
+   *
+   * Allowable values:
+   * provenance_sequence_identity, provenance_matching_uniprot_accession, provenance_matching_deposit_group_id
+   *
+   */
+  readonly group_provenance_id: Scalars['String'];
+  /** Member identifiers representing a higher level in the groping hierarchy that has parent-child relationship */
+  readonly parent_member_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+};
+
+export type RcsbGroupInfo = {
+  readonly group_description?: Maybe<Scalars['String']>;
+  readonly group_members_count: Scalars['Int'];
+  /**
+   * Granularity of group members identifiers
+   *
+   * Allowable values:
+   * assembly, entry, polymer_entity, polymer_entity_instance
+   *
+   */
+  readonly group_members_granularity: Scalars['String'];
+  readonly group_name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbGroupProvenanceContainerIdentifiers = {
+  /**
+   * A unique group provenance identifier
+   *
+   * Allowable values:
+   * provenance_sequence_identity, provenance_matching_uniprot_accession, provenance_matching_deposit_group_id
+   *
+   */
+  readonly group_provenance_id: Scalars['String'];
+};
+
+export type RcsbGroupRelated = {
+  /**
+   * A unique code assigned to a reference related the group
+   *
+   * Examples:
+   * P69905
+   *
+   */
+  readonly resource_accession_code?: Maybe<Scalars['String']>;
+  /**
+   * Defines the type of the resource describing related references
+   *
+   * Examples:
+   * UniProt
+   *
+   */
+  readonly resource_name?: Maybe<Scalars['String']>;
+};
+
+export type RcsbGroupStatistics = {
+  /** The desired lower limit for the similarity between two members that belong to the same group */
+  readonly similarity_cutoff?: Maybe<Scalars['Float']>;
+  /** Similarity score between two most similar group members */
+  readonly similarity_score_max?: Maybe<Scalars['Float']>;
+  /** Similarity score between two least similar group members */
+  readonly similarity_score_min?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbInterfaceContainerIdentifiers = {
+  /** This item references an assembly in pdbx_struct_assembly */
+  readonly assembly_id: Scalars['String'];
+  /** Entry identifier for the container. */
+  readonly entry_id: Scalars['String'];
+  /**
+   * Identifier for NCS-equivalent interfaces within the assembly (same entity_ids on both sides)
+   *
+   * Examples:
+   * 1, 2
+   *
+   */
+  readonly interface_entity_id?: Maybe<Scalars['String']>;
+  /**
+   * Identifier for the geometrically equivalent (same asym_ids on either side) interfaces within the assembly
+   *
+   * Examples:
+   * 1, 2
+   *
+   */
+  readonly interface_id: Scalars['String'];
+  /**
+   * Unique identifier for the document
+   *
+   * Examples:
+   * 2UZI-1.A.B?1
+   *
+   */
+  readonly rcsb_id: Scalars['String'];
+};
+
+export type RcsbInterfaceInfo = {
+  /** Total interface buried surface area */
+  readonly interface_area?: Maybe<Scalars['Float']>;
+  /** Allowable values: homo, hetero. */
+  readonly interface_character?: Maybe<Scalars['String']>;
+  /** Number of core interface residues, defined as those that bury >90% accessible surface area with respect to the unbound state */
+  readonly num_core_interface_residues?: Maybe<Scalars['Int']>;
+  /** Number of interface residues, defined as those with burial fraction > 0 */
+  readonly num_interface_residues?: Maybe<Scalars['Int']>;
+  /** Allowable values: Nucleic acid (only), Protein (only), Protein/NA. */
+  readonly polymer_composition?: Maybe<Scalars['String']>;
+  /** The Jaccard score (intersection over union) of interface contacts in homomeric interfaces, comparing contact sets left-right vs right-left. High values indicate isologous (symmetric) interfaces, with value=1 if perfectly symmetric (e.g. crystallographic symmetry) */
+  readonly self_jaccard_contact_score?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbInterfacePartner = {
+  readonly interface_partner_feature?: Maybe<ReadonlyArray<Maybe<RcsbInterfacePartnerInterfacePartnerFeature>>>;
+  readonly interface_partner_identifier?: Maybe<RcsbInterfacePartnerInterfacePartnerIdentifier>;
+};
+
+export type RcsbInterfacePartnerInterfacePartnerFeature = {
+  readonly additional_properties?: Maybe<ReadonlyArray<Maybe<InterfacePartnerFeatureAdditionalProperties>>>;
+  /**
+   * Identifies the version of the feature assignment.
+   *
+   * Examples:
+   * V4_0_2
+   *
+   */
+  readonly assignment_version?: Maybe<Scalars['String']>;
+  /** A description for the feature. */
+  readonly description?: Maybe<Scalars['String']>;
+  /** An identifier for the feature. */
+  readonly feature_id?: Maybe<Scalars['String']>;
+  readonly feature_positions?: Maybe<ReadonlyArray<Maybe<InterfacePartnerFeatureFeaturePositions>>>;
+  /** A name for the feature. */
+  readonly name?: Maybe<Scalars['String']>;
+  /**
+   * Code identifying the individual, organization or program that assigned the feature.
+   *
+   * Examples:
+   * NACCESS
+   *
+   */
+  readonly provenance_source?: Maybe<Scalars['String']>;
+  /**
+   * A type or category of the feature.
+   *
+   * Allowable values:
+   * ASA_UNBOUND, ASA_BOUND
+   *
+   */
+  readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbInterfacePartnerInterfacePartnerIdentifier = {
+  /** Instance identifier for this container. */
+  readonly asym_id: Scalars['String'];
+  /** Polymer entity identifier for the container. */
+  readonly entity_id: Scalars['String'];
+};
+
 export type RcsbLatestRevision = {
   /** The major version number of the latest revision. */
   readonly major_revision?: Maybe<Scalars['Int']>;
@@ -9733,6 +10136,7 @@ export type RcsbPolymerEntity = {
    *
    */
   readonly rcsb_multiple_source_flag?: Maybe<Scalars['String']>;
+  readonly rcsb_polymer_name_combined?: Maybe<RcsbPolymerEntityRcsbPolymerNameCombined>;
   /**
    * The number of biological sources for the polymer entity. Multiple source contributions
    *  may come from the same organism (taxonomy).
@@ -10059,6 +10463,69 @@ export type RcsbPolymerEntityFeatureSummary = {
   readonly type?: Maybe<Scalars['String']>;
 };
 
+export type RcsbPolymerEntityGroupMembersRankings = {
+  readonly group_members: ReadonlyArray<Maybe<RcsbPolymerEntityGroupMembersRankingsGroupMembers>>;
+  /**
+   * Defines ranking option applicable to group members
+   *
+   * Allowable values:
+   * coverage
+   *
+   */
+  readonly ranking_criteria_type: Scalars['String'];
+};
+
+export type RcsbPolymerEntityGroupMembersRankingsGroupMembers = {
+  readonly member_id: Scalars['String'];
+  /** Quantifies the criteria used for ranking */
+  readonly original_score?: Maybe<Scalars['Float']>;
+  /** Reflects a relationship between group members such that, for any two members the first is ranked higher (smaller rank value) than the second */
+  readonly rank: Scalars['Int'];
+};
+
+export type RcsbPolymerEntityGroupMembership = {
+  /**
+   * Method used to establish group membership
+   *
+   * Allowable values:
+   * sequence_identity, matching_uniprot_accession
+   *
+   */
+  readonly aggregation_method: Scalars['String'];
+  /**
+   * A unique identifier for a group of entities
+   *
+   * Examples:
+   * 1_100, P00003
+   *
+   */
+  readonly group_id: Scalars['String'];
+  /** Degree of similarity expressed as a floating-point number */
+  readonly similarity_cutoff?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbPolymerEntityGroupSequenceAlignment = {
+  /** Abstract reference where group members can be aligned to generate a MSA */
+  readonly abstract_reference: RcsbPolymerEntityGroupSequenceAlignmentAbstractReference;
+  /** Alignment with a core_entity canonical sequence */
+  readonly group_members_alignment: ReadonlyArray<Maybe<RcsbPolymerEntityGroupSequenceAlignmentGroupMembersAlignment>>;
+};
+
+export type RcsbPolymerEntityGroupSequenceAlignmentAbstractReference = {
+  /** Abstract reference length */
+  readonly length: Scalars['Int'];
+  /** Sequence that represents the abstract reference */
+  readonly sequence?: Maybe<Scalars['String']>;
+};
+
+export type RcsbPolymerEntityGroupSequenceAlignmentGroupMembersAlignment = {
+  /** 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;
+};
+
 export type RcsbPolymerEntityInstanceContainerIdentifiers = {
   /** Instance identifier for this container. */
   readonly asym_id: Scalars['String'];
@@ -10177,6 +10644,13 @@ export type RcsbPolymerEntityRcsbMacromolecularNamesCombined = {
   readonly provenance_source?: Maybe<Scalars['String']>;
 };
 
+export type RcsbPolymerEntityRcsbPolymerNameCombined = {
+  /** Protein name annotated by the UniProtKB or macromolecular name assigned by the PDB */
+  readonly names?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
+  /** Allowable values: PDB Preferred Name, PDB Description, UniProt Name. */
+  readonly provenance_source?: Maybe<Scalars['String']>;
+};
+
 export type RcsbPolymerInstanceAnnotation = {
   /** An identifier for the annotation. */
   readonly annotation_id?: Maybe<Scalars['String']>;
@@ -10263,7 +10737,7 @@ 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
+   * 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
    *
    */
   readonly type?: Maybe<Scalars['String']>;
@@ -13145,4 +13619,4 @@ export type AssemblySymmetryQueryVariables = Exact<{
 }>;
 
 
-export type AssemblySymmetryQuery = { readonly assembly?: { readonly rcsb_struct_symmetry?: ReadonlyArray<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<string | null | undefined>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<{ readonly avg_rmsd?: number | null | undefined, readonly members: ReadonlyArray<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null | undefined> | null | undefined } | null | undefined> } | null | undefined>, readonly rotation_axes?: ReadonlyArray<{ readonly order?: number | null | undefined, readonly start: ReadonlyArray<number | null | undefined>, readonly end: ReadonlyArray<number | null | undefined> } | null | undefined> | null | undefined } | null | undefined> | null | undefined } | null | undefined };
+export type AssemblySymmetryQuery = { readonly assembly?: { readonly rcsb_struct_symmetry?: ReadonlyArray<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<string | null>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<{ readonly avg_rmsd?: number | null, readonly members: ReadonlyArray<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null> | null } | null> } | null>, readonly rotation_axes?: ReadonlyArray<{ readonly order?: number | null, readonly start: ReadonlyArray<number | null>, readonly end: ReadonlyArray<number | null> } | null> | null } | null> | null } | null };

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

@@ -55,7 +55,16 @@ function createIntraUnitClashCylinderMesh(ctx: VisualContext, unit: Unit, struct
         radius: (edgeIndex: number) => magnitude[edgeIndex] * sizeFactor,
     };
 
-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
+
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else if (m.triangleCount > 0) {
+        const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+
+    return m;
 }
 
 export const IntraUnitClashParams = {
@@ -169,7 +178,16 @@ function createInterUnitClashCylinderMesh(ctx: VisualContext, structure: Structu
         radius: (edgeIndex: number) => edges[edgeIndex].props.magnitude * sizeFactor
     };
 
-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
+
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else {
+        const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+
+    return m;
 }
 
 export const InterUnitClashParams = {

src/extensions/zenodo/index.ts

@@ -0,0 +1,30 @@
+/**
+ * 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 { ZenodoImportUI } from './ui';
+
+export const ZenodoImport = PluginBehavior.create<{ }>({
+    name: 'extension-zenodo-import',
+    category: 'misc',
+    display: {
+        name: 'Zenodo Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.customImportControls.set('zenodo-import', ZenodoImportUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customImportControls.delete('zenodo-import');
+        }
+    },
+    params: () => ({ })
+});

src/extensions/zenodo/ui.tsx

@@ -0,0 +1,302 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { DownloadFile } from '../../mol-plugin-state/actions/file';
+import { DownloadStructure, LoadTrajectory } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { CoordinatesFormatCategory } from '../../mol-plugin-state/formats/coordinates';
+import { TopologyFormatCategory } from '../../mol-plugin-state/formats/topology';
+import { TrajectoryFormatCategory } from '../../mol-plugin-state/formats/trajectory';
+import { VolumeFormatCategory } from '../../mol-plugin-state/formats/volume';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { OpenInBrowserSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { PluginContext } from '../../mol-plugin/context';
+import { formatBytes } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+type ZenodoFile = {
+    bucket: string
+    checksum: string
+    key: string
+    links: {
+        [key: string]: string
+        self: string
+    }
+    size: number
+    type: string
+}
+
+type ZenodoRecord = {
+    id: number
+    conceptdoi: string
+    conceptrecid: string
+    created: string
+    doi: string
+    files: ZenodoFile[]
+    revision: number
+    updated: string
+    metadata: {
+        title: string
+    }
+}
+
+interface State {
+    busy?: boolean
+    recordValues: PD.Values<typeof ZenodoImportParams>
+    importValues?: PD.Values<ImportParams>
+    importParams?: ImportParams
+    record?: ZenodoRecord
+    files?: ZenodoFile[]
+}
+
+const ZenodoImportParams = {
+    record: PD.Text('', { description: 'Zenodo ID.' })
+};
+
+function createImportParams(files: ZenodoFile[], plugin: PluginContext) {
+    const modelOpts: [string, string][] = [];
+    const topologyOpts: [string, string][] = [];
+    const coordinatesOpts: [string, string][] = [];
+    const volumeOpts: [string, string][] = [];
+    const compressedOpts: [string, string][] = [];
+
+    const structureExts = new Map<string, { format: string, isBinary: boolean }>();
+    const coordinatesExts = new Map<string, { format: string, isBinary: boolean }>();
+    const topologyExts = new Map<string, { format: string, isBinary: boolean }>();
+    const volumeExts = new Map<string, { format: string, isBinary: boolean }>();
+
+    for (const { provider: { category, binaryExtensions, stringExtensions }, name } of plugin.dataFormats.list) {
+        if (category === TrajectoryFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) structureExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) structureExts.set(e, { format: name, isBinary: false });
+        } else if (category === VolumeFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) volumeExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) volumeExts.set(e, { format: name, isBinary: false });
+        } else if (category === CoordinatesFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) coordinatesExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) coordinatesExts.set(e, { format: name, isBinary: false });
+        } else if (category === TopologyFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) topologyExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) topologyExts.set(e, { format: name, isBinary: false });
+        }
+    }
+
+    for (const file of files) {
+        const label = `${file.key} (${formatBytes(file.size)})`;
+        if (structureExts.has(file.type)) {
+            const { format, isBinary } = structureExts.get(file.type)!;
+            modelOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+            topologyOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (volumeExts.has(file.type)) {
+            const { format, isBinary } = volumeExts.get(file.type)!;
+            volumeOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (topologyExts.has(file.type)) {
+            const { format, isBinary } = topologyExts.get(file.type)!;
+            topologyOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (coordinatesExts.has(file.type)) {
+            const { format, isBinary } = coordinatesExts.get(file.type)!;
+            coordinatesOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (file.type === 'zip') {
+            compressedOpts.push([`${file.links.self}|${file.type}|true`, label]);
+        }
+    }
+
+    const params: PD.Params = {};
+    let defaultType = '';
+
+    if (modelOpts.length) {
+        defaultType = 'structure';
+        params.structure = PD.Select(modelOpts[0][0], modelOpts);
+    }
+
+    if (topologyOpts.length && coordinatesOpts.length) {
+        if (!defaultType) defaultType = 'trajectory';
+        params.trajectory = PD.Group({
+            topology: PD.Select(topologyOpts[0][0], topologyOpts),
+            coordinates: PD.Select(coordinatesOpts[0][0], coordinatesOpts),
+        }, { isFlat: true });
+    }
+
+    if (volumeOpts.length) {
+        if (!defaultType) defaultType = 'volume';
+        params.volume = PD.Select(volumeOpts[0][0], volumeOpts);
+    }
+
+    if (compressedOpts.length) {
+        if (!defaultType) defaultType = 'compressed';
+        params.compressed = PD.Select(compressedOpts[0][0], compressedOpts);
+    }
+
+    return {
+        type: PD.MappedStatic(defaultType, Object.keys(params).length ? params : { '': PD.EmptyGroup() })
+    };
+}
+type ImportParams = ReturnType<typeof createImportParams>
+
+export class ZenodoImportUI extends CollapsableControls<{}, State> {
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Zenodo Import',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: OpenInBrowserSvg },
+            recordValues: PD.getDefaultValues(ZenodoImportParams),
+            importValues: undefined,
+            importParams: undefined,
+            record: undefined,
+            files: undefined,
+        };
+    }
+
+    private recordParamsOnChange = (values: any) => {
+        this.setState({ recordValues: values });
+    };
+
+    private importParamsOnChange = (values: any) => {
+        this.setState({ importValues: values });
+    };
+
+    private loadRecord = async () => {
+        try {
+            this.setState({ busy: true });
+            const record: ZenodoRecord = await this.plugin.runTask(this.plugin.fetch({ url: `https://zenodo.org/api/records/${this.state.recordValues.record}`, type: 'json' }));
+            const importParams = createImportParams(record.files, this.plugin);
+            this.setState({
+                record,
+                files: record.files,
+                busy: false,
+                importValues: PD.getDefaultValues(importParams),
+                importParams
+            });
+        } catch (e) {
+            console.error(e);
+            this.plugin.log.error(`Failed to load Zenodo record '${this.state.recordValues.record}'`);
+            this.setState({ busy: false });
+        }
+    };
+
+    private loadFile = async (values: PD.Values<ImportParams>) => {
+        try {
+            this.setState({ busy: true });
+
+            const t = values.type;
+            if (t.name === 'structure') {
+                const defaultParams = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            url,
+                            format: format as any,
+                            isBinary: isBinary === 'true',
+                            options: defaultParams.source.params.options,
+                        }
+                    }
+                }));
+            } else if (t.name === 'trajectory') {
+                const [topologyUrl, topologyFormat, topologyIsBinary] = t.params.topology.split('|');
+                const [coordinatesUrl, coordinatesFormat, coordinatesIsBinary] = t.params.coordinates.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(LoadTrajectory, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            model: {
+                                url: topologyUrl,
+                                format: topologyFormat as any,
+                                isBinary: topologyIsBinary === 'true',
+                            },
+                            coordinates: {
+                                url: coordinatesUrl,
+                                format: coordinatesFormat as any,
+                                isBinary: coordinatesIsBinary === 'true',
+                            },
+                        }
+                    }
+                }));
+            } else if (t.name === 'volume') {
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            url,
+                            format: format as any,
+                            isBinary: isBinary === 'true',
+                        }
+                    }
+                }));
+            } else if (t.name === 'compressed') {
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadFile, {
+                    url,
+                    format: format as any,
+                    isBinary: isBinary === 'true',
+                    visuals: true
+                }));
+            }
+        } catch (e) {
+            console.error(e);
+            this.plugin.log.error(`Failed to load Zenodo file`);
+        } finally {
+            this.setState({ busy: false });
+        }
+    };
+
+    private clearRecord = () => {
+        this.setState({
+            importValues: undefined,
+            importParams: undefined,
+            record: undefined,
+            files: undefined
+        });
+    };
+
+    private renderLoadRecord() {
+        return <div style={{ marginBottom: 10 }}>
+            <ParameterControls params={ZenodoImportParams} values={this.state.recordValues} onChangeValues={this.recordParamsOnChange} isDisabled={this.state.busy} />
+            <Button onClick={this.loadRecord} style={{ marginTop: 1 }} disabled={this.state.busy || !this.state.recordValues.record}>
+                Load Record
+            </Button>
+        </div>;
+    }
+
+    private renderRecordInfo(record: ZenodoRecord) {
+        return <div style={{ marginBottom: 10 }}>
+            <div className='msp-help-text'>
+                <div>Record {`${record.id}`}: <i>{`${record.metadata.title}`}</i></div>
+            </div>
+            <Button onClick={this.clearRecord} style={{ marginTop: 1 }} disabled={this.state.busy}>
+                Clear
+            </Button>
+        </div>;
+    }
+
+    private renderImportFile(params: ImportParams, values: PD.Values<ImportParams>) {
+        return values.type.name ? <div style={{ marginBottom: 10 }}>
+            <ParameterControls params={params} values={this.state.importValues} onChangeValues={this.importParamsOnChange} isDisabled={this.state.busy} />
+            <Button onClick={() => this.loadFile(values)} style={{ marginTop: 1 }} disabled={this.state.busy}>
+                Import File
+            </Button>
+        </div> : <div className='msp-help-text' style={{ marginBottom: 10 }}>
+            <div>No supported files</div>
+        </div>;
+    }
+
+    protected renderControls(): JSX.Element | null {
+        return <>
+            {!this.state.record ? this.renderLoadRecord() : null}
+            {this.state.record ? this.renderRecordInfo(this.state.record) : null}
+            {this.state.importParams && this.state.importValues ? this.renderImportFile(this.state.importParams, this.state.importValues) : null}
+        </>;
+    }
+}

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) 2018-2022 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>
@@ -10,6 +10,7 @@ import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 import { Scene } from '../mol-gl/scene';
+import { assertUnreachable } from '../mol-util/type-helpers';
 
 export { ICamera, Camera };
 
@@ -84,7 +85,7 @@ class Camera implements ICamera {
         switch (this.state.mode) {
             case 'orthographic': updateOrtho(this); break;
             case 'perspective': updatePers(this); break;
-            default: throw new Error('unknown camera mode');
+            default: assertUnreachable(this.state.mode);
         }
 
         const changed = !Mat4.areEqual(this.projection, this.prevProjection, EPSILON) || !Mat4.areEqual(this.view, this.prevView, EPSILON);
@@ -259,7 +260,8 @@ namespace Camera {
             radius: 0,
             radiusMax: 10,
             fog: 50,
-            clipFar: true
+            clipFar: true,
+            minNear: 5,
         };
     }
 
@@ -275,6 +277,7 @@ namespace Camera {
         radiusMax: number
         fog: number
         clipFar: boolean
+        minNear: number
     }
 
     export function copySnapshot(out: Snapshot, source?: Partial<Snapshot>) {
@@ -291,6 +294,7 @@ 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;
     }
@@ -302,6 +306,7 @@ 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);
@@ -369,7 +374,7 @@ 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;
@@ -383,12 +388,12 @@ 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) 2018-2021 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 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 { isDebugMode, isTimingMode } 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: 10, 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 +114,13 @@ 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 = {
+        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 +130,19 @@ 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 { failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
         const gl = getGLContext(canvas, {
+            failIfMajorPerformanceCaveat,
             antialias,
             preserveDrawingBuffer,
             alpha: true, // the renderer requires an alpha channel
@@ -139,7 +154,7 @@ 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 +207,7 @@ namespace Canvas3DContext {
             attribs: a,
             contextLost,
             contextRestored: webgl.contextRestored,
+            assetManager,
             dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => {
                 input.dispose();
 
@@ -236,7 +252,7 @@ interface Canvas3D {
     /** Sets drawPaused = false without starting the built in animation loop */
     resume(): void
     identify(x: number, y: number): PickData | undefined
-    mark(loci: Representation.Loci, action: MarkerAction, noDraw?: boolean): void
+    mark(loci: Representation.Loci, action: MarkerAction): void
     getLoci(pickingId: PickingId | undefined): Representation.Loci
 
     notifyDidDraw: boolean,
@@ -278,8 +294,8 @@ 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>();
@@ -296,14 +312,19 @@ 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 +336,10 @@ 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;
@@ -345,34 +370,43 @@ namespace Canvas3D {
             return { loci, repr };
         }
 
-        function mark(reprLoci: Representation.Loci, action: MarkerAction, noDraw = false) {
+        let markBuffer: [reprLoci: Representation.Loci, action: MarkerAction][] = [];
+
+        function mark(reprLoci: Representation.Loci, action: MarkerAction) {
+            // NOTE: might try to optimize a case with opposite actions for the
+            //       same loci. Tho this might end up being more expensive (and error prone)
+            //       then just applying everything "naively".
+            markBuffer.push([reprLoci, action]);
+        }
+
+        function resolveMarking() {
+            let changed = false;
+            for (const [r, l] of markBuffer) {
+                changed = applyMark(r, l) || changed;
+            }
+            markBuffer = [];
+            if (changed) {
+                scene.update(void 0, true);
+                helper.handle.scene.update(void 0, true);
+                helper.camera.scene.update(void 0, true);
+            }
+            return changed;
+        }
+
+        function applyMark(reprLoci: Representation.Loci, action: MarkerAction) {
             const { repr, loci } = reprLoci;
             let changed = false;
             if (repr) {
-                changed = repr.mark(loci, action);
+                changed = repr.mark(loci, action) || changed;
             } else {
-                changed = helper.handle.mark(loci, action);
-                changed = helper.camera.mark(loci, action) || changed;
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
-            if (changed) {
-                if (noDraw) {
-                    // Even with `noDraw` make sure changes will be rendered.
-                    // Note that with this calling mark (with or without `noDraw`) multiple times
-                    // during a JS event loop iteration will only result in a single render call.
-                    forceNextRender = true;
-                } else {
-                    scene.update(void 0, true);
-                    helper.handle.scene.update(void 0, true);
-                    helper.camera.scene.update(void 0, true);
-                    const prevPickDirty = pickHelper.dirty;
-                    draw({ force: true, allowMulti: true });
-                    pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
-                }
-            }
+            changed = helper.handle.mark(loci, action) || changed;
+            changed = helper.camera.mark(loci, action) || changed;
+            return changed;
         }
 
-        function render(force: boolean, allowMulti: boolean) {
+        function render(force: boolean) {
             if (webgl.isContextLost) return false;
 
             let resized = false;
@@ -386,6 +420,8 @@ namespace Canvas3D {
                 y > gl.drawingBufferHeight || y + height < 0
             ) return false;
 
+            const markingUpdated = resolveMarking() && (renderer.props.colorMarker || p.marking.enabled);
+
             let didRender = false;
             controls.update(currentTime);
             const cameraChanged = camera.update();
@@ -393,23 +429,27 @@ namespace Canvas3D {
             const shouldRender = force || cameraChanged || resized || forceNextRender;
             forceNextRender = false;
 
-            const multiSampleChanged = multiSampleHelper.update(shouldRender, p.multiSample);
+            const multiSampleChanged = multiSampleHelper.update(markingUpdated || shouldRender, p.multiSample);
 
-            if (shouldRender || multiSampleChanged) {
+            if (shouldRender || multiSampleChanged || markingUpdated) {
                 let cam: Camera | StereoCamera = camera;
                 if (p.camera.stereo.name === 'on') {
                     stereoCamera.update();
                     cam = stereoCamera;
                 }
 
+                if (isTimingMode) webgl.timer.mark('Canvas3D.render');
                 const ctx = { renderer, camera: cam, scene, helper };
                 if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    const forceOn = !cameraChanged && allowMulti && !controls.isAnimating;
+                    const forceOn = !cameraChanged && markingUpdated && !controls.isAnimating;
                     multiSampleHelper.render(ctx, p, true, forceOn);
                 } else {
                     passes.draw.render(ctx, p, true);
                 }
-                pickHelper.dirty = 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;
             }
 
@@ -421,9 +461,9 @@ namespace Canvas3D {
         let currentTime = 0;
         let drawPaused = false;
 
-        function draw(options?: { force?: boolean, allowMulti?: boolean }) {
+        function draw(options?: { force?: boolean }) {
             if (drawPaused) return;
-            if (render(!!options?.force, !!options?.allowMulti) && notifyDidDraw) {
+            if (render(!!options?.force) && notifyDidDraw) {
                 didDraw.next(now() - startTime as now.Timestamp);
             }
         }
@@ -508,7 +548,7 @@ 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;
@@ -559,7 +599,7 @@ 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();
 
@@ -635,7 +675,7 @@ 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 {
@@ -643,14 +683,17 @@ 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 },
@@ -752,10 +795,19 @@ 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;
@@ -764,8 +816,11 @@ 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);
@@ -776,9 +831,13 @@ 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));
@@ -790,6 +849,12 @@ 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);
@@ -808,7 +873,7 @@ 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[] = [];
@@ -831,6 +896,8 @@ namespace Canvas3D {
             dispose: () => {
                 contextRestoredSub.unsubscribe();
 
+                markBuffer = [];
+
                 scene.clear();
                 helper.debug.clear();
                 controls.dispose();
@@ -871,4 +938,4 @@ namespace Canvas3D {
             Viewport.set(controls.viewport, x, y, width, height);
         }
     }
-}
+}

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 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>
  */
@@ -17,7 +17,7 @@ import { WebGLContext } from '../../mol-gl/webgl/context';
 import { GraphicsRenderVariantsBlended } from '../../mol-gl/webgl/render-item';
 import { Sphere3D } from '../../mol-math/geometry';
 import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { DataLoci, EmptyLoci, Loci } from '../../mol-model/loci';
+import { DataLoci, EmptyLoci, isEveryLoci, Loci } from '../../mol-model/loci';
 import { Shape } from '../../mol-model/shape';
 import { Visual } from '../../mol-repr/visual';
 import { ColorNames } from '../../mol-util/color/names';
@@ -113,8 +113,10 @@ export class CameraHelper {
 
     mark(loci: Loci, action: MarkerAction) {
         if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
-        if (!isCameraAxesLoci(loci)) return false;
-        if (loci.data !== this) return false;
+        if (!isEveryLoci(loci)) {
+            if (!isCameraAxesLoci(loci)) return false;
+            if (loci.data !== this) return false;
+        }
         return Visual.mark(this.renderObject, loci, action, this.eachGroup);
     }
 

src/mol-canvas3d/helper/handle-helper.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -20,7 +20,7 @@ import produce from 'immer';
 import { Shape } from '../../mol-model/shape';
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { Camera } from '../camera';
-import { DataLoci, EmptyLoci, Loci } from '../../mol-model/loci';
+import { DataLoci, EmptyLoci, isEveryLoci, Loci } from '../../mol-model/loci';
 import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
 import { Visual } from '../../mol-repr/visual';
 import { Interval } from '../../mol-data/int';
@@ -121,8 +121,10 @@ export class HandleHelper {
 
     mark(loci: Loci, action: MarkerAction) {
         if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
-        if (!isHandleLoci(loci)) return false;
-        if (loci.data !== this) return false;
+        if (!isEveryLoci(loci)) {
+            if (!isHandleLoci(loci)) return false;
+            if (loci.data !== this) return false;
+        }
         return Visual.mark(this.renderObject, loci, action, this.eachGroup);
     }
 

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

@@ -71,7 +71,7 @@ export class Canvas3dInteractionHelper {
         const xyChanged = this.startX !== this.endX || this.startY !== this.endY;
 
         if (e === InputEvent.Drag) {
-            if (xyChanged && !Representation.Loci.isEmpty(this.prevLoci)) {
+            if (xyChanged && !this.outsideViewport(this.startX, this.startY)) {
                 this.events.drag.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, pageStart: Vec2.create(this.startX, this.startY), pageEnd: Vec2.create(this.endX, this.endY) });
 
                 this.startX = this.endX;

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) 2019-2021 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 Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
@@ -11,52 +12,24 @@ import { Renderer } from '../../mol-gl/renderer';
 import { Scene } from '../../mol-gl/scene';
 import { Texture } from '../../mol-gl/webgl/texture';
 import { Camera, ICamera } from '../camera';
-import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
-import { DefineSpec, TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
-import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
-import { ShaderCode } from '../../mol-gl/shader-code';
-import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
 import { ValueCell } from '../../mol-util';
 import { Vec2 } from '../../mol-math/linear-algebra';
 import { Helper } from '../helper/helper';
 
-import { quad_vert } from '../../mol-gl/shader/quad.vert';
-import { depthMerge_frag } from '../../mol-gl/shader/depth-merge.frag';
 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';
-
-const DepthMergeSchema = {
-    ...QuadSchema,
-    tDepthPrimitives: TextureSpec('texture', 'depth', 'ushort', 'nearest'),
-    tDepthVolumes: TextureSpec('texture', 'depth', 'ushort', 'nearest'),
-    uTexSize: UniformSpec('v2'),
-    dPackedDepth: DefineSpec('boolean'),
-};
-const DepthMergeShaderCode = ShaderCode('depth-merge', quad_vert, depthMerge_frag);
-type DepthMergeRenderable = ComputeRenderable<Values<typeof DepthMergeSchema>>
-
-function getDepthMergeRenderable(ctx: WebGLContext, depthTexturePrimitives: Texture, depthTextureVolumes: Texture, packedDepth: boolean): DepthMergeRenderable {
-    const values: Values<typeof DepthMergeSchema> = {
-        ...QuadValues,
-        tDepthPrimitives: ValueCell.create(depthTexturePrimitives),
-        tDepthVolumes: ValueCell.create(depthTextureVolumes),
-        uTexSize: ValueCell.create(Vec2.create(depthTexturePrimitives.getWidth(), depthTexturePrimitives.getHeight())),
-        dPackedDepth: ValueCell.create(packedDepth),
-    };
-
-    const schema = { ...DepthMergeSchema };
-    const renderItem = createComputeRenderItem(ctx, 'triangles', DepthMergeShaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
+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 = {
@@ -70,21 +43,19 @@ export class DrawPass {
     private readonly drawTarget: RenderTarget;
 
     readonly colorTarget: RenderTarget;
-    readonly depthTexture: Texture;
-    readonly depthTexturePrimitives: Texture;
+    readonly depthTextureTransparent: Texture;
+    readonly depthTextureOpaque: Texture;
 
     readonly packedDepth: boolean;
 
-    private depthTarget: RenderTarget;
-    private depthTargetPrimitives: RenderTarget | null;
-    private depthTargetVolumes: RenderTarget | null;
-    private depthTextureVolumes: Texture;
-    private depthMerge: DepthMergeRenderable;
+    private depthTargetTransparent: RenderTarget;
+    private depthTargetOpaque: RenderTarget | null;
 
     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;
@@ -93,31 +64,30 @@ 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;
 
-        this.depthTarget = webgl.createRenderTarget(width, height);
-        this.depthTexture = this.depthTarget.texture;
+        this.depthTargetTransparent = webgl.createRenderTarget(width, height);
+        this.depthTextureTransparent = this.depthTargetTransparent.texture;
 
-        this.depthTargetPrimitives = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
-        this.depthTargetVolumes = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
+        this.depthTargetOpaque = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
 
-        this.depthTexturePrimitives = this.depthTargetPrimitives ? this.depthTargetPrimitives.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
-        this.depthTextureVolumes = this.depthTargetVolumes ? this.depthTargetVolumes.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
+        this.depthTextureOpaque = this.depthTargetOpaque ? this.depthTargetOpaque.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
         if (!this.packedDepth) {
-            this.depthTexturePrimitives.define(width, height);
-            this.depthTextureVolumes.define(width, height);
+            this.depthTextureOpaque.define(width, height);
         }
-        this.depthMerge = getDepthMergeRenderable(webgl, this.depthTexturePrimitives, this.depthTextureVolumes, this.packedDepth);
 
         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);
@@ -126,6 +96,7 @@ export class DrawPass {
 
     reset() {
         this.wboit?.reset();
+        this.dpoit?.reset();
     }
 
     setSize(width: number, height: number) {
@@ -134,22 +105,14 @@ export class DrawPass {
 
         if (width !== w || height !== h) {
             this.colorTarget.setSize(width, height);
-            this.depthTarget.setSize(width, height);
+            this.depthTargetTransparent.setSize(width, height);
 
-            if (this.depthTargetPrimitives) {
-                this.depthTargetPrimitives.setSize(width, height);
+            if (this.depthTargetOpaque) {
+                this.depthTargetOpaque.setSize(width, height);
             } else {
-                this.depthTexturePrimitives.define(width, height);
+                this.depthTextureOpaque.define(width, height);
             }
 
-            if (this.depthTargetVolumes) {
-                this.depthTargetVolumes.setSize(width, height);
-            } else {
-                this.depthTextureVolumes.define(width, height);
-            }
-
-            ValueCell.update(this.depthMerge.values.uTexSize, Vec2.set(this.depthMerge.values.uTexSize.ref.value, width, height));
-
             ValueCell.update(this.copyFboTarget.values.uTexSize, Vec2.set(this.copyFboTarget.values.uTexSize.ref.value, width, height));
             ValueCell.update(this.copyFboPostprocessing.values.uTexSize, Vec2.set(this.copyFboPostprocessing.values.uTexSize.ref.value, width, height));
 
@@ -157,127 +120,191 @@ 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 _depthMerge() {
-        const { state, gl } = this.webgl;
+    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.depthMerge.update();
-        this.depthTarget.bind();
-        state.disable(gl.BLEND);
-        state.disable(gl.DEPTH_TEST);
-        state.disable(gl.CULL_FACE);
-        state.depthMask(false);
-        state.clearColor(1, 1, 1, 1);
-        gl.clear(gl.COLOR_BUFFER_BIT);
-        this.depthMerge.render();
+        this.depthTextureOpaque.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+        renderer.clear(true);
+
+        // render opaque primitives
+        if (scene.hasOpaque) {
+            renderer.renderDpoitOpaque(scene.primitives, camera, null);
+        }
+
+        if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isOutlineEnabled(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);
+        }
+
+        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.colorTarget.bind();
+        this.depthTextureOpaque.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
         renderer.clear(true);
 
         // render opaque primitives
-        this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-        this.colorTarget.bind();
-        renderer.clearDepth();
-        renderer.renderWboitOpaque(scene.primitives, camera, null);
-
-        // render opaque volumes
-        this.depthTextureVolumes.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-        this.colorTarget.bind();
-        renderer.clearDepth();
-        renderer.renderWboitOpaque(scene.volumes, camera, this.depthTexturePrimitives);
-
-        // merge depth of opaque primitives and volumes
-        this._depthMerge();
+        if (scene.hasOpaque) {
+            renderer.renderWboitOpaque(scene.primitives, camera, null);
+        }
 
         if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isOutlineEnabled(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);
         }
 
         // render transparent primitives and volumes
-        this.wboit.bind();
-        renderer.renderWboitTransparent(scene.primitives, camera, this.depthTexture);
-        renderer.renderWboitTransparent(scene.volumes, camera, this.depthTexture);
+        if (scene.opacityAverage < 1 || scene.volumes.renderables.length > 0) {
+            this.wboit.bind();
+            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)) {
-            this.depthTexturePrimitives.attachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
-            this.postprocessing.target.bind();
-        } else {
-            this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-            this.colorTarget.bind();
+            // evaluate wboit
+            if (PostprocessingPass.isEnabled(postprocessingProps)) {
+                this.postprocessing.target.bind();
+            } else {
+                this.colorTarget.bind();
+            }
+            this.wboit.render();
         }
-        this.wboit.render();
     }
 
     private _renderBlended(renderer: Renderer, camera: ICamera, scene: Scene, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
         if (toDrawingBuffer) {
             this.drawTarget.bind();
         } else {
-            this.colorTarget.bind();
             if (!this.packedDepth) {
-                this.depthTexturePrimitives.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
+                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
             // extensions.depthTexture is unsupported (i.e. depthTarget is set)
-            if (this.depthTargetPrimitives) {
-                this.depthTargetPrimitives.bind();
-                renderer.clear(false);
-                // TODO: this should only render opaque
-                renderer.renderDepth(scene.primitives, camera, null);
+            if (this.depthTargetOpaque) {
+                this.depthTargetOpaque.bind();
+                renderer.clearDepth(true);
+                renderer.renderDepthOpaque(scene.primitives, camera, null);
                 this.colorTarget.bind();
             }
 
-            // do direct-volume rendering
-            if (!this.packedDepth) {
-                this.depthTextureVolumes.attachFramebuffer(this.colorTarget.framebuffer, 'depth');
-                renderer.clearDepth(); // from previous frame
-            }
-            renderer.renderBlendedVolumeOpaque(scene.volumes, camera, this.depthTexturePrimitives);
-
-            // do volume depth pass if extensions.depthTexture is unsupported (i.e. depthTarget is set)
-            if (this.depthTargetVolumes) {
-                this.depthTargetVolumes.bind();
-                renderer.clear(false);
-                renderer.renderDepth(scene.volumes, camera, this.depthTexturePrimitives);
-                this.colorTarget.bind();
-            }
-
-            // merge depths from primitive and volume rendering
-            this._depthMerge();
-            this.colorTarget.bind();
-
             if (PostprocessingPass.isEnabled(postprocessingProps)) {
-                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
-            }
-            renderer.renderBlendedVolumeTransparent(scene.volumes, camera, this.depthTexturePrimitives);
+                if (!this.packedDepth) {
+                    this.depthTextureOpaque.detachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
+                } else {
+                    this.colorTarget.depthRenderbuffer?.detachFramebuffer(this.postprocessing.target.framebuffer);
+                }
 
-            const target = PostprocessingPass.isEnabled(postprocessingProps)
-                ? this.postprocessing.target : this.colorTarget;
-            if (!this.packedDepth) {
-                this.depthTexturePrimitives.attachFramebuffer(target.framebuffer, 'depth');
+                if (PostprocessingPass.isOutlineEnabled(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);
+
+                if (!this.packedDepth) {
+                    this.depthTextureOpaque.attachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
+                } else {
+                    this.colorTarget.depthRenderbuffer?.attachFramebuffer(this.postprocessing.target.framebuffer);
+                }
+            }
+
+            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();
             }
-            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);
@@ -287,52 +314,54 @@ export class DrawPass {
         renderer.setViewport(x, y, width, height);
         renderer.update(camera);
 
-        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 (markingEnabled && scene.markerAverage > 0) {
             const markingDepthTest = props.marking.ghostEdgeStrength < 1;
-            if (markingDepthTest) {
+            if (markingDepthTest && scene.markerAverage !== 1) {
                 this.marking.depthTarget.bind();
-                renderer.clear(false);
+                renderer.clear(false, true);
                 renderer.renderMarkingDepth(scene.primitives, camera, null);
             }
 
             this.marking.maskTarget.bind();
-            renderer.clear(false);
+            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);
+            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.renderBlended(helper.camera.scene, helper.camera.camera);
         }
 
         if (antialiasingEnabled) {
@@ -343,7 +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();
             }
         }
@@ -352,17 +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 {
@@ -373,4 +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;
 

src/mol-canvas3d/passes/marking.ts

@@ -20,6 +20,7 @@ import { Viewport } from '../camera/util';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { Color } from '../../mol-util/color';
 import { edge_frag } from '../../mol-gl/shader/marking/edge.frag';
+import { isTimingMode } from '../../mol-util/debug';
 
 export const MarkingParams = {
     enabled: PD.Boolean(true),
@@ -63,8 +64,8 @@ export class MarkingPass {
         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, 0);
         gl.clear(gl.COLOR_BUFFER_BIT);
@@ -81,8 +82,8 @@ export class MarkingPass {
         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);
     }
 
     setSize(width: number, height: number) {
@@ -117,6 +118,7 @@ export class MarkingPass {
     }
 
     render(viewport: Viewport, target: RenderTarget | undefined) {
+        if (isTimingMode) this.webgl.timer.mark('MarkingPass.render');
         this.edgesTarget.bind();
         this.setEdgeState(viewport);
         this.edge.render();
@@ -128,6 +130,7 @@ export class MarkingPass {
         }
         this.setOverlayState(viewport);
         this.overlay.render();
+        if (isTimingMode) this.webgl.timer.markEnd('MarkingPass.render');
     }
 }
 

src/mol-canvas3d/passes/multi-sample.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>
  */
@@ -25,6 +25,7 @@ import { StereoCamera } from '../camera/stereo';
 import { quad_vert } from '../../mol-gl/shader/quad.vert';
 import { compose_frag } from '../../mol-gl/shader/compose.frag';
 import { MarkingProps } from './marking';
+import { isTimingMode } from '../../mol-util/debug';
 
 const ComposeSchema = {
     ...QuadSchema,
@@ -60,6 +61,7 @@ type Props = {
     postprocessing: PostprocessingProps
     marking: MarkingProps
     transparentBackground: boolean;
+    dpoitIterations: number;
 }
 
 type RenderContext = {
@@ -126,6 +128,7 @@ export class MultiSamplePass {
         const { camera } = ctx;
         const { compose, composeTarget, drawPass, webgl } = this;
         const { gl, state } = webgl;
+        if (isTimingMode) webgl.timer.mark('MultiSamplePass.renderMultiSample');
 
         // based on the Multisample Anti-Aliasing Render Pass
         // contributed to three.js by bhouston / http://clara.io/
@@ -157,6 +160,14 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, sampleWeight);
 
             // render scene
+            if (i === 0) {
+                drawPass.postprocessing.setOcclusionOffset(0, 0);
+            } else {
+                drawPass.postprocessing.setOcclusionOffset(
+                    offset[0] / width,
+                    offset[1] / height
+                );
+            }
             drawPass.render(ctx, props, false);
 
             // compose rendered scene with compose target
@@ -166,8 +177,8 @@ export class MultiSamplePass {
             state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ONE, gl.ONE);
             state.disable(gl.DEPTH_TEST);
             state.depthMask(false);
-            gl.viewport(x, y, width, height);
-            gl.scissor(x, y, width, height);
+            state.viewport(x, y, width, height);
+            state.scissor(x, y, width, height);
             if (i === 0) {
                 state.clearColor(0, 0, 0, 0);
                 gl.clear(gl.COLOR_BUFFER_BIT);
@@ -175,25 +186,29 @@ export class MultiSamplePass {
             compose.render();
         }
 
+        drawPass.postprocessing.setOcclusionOffset(0, 0);
+
         ValueCell.update(compose.values.uWeight, 1.0);
         ValueCell.update(compose.values.tColor, composeTarget.texture);
         compose.update();
 
         this.bindOutputTarget(toDrawingBuffer);
-        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.disable(gl.BLEND);
         compose.render();
 
         camera.viewOffset.enabled = false;
         camera.update();
+        if (isTimingMode) webgl.timer.markEnd('MultiSamplePass.renderMultiSample');
     }
 
     private renderTemporalMultiSample(sampleIndex: number, ctx: RenderContext, props: Props, toDrawingBuffer: boolean) {
         const { camera } = ctx;
         const { compose, composeTarget, holdTarget, drawPass, webgl } = this;
         const { gl, state } = webgl;
+        if (isTimingMode) webgl.timer.mark('MultiSamplePass.renderTemporalMultiSample');
 
         // based on the Multisample Anti-Aliasing Render Pass
         // contributed to three.js by bhouston / http://clara.io/
@@ -217,8 +232,8 @@ export class MultiSamplePass {
             state.disable(gl.BLEND);
             state.disable(gl.DEPTH_TEST);
             state.depthMask(false);
-            gl.viewport(x, y, width, height);
-            gl.scissor(x, y, width, height);
+            state.viewport(x, y, width, height);
+            state.scissor(x, y, width, height);
             compose.render();
             sampleIndex += 1;
         } else {
@@ -236,6 +251,14 @@ export class MultiSamplePass {
                 camera.update();
 
                 // render scene
+                if (sampleIndex === 0) {
+                    drawPass.postprocessing.setOcclusionOffset(0, 0);
+                } else {
+                    drawPass.postprocessing.setOcclusionOffset(
+                        offset[0] / width,
+                        offset[1] / height
+                    );
+                }
                 drawPass.render(ctx, props, false);
 
                 // compose rendered scene with compose target
@@ -245,8 +268,8 @@ export class MultiSamplePass {
                 state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ONE, gl.ONE);
                 state.disable(gl.DEPTH_TEST);
                 state.depthMask(false);
-                gl.viewport(x, y, width, height);
-                gl.scissor(x, y, width, height);
+                state.viewport(x, y, width, height);
+                state.scissor(x, y, width, height);
                 if (sampleIndex === 0) {
                     state.clearColor(0, 0, 0, 0);
                     gl.clear(gl.COLOR_BUFFER_BIT);
@@ -258,9 +281,11 @@ export class MultiSamplePass {
             }
         }
 
+        drawPass.postprocessing.setOcclusionOffset(0, 0);
+
         this.bindOutputTarget(toDrawingBuffer);
-        gl.viewport(x, y, width, height);
-        gl.scissor(x, y, width, height);
+        state.viewport(x, y, width, height);
+        state.scissor(x, y, width, height);
 
         const accumulationWeight = sampleIndex * sampleWeight;
         if (accumulationWeight > 0) {
@@ -281,6 +306,7 @@ export class MultiSamplePass {
 
         camera.viewOffset.enabled = false;
         camera.update();
+        if (isTimingMode) webgl.timer.markEnd('MultiSamplePass.renderTemporalMultiSample');
 
         return sampleIndex >= offsetList.length ? -2 : sampleIndex;
     }
@@ -291,23 +317,23 @@ const JitterVectors = [
         [0, 0]
     ],
     [
-        [4, 4], [-4, -4]
+        [0, 0], [-4, -4]
     ],
     [
-        [-2, -6], [6, -2], [-6, 2], [2, 6]
+        [0, 0], [6, -2], [-6, 2], [2, 6]
     ],
     [
-        [1, -3], [-1, 3], [5, 1], [-3, -5],
+        [0, 0], [-1, 3], [5, 1], [-3, -5],
         [-5, 5], [-7, -1], [3, 7], [7, -7]
     ],
     [
-        [1, 1], [-1, -3], [-3, 2], [4, -1],
+        [0, 0], [-1, -3], [-3, 2], [4, -1],
         [-5, -2], [2, 5], [5, 3], [3, -5],
         [-2, 6], [0, -7], [-4, -6], [-6, 4],
         [-8, 0], [7, -4], [6, 7], [-7, -8]
     ],
     [
-        [-4, -7], [-7, -5], [-3, -5], [-5, -4],
+        [0, 0], [-7, -5], [-3, -5], [-5, -4],
         [-1, -4], [-2, -2], [-6, -1], [-4, 0],
         [-7, 1], [-1, 2], [-6, 3], [-3, 3],
         [-7, 6], [-3, 6], [-5, 7], [-1, 7],

src/mol-canvas3d/passes/passes.ts

@@ -8,22 +8,26 @@ import { DrawPass } from './draw';
 import { PickPass } from './pick';
 import { MultiSamplePass } from './multi-sample';
 import { WebGLContext } from '../../mol-gl/webgl/context';
+import { AssetManager } from '../../mol-util/assets';
 
 export class Passes {
     readonly draw: DrawPass;
     readonly pick: PickPass;
     readonly multiSample: MultiSamplePass;
 
-    constructor(private webgl: WebGLContext, attribs: Partial<{ pickScale: number, enableWboit: boolean }> = {}) {
+    constructor(private webgl: WebGLContext, assetManager: AssetManager, attribs: Partial<{ pickScale: number, enableWboit: boolean, enableDpoit: boolean }> = {}) {
         const { gl } = webgl;
-        this.draw = new DrawPass(webgl, gl.drawingBufferWidth, gl.drawingBufferHeight, attribs.enableWboit || false);
+        this.draw = new DrawPass(webgl, assetManager, gl.drawingBufferWidth, gl.drawingBufferHeight, attribs.enableWboit || false, attribs.enableDpoit || false);
         this.pick = new PickPass(webgl, this.draw, attribs.pickScale || 0.25);
         this.multiSample = new MultiSamplePass(webgl, this.draw);
     }
 
     updateSize() {
         const { gl } = this.webgl;
-        this.draw.setSize(gl.drawingBufferWidth, gl.drawingBufferHeight);
+        // Avoid setting dimensions to 0x0 because it causes "empty textures are not allowed" error.
+        const width = Math.max(gl.drawingBufferWidth, 2);
+        const height = Math.max(gl.drawingBufferHeight, 2);
+        this.draw.setSize(width, height);
         this.pick.syncSize();
         this.multiSample.syncSize();
     }

src/mol-canvas3d/passes/pick.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>
  */
@@ -7,11 +7,15 @@
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { PickType, Renderer } from '../../mol-gl/renderer';
 import { Scene } from '../../mol-gl/scene';
+import { isWebGL2 } from '../../mol-gl/webgl/compat';
 import { WebGLContext } from '../../mol-gl/webgl/context';
-import { GraphicsRenderVariant } from '../../mol-gl/webgl/render-item';
+import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { Renderbuffer } from '../../mol-gl/webgl/renderbuffer';
+import { Texture } from '../../mol-gl/webgl/texture';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { spiral2d } from '../../mol-math/misc';
+import { isTimingMode } from '../../mol-util/debug';
 import { unpackRGBToInt, unpackRGBAToDepth } from '../../mol-util/number-packing';
 import { Camera, ICamera } from '../camera';
 import { StereoCamera } from '../camera/stereo';
@@ -25,10 +29,24 @@ const NullId = Math.pow(2, 24) - 2;
 export type PickData = { id: PickingId, position: Vec3 }
 
 export class PickPass {
-    readonly objectPickTarget: RenderTarget;
-    readonly instancePickTarget: RenderTarget;
-    readonly groupPickTarget: RenderTarget;
-    readonly depthPickTarget: RenderTarget;
+    private readonly objectPickTarget: RenderTarget;
+    private readonly instancePickTarget: RenderTarget;
+    private readonly groupPickTarget: RenderTarget;
+    private readonly depthPickTarget: RenderTarget;
+
+    private readonly framebuffer: Framebuffer;
+
+    private readonly objectPickTexture: Texture;
+    private readonly instancePickTexture: Texture;
+    private readonly groupPickTexture: Texture;
+    private readonly depthPickTexture: Texture;
+
+    private readonly objectPickFramebuffer: Framebuffer;
+    private readonly instancePickFramebuffer: Framebuffer;
+    private readonly groupPickFramebuffer: Framebuffer;
+    private readonly depthPickFramebuffer: Framebuffer;
+
+    private readonly depthRenderbuffer: Renderbuffer;
 
     private pickWidth: number;
     private pickHeight: number;
@@ -38,10 +56,89 @@ export class PickPass {
         this.pickWidth = Math.ceil(drawPass.colorTarget.getWidth() * pickScale);
         this.pickHeight = Math.ceil(drawPass.colorTarget.getHeight() * pickScale);
 
-        this.objectPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
-        this.instancePickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
-        this.groupPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
-        this.depthPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
+        const { resources, extensions: { drawBuffers }, gl } = webgl;
+
+        if (drawBuffers) {
+            this.objectPickTexture = resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+            this.objectPickTexture.define(this.pickWidth, this.pickHeight);
+
+            this.instancePickTexture = resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+            this.instancePickTexture.define(this.pickWidth, this.pickHeight);
+
+            this.groupPickTexture = resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+            this.groupPickTexture.define(this.pickWidth, this.pickHeight);
+
+            this.depthPickTexture = resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+            this.depthPickTexture.define(this.pickWidth, this.pickHeight);
+
+            this.framebuffer = resources.framebuffer();
+
+            this.objectPickFramebuffer = resources.framebuffer();
+            this.instancePickFramebuffer = resources.framebuffer();
+            this.groupPickFramebuffer = resources.framebuffer();
+            this.depthPickFramebuffer = resources.framebuffer();
+
+            this.framebuffer.bind();
+            drawBuffers!.drawBuffers([
+                drawBuffers!.COLOR_ATTACHMENT0,
+                drawBuffers!.COLOR_ATTACHMENT1,
+                drawBuffers!.COLOR_ATTACHMENT2,
+                drawBuffers!.COLOR_ATTACHMENT3,
+            ]);
+
+            this.objectPickTexture.attachFramebuffer(this.framebuffer, 'color0');
+            this.instancePickTexture.attachFramebuffer(this.framebuffer, 'color1');
+            this.groupPickTexture.attachFramebuffer(this.framebuffer, 'color2');
+            this.depthPickTexture.attachFramebuffer(this.framebuffer, 'color3');
+
+            this.depthRenderbuffer = isWebGL2(gl)
+                ? resources.renderbuffer('depth32f', 'depth', this.pickWidth, this.pickHeight)
+                : resources.renderbuffer('depth16', 'depth', this.pickWidth, this.pickHeight);
+
+            this.depthRenderbuffer.attachFramebuffer(this.framebuffer);
+
+            this.objectPickTexture.attachFramebuffer(this.objectPickFramebuffer, 'color0');
+            this.instancePickTexture.attachFramebuffer(this.instancePickFramebuffer, 'color0');
+            this.groupPickTexture.attachFramebuffer(this.groupPickFramebuffer, 'color0');
+            this.depthPickTexture.attachFramebuffer(this.depthPickFramebuffer, 'color0');
+        } else {
+            this.objectPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
+            this.instancePickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
+            this.groupPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
+            this.depthPickTarget = webgl.createRenderTarget(this.pickWidth, this.pickHeight);
+        }
+    }
+
+    bindObject() {
+        if (this.webgl.extensions.drawBuffers) {
+            this.objectPickFramebuffer.bind();
+        } else {
+            this.objectPickTarget.bind();
+        }
+    }
+
+    bindInstance() {
+        if (this.webgl.extensions.drawBuffers) {
+            this.instancePickFramebuffer.bind();
+        } else {
+            this.instancePickTarget.bind();
+        }
+    }
+
+    bindGroup() {
+        if (this.webgl.extensions.drawBuffers) {
+            this.groupPickFramebuffer.bind();
+        } else {
+            this.groupPickTarget.bind();
+        }
+    }
+
+    bindDepth() {
+        if (this.webgl.extensions.drawBuffers) {
+            this.depthPickFramebuffer.bind();
+        } else {
+            this.depthPickTarget.bind();
+        }
     }
 
     get drawingBufferHeight() {
@@ -57,21 +154,30 @@ export class PickPass {
             this.pickWidth = pickWidth;
             this.pickHeight = pickHeight;
 
-            this.objectPickTarget.setSize(this.pickWidth, this.pickHeight);
-            this.instancePickTarget.setSize(this.pickWidth, this.pickHeight);
-            this.groupPickTarget.setSize(this.pickWidth, this.pickHeight);
-            this.depthPickTarget.setSize(this.pickWidth, this.pickHeight);
+            if (this.webgl.extensions.drawBuffers) {
+                this.objectPickTexture.define(this.pickWidth, this.pickHeight);
+                this.instancePickTexture.define(this.pickWidth, this.pickHeight);
+                this.groupPickTexture.define(this.pickWidth, this.pickHeight);
+                this.depthPickTexture.define(this.pickWidth, this.pickHeight);
+
+                this.depthRenderbuffer.setSize(this.pickWidth, this.pickHeight);
+            } else {
+                this.objectPickTarget.setSize(this.pickWidth, this.pickHeight);
+                this.instancePickTarget.setSize(this.pickWidth, this.pickHeight);
+                this.groupPickTarget.setSize(this.pickWidth, this.pickHeight);
+                this.depthPickTarget.setSize(this.pickWidth, this.pickHeight);
+            }
         }
     }
 
-    private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: GraphicsRenderVariant, pickType: number) {
-        const depth = this.drawPass.depthTexturePrimitives;
+    private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: 'pick' | 'depth', pickType: number) {
         renderer.clear(false);
-
         renderer.update(camera);
         renderer.renderPick(scene.primitives, camera, variant, null, pickType);
-        renderer.renderPick(scene.volumes, camera, variant, depth, pickType);
-        renderer.renderPick(helper.handle.scene, camera, variant, null, pickType);
+
+        if (helper.handle.isEnabled) {
+            renderer.renderPick(helper.handle.scene, camera, variant, null, pickType);
+        }
 
         if (helper.camera.isEnabled) {
             helper.camera.update(camera);
@@ -81,18 +187,23 @@ export class PickPass {
     }
 
     render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper) {
-        this.objectPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Object);
+        if (this.webgl.extensions.drawBuffers) {
+            this.framebuffer.bind();
+            this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.None);
+        } else {
+            this.objectPickTarget.bind();
+            this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Object);
 
-        this.instancePickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Instance);
+            this.instancePickTarget.bind();
+            this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Instance);
 
-        this.groupPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Group);
-        // printTexture(this.webgl, this.groupPickTarget.texture, { id: 'group' })
+            this.groupPickTarget.bind();
+            this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Group);
+            // printTexture(this.webgl, this.groupPickTarget.texture, { id: 'group' })
 
-        this.depthPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'depth', PickType.None);
+            this.depthPickTarget.bind();
+            this.renderVariant(renderer, camera, scene, helper, 'depth', PickType.None);
+        }
     }
 }
 
@@ -147,19 +258,21 @@ export class PickHelper {
     }
 
     private syncBuffers() {
+        if (isTimingMode) this.webgl.timer.mark('PickHelper.syncBuffers');
         const { pickX, pickY, pickWidth, pickHeight } = this;
 
-        this.pickPass.objectPickTarget.bind();
+        this.pickPass.bindObject();
         this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.objectBuffer);
 
-        this.pickPass.instancePickTarget.bind();
+        this.pickPass.bindInstance();
         this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.instanceBuffer);
 
-        this.pickPass.groupPickTarget.bind();
+        this.pickPass.bindGroup();
         this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.groupBuffer);
 
-        this.pickPass.depthPickTarget.bind();
+        this.pickPass.bindDepth();
         this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.depthBuffer);
+        if (isTimingMode) this.webgl.timer.markEnd('PickHelper.syncBuffers');
     }
 
     private getBufferIdx(x: number, y: number): number {
@@ -178,11 +291,12 @@ export class PickHelper {
     }
 
     private render(camera: Camera | StereoCamera) {
+        if (isTimingMode) this.webgl.timer.mark('PickHelper.render');
         const { pickX, pickY, pickWidth, pickHeight, halfPickWidth } = this;
         const { renderer, scene, helper } = this;
 
         renderer.setTransparentBackground(false);
-        renderer.setDrawingBufferSize(this.pickPass.objectPickTarget.getWidth(), this.pickPass.objectPickTarget.getHeight());
+        renderer.setDrawingBufferSize(pickWidth, pickHeight);
         renderer.setPixelRatio(this.pickScale);
 
         if (StereoCamera.is(camera)) {
@@ -197,6 +311,7 @@ export class PickHelper {
         }
 
         this.dirty = false;
+        if (isTimingMode) this.webgl.timer.markEnd('PickHelper.render');
     }
 
     private identifyInternal(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
@@ -217,8 +332,10 @@ export class PickHelper {
         ) return;
 
         if (this.dirty) {
+            if (isTimingMode) this.webgl.timer.mark('PickHelper.identify');
             this.render(camera);
             this.syncBuffers();
+            if (isTimingMode) this.webgl.timer.markEnd('PickHelper.identify');
         }
 
         const xv = x - viewport.x;
@@ -240,6 +357,7 @@ export class PickHelper {
         if (groupId === -1 || groupId === NullId) return;
 
         const z = this.getDepth(xp, yp);
+        // console.log('z', z);
         const position = Vec3.create(x, viewport.height - y, z);
         if (StereoCamera.is(camera)) {
             const halfWidth = Math.floor(viewport.width / 2);
@@ -254,7 +372,7 @@ export class PickHelper {
             cameraUnproject(position, position, viewport, camera.inverseProjectionView);
         }
 
-        // console.log({ { objectId, instanceId, groupId }, position} );
+        // console.log({ id: { objectId, instanceId, groupId }, position });
         return { id: { objectId, instanceId, groupId }, position };
     }
 

src/mol-canvas3d/passes/postprocessing.ts

@@ -1,11 +1,11 @@
 /**
- * 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 Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
  */
 
-import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
 import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
 import { ShaderCode } from '../../mol-gl/shader-code';
 import { WebGLContext } from '../../mol-gl/webgl/context';
@@ -27,10 +27,14 @@ import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
 import { Color } from '../../mol-util/color';
 import { FxaaParams, FxaaPass } from './fxaa';
 import { SmaaParams, SmaaPass } from './smaa';
+import { isTimingMode } from '../../mol-util/debug';
+import { BackgroundParams, BackgroundPass } from './background';
+import { AssetManager } from '../../mol-util/assets';
 
 const OutlinesSchema = {
     ...QuadSchema,
-    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     uTexSize: UniformSpec('v2'),
 
     dOrthographic: DefineSpec('number'),
@@ -41,11 +45,15 @@ const OutlinesSchema = {
 };
 type OutlinesRenderable = ComputeRenderable<Values<typeof OutlinesSchema>>
 
-function getOutlinesRenderable(ctx: WebGLContext, depthTexture: Texture): OutlinesRenderable {
+function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture): OutlinesRenderable {
+    const width = depthTextureOpaque.getWidth();
+    const height = depthTextureOpaque.getHeight();
+
     const values: Values<typeof OutlinesSchema> = {
         ...QuadValues,
-        tDepth: ValueCell.create(depthTexture),
-        uTexSize: ValueCell.create(Vec2.create(depthTexture.getWidth(), depthTexture.getHeight())),
+        tDepthOpaque: ValueCell.create(depthTextureOpaque),
+        tDepthTransparent: ValueCell.create(depthTextureTransparent),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
 
         dOrthographic: ValueCell.create(0),
         uNear: ValueCell.create(1),
@@ -85,7 +93,7 @@ function getSsaoRenderable(ctx: WebGLContext, depthTexture: Texture): SsaoRender
         ...QuadValues,
         tDepth: ValueCell.create(depthTexture),
 
-        uSamples: ValueCell.create([0.0, 0.0, 1.0]),
+        uSamples: ValueCell.create(getSamples(32)),
         dNSamples: ValueCell.create(32),
 
         uProjection: ValueCell.create(Mat4.identity()),
@@ -132,7 +140,7 @@ function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, dir
         tSsaoDepth: ValueCell.create(ssaoDepthTexture),
         uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())),
 
-        uKernel: ValueCell.create([0.0]),
+        uKernel: ValueCell.create(getBlurKernel(15)),
         dOcclusionKernelSize: ValueCell.create(15),
 
         uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0),
@@ -165,15 +173,26 @@ function getBlurKernel(kernelSize: number): number[] {
     return kernel;
 }
 
-function getSamples(vectorSamples: Vec3[], nSamples: number): number[] {
+const RandomHemisphereVector: Vec3[] = [];
+for (let i = 0; i < 256; i++) {
+    const v = Vec3();
+    v[0] = Math.random() * 2.0 - 1.0;
+    v[1] = Math.random() * 2.0 - 1.0;
+    v[2] = Math.random();
+    Vec3.normalize(v, v);
+    Vec3.scale(v, v, Math.random());
+    RandomHemisphereVector.push(v);
+}
+
+function getSamples(nSamples: number): number[] {
     const samples = [];
     for (let i = 0; i < nSamples; i++) {
         let scale = (i * i + 2.0 * i + 1) / (nSamples * nSamples);
         scale = 0.1 + scale * (1.0 - 0.1);
 
-        samples.push(vectorSamples[i][0] * scale);
-        samples.push(vectorSamples[i][1] * scale);
-        samples.push(vectorSamples[i][2] * scale);
+        samples.push(RandomHemisphereVector[i][0] * scale);
+        samples.push(RandomHemisphereVector[i][1] * scale);
+        samples.push(RandomHemisphereVector[i][2] * scale);
     }
 
     return samples;
@@ -183,7 +202,8 @@ const PostprocessingSchema = {
     ...QuadSchema,
     tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tOutlines: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     uTexSize: UniformSpec('v2'),
 
@@ -199,6 +219,7 @@ const PostprocessingSchema = {
     uMaxPossibleViewZDiff: UniformSpec('f'),
 
     dOcclusionEnable: DefineSpec('boolean'),
+    uOcclusionOffset: UniformSpec('v2'),
 
     dOutlineEnable: DefineSpec('boolean'),
     dOutlineScale: DefineSpec('number'),
@@ -206,12 +227,13 @@ const PostprocessingSchema = {
 };
 type PostprocessingRenderable = ComputeRenderable<Values<typeof PostprocessingSchema>>
 
-function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTexture: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture): PostprocessingRenderable {
+function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture): PostprocessingRenderable {
     const values: Values<typeof PostprocessingSchema> = {
         ...QuadValues,
         tSsaoDepth: ValueCell.create(ssaoDepthTexture),
         tColor: ValueCell.create(colorTexture),
-        tDepth: ValueCell.create(depthTexture),
+        tDepthOpaque: ValueCell.create(depthTextureOpaque),
+        tDepthTransparent: ValueCell.create(depthTextureTransparent),
         tOutlines: ValueCell.create(outlinesTexture),
         uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
 
@@ -227,6 +249,7 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
         uMaxPossibleViewZDiff: ValueCell.create(0.5),
 
         dOcclusionEnable: ValueCell.create(true),
+        uOcclusionOffset: ValueCell.create(Vec2.create(0, 0)),
 
         dOutlineEnable: ValueCell.create(false),
         dOutlineScale: ValueCell.create(1),
@@ -244,9 +267,10 @@ export const PostprocessingParams = {
     occlusion: PD.MappedStatic('on', {
         on: PD.Group({
             samples: PD.Numeric(32, { min: 1, max: 256, step: 1 }),
-            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final radius is 2^x.' }),
+            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final occlusion radius is 2^x' }),
             bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
             blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
+            resolutionScale: PD.Numeric(1, { min: 0.1, max: 1, step: 0.05 }, { description: 'Adjust resolution of occlusion calculation' }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
@@ -263,12 +287,17 @@ export const PostprocessingParams = {
         smaa: PD.Group(SmaaParams),
         off: PD.Group({})
     }, { options: [['fxaa', 'FXAA'], ['smaa', 'SMAA'], ['off', 'Off']], description: 'Smooth pixel edges' }),
+    background: PD.Group(BackgroundParams, { isFlat: true }),
 };
 export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
 
 export class PostprocessingPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.occlusion.name === 'on' || props.outline.name === 'on';
+        return props.occlusion.name === 'on' || props.outline.name === 'on' || props.background.variant.name !== 'off';
+    }
+
+    static isOutlineEnabled(props: PostprocessingProps) {
+        return props.outline.name === 'on';
     }
 
     readonly target: RenderTarget;
@@ -276,11 +305,13 @@ export class PostprocessingPass {
     private readonly outlinesTarget: RenderTarget;
     private readonly outlinesRenderable: OutlinesRenderable;
 
-    private readonly randomHemisphereVector: Vec3[];
     private readonly ssaoFramebuffer: Framebuffer;
     private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
     private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;
 
+    private readonly downsampledDepthTarget: RenderTarget;
+    private readonly downsampleDepthRenderable: CopyRenderable;
+
     private readonly ssaoDepthTexture: Texture;
     private readonly ssaoDepthBlurProxyTexture: Texture;
 
@@ -290,41 +321,35 @@ export class PostprocessingPass {
 
     private nSamples: number;
     private blurKernelSize: number;
+    private downsampleFactor: number;
 
     private readonly renderable: PostprocessingRenderable;
 
     private ssaoScale: number;
     private calcSsaoScale() {
         // downscale ssao for high pixel-ratios
-        return Math.min(1, 1 / this.webgl.pixelRatio);
+        return Math.min(1, 1 / this.webgl.pixelRatio) * this.downsampleFactor;
     }
 
-    constructor(private webgl: WebGLContext, drawPass: DrawPass) {
-        this.ssaoScale = this.calcSsaoScale();
+    private readonly bgColor = Vec3();
+    readonly background: BackgroundPass;
 
-        const { colorTarget, depthTexture } = drawPass;
+    constructor(private readonly webgl: WebGLContext, assetManager: AssetManager, private readonly drawPass: DrawPass) {
+        const { colorTarget, depthTextureTransparent, depthTextureOpaque } = drawPass;
         const width = colorTarget.getWidth();
         const height = colorTarget.getHeight();
 
         this.nSamples = 1;
         this.blurKernelSize = 1;
+        this.downsampleFactor = 1;
+        this.ssaoScale = this.calcSsaoScale();
 
         // needs to be linear for anti-aliasing pass
         this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
 
         this.outlinesTarget = webgl.createRenderTarget(width, height, false);
-        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTexture);
+        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent);
 
-        this.randomHemisphereVector = [];
-        for (let i = 0; i < 256; i++) {
-            const v = Vec3();
-            v[0] = Math.random() * 2.0 - 1.0;
-            v[1] = Math.random() * 2.0 - 1.0;
-            v[2] = Math.random();
-            Vec3.normalize(v, v);
-            Vec3.scale(v, v, Math.random());
-            this.randomHemisphereVector.push(v);
-        }
         this.ssaoFramebuffer = webgl.resources.framebuffer();
         this.ssaoBlurFirstPassFramebuffer = webgl.resources.framebuffer();
         this.ssaoBlurSecondPassFramebuffer = webgl.resources.framebuffer();
@@ -332,20 +357,25 @@ export class PostprocessingPass {
         const sw = Math.floor(width * this.ssaoScale);
         const sh = Math.floor(height * this.ssaoScale);
 
-        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        this.downsampledDepthTarget = webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear');
+        this.downsampleDepthRenderable = createCopyRenderable(webgl, depthTextureOpaque);
+
+        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
         this.ssaoDepthTexture.define(sw, sh);
         this.ssaoDepthTexture.attachFramebuffer(this.ssaoFramebuffer, 'color0');
 
-        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
         this.ssaoDepthBlurProxyTexture.define(sw, sh);
         this.ssaoDepthBlurProxyTexture.attachFramebuffer(this.ssaoBlurFirstPassFramebuffer, 'color0');
 
         this.ssaoDepthTexture.attachFramebuffer(this.ssaoBlurSecondPassFramebuffer, 'color0');
 
-        this.ssaoRenderable = getSsaoRenderable(webgl, depthTexture);
+        this.ssaoRenderable = getSsaoRenderable(webgl, this.downsampleFactor === 1 ? depthTextureOpaque : this.downsampledDepthTarget.texture);
         this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
         this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
-        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture, this.outlinesTarget.texture, this.ssaoDepthTexture);
+        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.outlinesTarget.texture, this.ssaoDepthTexture);
+
+        this.background = new BackgroundPass(webgl, assetManager, width, height);
     }
 
     setSize(width: number, height: number) {
@@ -359,14 +389,18 @@ export class PostprocessingPass {
             const sh = Math.floor(height * this.ssaoScale);
             this.target.setSize(width, height);
             this.outlinesTarget.setSize(width, height);
+            this.downsampledDepthTarget.setSize(sw, sh);
             this.ssaoDepthTexture.define(sw, sh);
             this.ssaoDepthBlurProxyTexture.define(sw, sh);
 
             ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
             ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
             ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
+
+            this.background.setSize(width, height);
         }
     }
 
@@ -416,7 +450,7 @@ export class PostprocessingPass {
                 needsUpdateSsao = true;
 
                 this.nSamples = props.occlusion.params.samples;
-                ValueCell.update(this.ssaoRenderable.values.uSamples, getSamples(this.randomHemisphereVector, this.nSamples));
+                ValueCell.update(this.ssaoRenderable.values.uSamples, getSamples(this.nSamples));
                 ValueCell.updateIfChanged(this.ssaoRenderable.values.dNSamples, this.nSamples);
             }
             ValueCell.updateIfChanged(this.ssaoRenderable.values.uRadius, Math.pow(2, props.occlusion.params.radius));
@@ -434,6 +468,30 @@ export class PostprocessingPass {
                 ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
             }
 
+            if (this.downsampleFactor !== props.occlusion.params.resolutionScale) {
+                needsUpdateSsao = true;
+
+                this.downsampleFactor = props.occlusion.params.resolutionScale;
+                this.ssaoScale = this.calcSsaoScale();
+
+                const sw = Math.floor(w * this.ssaoScale);
+                const sh = Math.floor(h * this.ssaoScale);
+
+                this.downsampledDepthTarget.setSize(sw, sh);
+                this.ssaoDepthTexture.define(sw, sh);
+                this.ssaoDepthBlurProxyTexture.define(sw, sh);
+
+                if (this.ssaoScale === 1) {
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.drawPass.depthTextureTransparent);
+                } else {
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.downsampledDepthTarget.texture);
+                }
+
+                ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
+            }
         }
 
         if (props.outline.name === 'on') {
@@ -490,11 +548,24 @@ export class PostprocessingPass {
         state.depthMask(false);
 
         const { x, y, width, height } = camera.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);
+    }
+
+    private occlusionOffset: [x: number, y: number] = [0, 0];
+    setOcclusionOffset(x: number, y: number) {
+        this.occlusionOffset[0] = x;
+        this.occlusionOffset[1] = y;
+        ValueCell.update(this.renderable.values.uOcclusionOffset, Vec2.set(this.renderable.values.uOcclusionOffset.ref.value, x, y));
+    }
+
+    private transparentBackground = false;
+    setTransparentBackground(value: boolean) {
+        this.transparentBackground = value;
     }
 
     render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
+        if (isTimingMode) this.webgl.timer.mark('PostprocessingPass.render');
         this.updateState(camera, transparentBackground, backgroundColor, props);
 
         if (props.outline.name === 'on') {
@@ -502,14 +573,13 @@ export class PostprocessingPass {
             this.outlinesRenderable.render();
         }
 
-        if (props.occlusion.name === 'on') {
-            const { x, y, width, height } = camera.viewport;
-            const sx = Math.floor(x * this.ssaoScale);
-            const sy = Math.floor(y * this.ssaoScale);
-            const sw = Math.ceil(width * this.ssaoScale);
-            const sh = Math.ceil(height * this.ssaoScale);
-            this.webgl.gl.viewport(sx, sy, sw, sh);
-            this.webgl.gl.scissor(sx, sy, sw, sh);
+        // don't render occlusion if offset is given,
+        // which will reuse the existing occlusion
+        if (props.occlusion.name === 'on' && this.occlusionOffset[0] === 0 && this.occlusionOffset[1] === 0) {
+            if (this.ssaoScale < 1) {
+                this.downsampledDepthTarget.bind();
+                this.downsampleDepthRenderable.render();
+            }
 
             this.ssaoFramebuffer.bind();
             this.ssaoRenderable.render();
@@ -519,9 +589,6 @@ export class PostprocessingPass {
 
             this.ssaoBlurSecondPassFramebuffer.bind();
             this.ssaoBlurSecondPassRenderable.render();
-
-            this.webgl.gl.viewport(x, y, width, height);
-            this.webgl.gl.scissor(x, y, width, height);
         }
 
         if (toDrawingBuffer) {
@@ -531,10 +598,26 @@ export class PostprocessingPass {
         }
 
         const { gl, state } = this.webgl;
-        state.clearColor(0, 0, 0, 1);
-        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.background.update(camera, props.background);
+        if (this.background.isEnabled(props.background)) {
+            if (this.transparentBackground) {
+                state.clearColor(0, 0, 0, 0);
+            } else {
+                Color.toVec3Normalized(this.bgColor, backgroundColor);
+                state.clearColor(this.bgColor[0], this.bgColor[1], this.bgColor[2], 1);
+            }
+            gl.clear(gl.COLOR_BUFFER_BIT);
+            state.enable(gl.BLEND);
+            state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
+            this.background.render();
+        } else {
+            state.clearColor(0, 0, 0, 1);
+            gl.clear(gl.COLOR_BUFFER_BIT);
+        }
 
         this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('PostprocessingPass.render');
     }
 }
 

src/mol-canvas3d/passes/smaa.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,7 +11,7 @@ import { ShaderCode } from '../../mol-gl/shader-code';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
-import { createTexture, loadImageTexture, Texture } from '../../mol-gl/webgl/texture';
+import { loadImageTexture, Texture } from '../../mol-gl/webgl/texture';
 import { Vec2, Vec4 } from '../../mol-math/linear-algebra';
 import { ValueCell } from '../../mol-util';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -22,7 +22,7 @@ import { weights_frag } from '../../mol-gl/shader/smaa/weights.frag';
 import { edges_vert } from '../../mol-gl/shader/smaa/edges.vert';
 import { edges_frag } from '../../mol-gl/shader/smaa/edges.frag';
 import { Viewport } from '../camera/util';
-import { isDebugMode } from '../../mol-util/debug';
+import { isDebugMode, isTimingMode } from '../../mol-util/debug';
 
 export const SmaaParams = {
     edgeThreshold: PD.Numeric(0.1, { min: 0.05, max: 0.15, step: 0.01 }),
@@ -71,9 +71,10 @@ export class SmaaPass {
         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.colorMask(true, true, true, true);
         state.clearColor(0, 0, 0, 1);
         gl.clear(gl.COLOR_BUFFER_BIT);
 
@@ -120,6 +121,7 @@ export class SmaaPass {
     }
 
     render(viewport: Viewport, target: RenderTarget | undefined) {
+        if (isTimingMode) this.webgl.timer.mark('SmaaPass.render');
         this.edgesTarget.bind();
         this.updateState(viewport);
         this.edgesRenderable.render();
@@ -135,8 +137,8 @@ export class SmaaPass {
         }
         this.updateState(viewport);
         this.blendRenderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('SmaaPass.render');
     }
-
 }
 
 //
@@ -190,8 +192,8 @@ function getWeightsRenderable(ctx: WebGLContext, edgesTexture: Texture): Weights
     const width = edgesTexture.getWidth();
     const height = edgesTexture.getHeight();
 
-    const areaTexture = createTexture(ctx.gl, ctx.extensions, 'image-uint8', 'rgb', 'ubyte', 'linear');
-    const searchTexture = createTexture(ctx.gl, ctx.extensions, 'image-uint8', 'rgba', 'ubyte', 'nearest');
+    const areaTexture = ctx.resources.texture('image-uint8', 'rgb', 'ubyte', 'linear');
+    const searchTexture = ctx.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
 
     const values: Values<typeof WeightsSchema> = {
         ...QuadValues,

src/mol-canvas3d/passes/wboit.ts

@@ -17,7 +17,9 @@ import { quad_vert } from '../../mol-gl/shader/quad.vert';
 import { evaluateWboit_frag } from '../../mol-gl/shader/evaluate-wboit.frag';
 import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
 import { Vec2 } from '../../mol-math/linear-algebra';
-import { isDebugMode } from '../../mol-util/debug';
+import { isDebugMode, isTimingMode } from '../../mol-util/debug';
+import { isWebGL2 } from '../../mol-gl/webgl/compat';
+import { Renderbuffer } from '../../mol-gl/webgl/renderbuffer';
 
 const EvaluateWboitSchema = {
     ...QuadSchema,
@@ -50,6 +52,7 @@ export class WboitPass {
     private readonly framebuffer: Framebuffer;
     private readonly textureA: Texture;
     private readonly textureB: Texture;
+    private readonly depthRenderbuffer: Renderbuffer;
 
     private _supported = false;
     get supported() {
@@ -71,6 +74,7 @@ export class WboitPass {
     }
 
     render() {
+        if (isTimingMode) this.webgl.timer.mark('WboitPass.render');
         const { state, gl } = this.webgl;
 
         state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
@@ -78,6 +82,7 @@ export class WboitPass {
 
         this.renderable.update();
         this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('WboitPass.render');
     }
 
     setSize(width: number, height: number) {
@@ -85,6 +90,7 @@ export class WboitPass {
         if (width !== w || height !== h) {
             this.textureA.define(width, height);
             this.textureB.define(width, height);
+            this.depthRenderbuffer.setSize(width, height);
             ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
         }
     }
@@ -104,6 +110,8 @@ export class WboitPass {
 
         this.textureA.attachFramebuffer(this.framebuffer, 'color0');
         this.textureB.attachFramebuffer(this.framebuffer, 'color1');
+
+        this.depthRenderbuffer.attachFramebuffer(this.framebuffer);
     }
 
     static isSupported(webgl: WebGLContext) {
@@ -126,7 +134,7 @@ export class WboitPass {
     constructor(private webgl: WebGLContext, width: number, height: number) {
         if (!WboitPass.isSupported(webgl)) return;
 
-        const { resources } = webgl;
+        const { resources, gl } = webgl;
 
         this.textureA = resources.texture('image-float32', 'rgba', 'float', 'nearest');
         this.textureA.define(width, height);
@@ -134,6 +142,10 @@ export class WboitPass {
         this.textureB = resources.texture('image-float32', 'rgba', 'float', 'nearest');
         this.textureB.define(width, height);
 
+        this.depthRenderbuffer = isWebGL2(gl)
+            ? resources.renderbuffer('depth32f', 'depth', width, height)
+            : resources.renderbuffer('depth16', 'depth', width, height);
+
         this.renderable = getEvaluateWboitRenderable(webgl, this.textureA, this.textureB);
         this.framebuffer = resources.framebuffer();
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -61,6 +61,29 @@ describe('column', () => {
     });
 });
 
+describe('string column', () => {
+    const xs = ['A', 'b', null, undefined];
+    const xsArr = xs.map(x => x ?? '');
+    const xsLC = xs.map(x => (x ?? '').toLowerCase());
+    const arr = Column.ofArray({ array: xs as any, schema: Column.Schema.str });
+    const arrLC = Column.ofArray({ array: xs as any, schema: Column.Schema.Str({ transform: 'lowercase' }) });
+    const aliasedLC = Column.ofArray({ array: xs as any, schema: Column.Schema.Aliased<'a' | 'b'>(Column.Schema.lstr) });
+
+    it('value', () => {
+        for (let i = 0; i < xs.length; i++) {
+            expect(arr.value(i)).toBe(xs[i] ?? '');
+            expect(arrLC.value(i)).toBe(xsLC[i] ?? '');
+            expect(aliasedLC.value(i)).toBe(xsLC[i]);
+        }
+    });
+
+    it('array', () => {
+        expect(arr.toArray()).toEqual(xsArr);
+        expect(arrLC.toArray()).toEqual(xsLC);
+        expect(aliasedLC.toArray()).toEqual(xsLC);
+    });
+});
+
 describe('table', () => {
     const schema = {
         x: Column.Schema.int,

src/mol-data/db/column.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -25,38 +25,39 @@ interface Column<T> {
 namespace Column {
     export type ArrayCtor<T> = { new(size: number): ArrayLike<T> }
 
-    export type Schema<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T> | Schema.Tensor | Schema.List<number|string>
+    export type Schema<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T> | Schema.Tensor | Schema.List<number | string>
 
     export namespace Schema {
         // T also serves as a default value for undefined columns
 
         type Base<T extends string> = { valueType: T }
-        export type Str = { '@type': 'str', T: string } & Base<'str'>
+        export type Str = { '@type': 'str', T: string, transform?: 'uppercase' | 'lowercase' } & Base<'str'>
         export type Int = { '@type': 'int', T: number } & Base<'int'>
         export type Float = { '@type': 'float', T: number } & Base<'float'>
         export type Coordinate = { '@type': 'coord', T: number } & Base<'float'>
 
         export type Tensor = { '@type': 'tensor', T: Tensors.Data, space: Tensors.Space, baseType: Int | Float } & Base<'tensor'>
-        export type Aliased<T> = { '@type': 'aliased', T: T } & Base<T extends string ? 'str' : 'int'>
-        export type List<T extends number|string> = { '@type': 'list', T: T[], separator: string, itemParse: (x: string) => T } & Base<'list'>
+        export type Aliased<T> = { '@type': 'aliased', T: T, transform?: T extends string ? 'uppercase' | 'lowercase' : never } & Base<T extends string ? 'str' : 'int'>
+        export type List<T extends number | string> = { '@type': 'list', T: T[], separator: string, itemParse: (x: string) => T } & Base<'list'>
 
         export const str: Str = { '@type': 'str', T: '', valueType: 'str' };
+        export const ustr: Str = { '@type': 'str', T: '', valueType: 'str', transform: 'uppercase' };
+        export const lstr: Str = { '@type': 'str', T: '', valueType: 'str', transform: 'lowercase' };
         export const int: Int = { '@type': 'int', T: 0, valueType: 'int' };
         export const coord: Coordinate = { '@type': 'coord', T: 0, valueType: 'float' };
         export const float: Float = { '@type': 'float', T: 0, valueType: 'float' };
 
-        export function Str(defaultValue = ''): Str { return { '@type': 'str', T: defaultValue, valueType: 'str' }; };
+        export function Str(options?: { defaultValue?: string, transform?: 'uppercase' | 'lowercase' }): Str { return { '@type': 'str', T: options?.defaultValue ?? '', transform: options?.transform, valueType: 'str' }; };
         export function Int(defaultValue = 0): Int { return { '@type': 'int', T: defaultValue, valueType: 'int' }; };
         export function Float(defaultValue = 0): Float { return { '@type': 'float', T: defaultValue, valueType: 'float' }; };
         export function Tensor(space: Tensors.Space, baseType: Int | Float = float): Tensor { return { '@type': 'tensor', T: space.create(), space, valueType: 'tensor', baseType }; }
         export function Vector(dim: number, baseType: Int | Float = float): Tensor { return Tensor(Tensors.Vector(dim, baseType['@type'] === 'int' ? Int32Array : Float64Array), baseType); }
         export function Matrix(rows: number, cols: number, baseType: Int | Float = float): Tensor { return Tensor(Tensors.ColumnMajorMatrix(rows, cols, baseType['@type'] === 'int' ? Int32Array : Float64Array), baseType); }
 
-        export function Aliased<T>(t: Str | Int, defaultValue?: T): Aliased<T> {
-            if (typeof defaultValue !== 'undefined') return { ...t, T: defaultValue } as any as Aliased<T>;
+        export function Aliased<T>(t: Str | Int): Aliased<T> {
             return t as any as Aliased<T>;
         }
-        export function List<T extends number|string>(separator: string, itemParse: (x: string) => T, defaultValue: T[] = []): List<T> {
+        export function List<T extends number | string>(separator: string, itemParse: (x: string) => T, defaultValue: T[] = []): List<T> {
             return { '@type': 'list', T: defaultValue, separator, itemParse, valueType: 'list' };
         }
     }
@@ -287,8 +288,13 @@ function lambdaColumn<T extends Column.Schema>({ value, valueKind, areValuesEqua
 
 function arrayColumn<T extends Column.Schema>({ array, schema, valueKind }: Column.ArraySpec<T>): Column<T['T']> {
     const rowCount = array.length;
+    const defaultValue = schema.T;
     const value: Column<T['T']>['value'] = schema.valueType === 'str'
-        ? row => { const v = array[row]; return typeof v === 'string' ? v : '' + v; }
+        ? (schema as Column.Schema.Str).transform === 'lowercase'
+            ? row => { const v = array[row]; return typeof v === 'string' ? v.toLowerCase() : `${v ?? defaultValue}`.toLowerCase(); }
+            : (schema as Column.Schema.Str).transform === 'uppercase'
+                ? row => { const v = array[row]; return typeof v === 'string' ? v.toUpperCase() : `${v ?? defaultValue}`.toUpperCase(); }
+                : row => { const v = array[row]; return typeof v === 'string' ? v : `${v ?? defaultValue}`; }
         : row => array[row];
 
     const isTyped = ColumnHelpers.isTypedArray(array);
@@ -300,15 +306,35 @@ function arrayColumn<T extends Column.Schema>({ array, schema, valueKind }: Colu
         value,
         valueKind: valueKind ? valueKind : row => Column.ValueKind.Present,
         toArray: schema.valueType === 'str'
-            ? params => {
-                const { start, end } = ColumnHelpers.getArrayBounds(rowCount, params);
-                const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
-                for (let i = 0, _i = end - start; i < _i; i++) {
-                    const v = array[start + i];
-                    ret[i] = typeof v === 'string' ? v : '' + v;
+            ? (schema as Column.Schema.Str).transform === 'lowercase'
+                ? params => {
+                    const { start, end } = ColumnHelpers.getArrayBounds(rowCount, params);
+                    const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
+                    for (let i = 0, _i = end - start; i < _i; i++) {
+                        const v = array[start + i];
+                        ret[i] = typeof v === 'string' ? v.toLowerCase() : `${v ?? defaultValue}`.toLowerCase();
+                    }
+                    return ret;
                 }
-                return ret;
-            }
+                : (schema as Column.Schema.Str).transform === 'uppercase'
+                    ? params => {
+                        const { start, end } = ColumnHelpers.getArrayBounds(rowCount, params);
+                        const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
+                        for (let i = 0, _i = end - start; i < _i; i++) {
+                            const v = array[start + i];
+                            ret[i] = typeof v === 'string' ? v.toUpperCase() : `${v ?? defaultValue}`.toUpperCase();
+                        }
+                        return ret;
+                    }
+                    : params => {
+                        const { start, end } = ColumnHelpers.getArrayBounds(rowCount, params);
+                        const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
+                        for (let i = 0, _i = end - start; i < _i; i++) {
+                            const v = array[start + i];
+                            ret[i] = typeof v === 'string' ? v : `${v ?? defaultValue}`;
+                        }
+                        return ret;
+                    }
             : isTyped
                 ? params => ColumnHelpers.typedArrayWindow(array, params) as any as ReadonlyArray<T>
                 : params => {

src/mol-geo/geometry/base.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -83,6 +83,7 @@ export namespace BaseGeometry {
         quality: PD.Select<VisualQuality>('auto', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }),
         material: Material.getParam(),
         clip: PD.Group(Clip.Params),
+        instanceGranularity: PD.Boolean(false, { description: 'Use instance granularity for marker, transparency, clipping, overpaint, substance data to save memory.' }),
     };
     export type Params = typeof Params
 
@@ -110,6 +111,7 @@ export namespace BaseGeometry {
             uRoughness: ValueCell.create(props.material.roughness),
             uBumpiness: ValueCell.create(props.material.bumpiness),
             dLightCount: ValueCell.create(1),
+            dColorMarker: ValueCell.create(true),
 
             dClipObjectCount: ValueCell.create(clip.objects.count),
             dClipVariant: ValueCell.create(clip.variant),
@@ -118,6 +120,8 @@ export namespace BaseGeometry {
             uClipObjectPosition: ValueCell.create(clip.objects.position),
             uClipObjectRotation: ValueCell.create(clip.objects.rotation),
             uClipObjectScale: ValueCell.create(clip.objects.scale),
+
+            instanceGranularity: ValueCell.create(props.instanceGranularity),
         };
     }
 
@@ -135,6 +139,8 @@ export namespace BaseGeometry {
         ValueCell.update(values.uClipObjectPosition, clip.objects.position);
         ValueCell.update(values.uClipObjectRotation, clip.objects.rotation);
         ValueCell.update(values.uClipObjectScale, clip.objects.scale);
+
+        ValueCell.updateIfChanged(values.instanceGranularity, props.instanceGranularity);
     }
 
     export function createRenderableState(props: Partial<PD.Values<Params>> = {}): RenderableState {

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

@@ -9,10 +9,13 @@ import { Vec2 } from '../../mol-math/linear-algebra';
 import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
 import { Clipping } from '../../mol-theme/clipping';
 
+export type ClippingType = 'instance' | 'groupInstance';
+
 export type ClippingData = {
     tClipping: ValueCell<TextureImage<Uint8Array>>
     uClippingTexDim: ValueCell<Vec2>
-    dClipping: ValueCell<boolean>,
+    dClipping: ValueCell<boolean>
+    dClippingType: ValueCell<string>
 }
 
 export function applyClippingGroups(array: Uint8Array, start: number, end: number, groups: Clipping.Groups) {
@@ -24,18 +27,20 @@ export function clearClipping(array: Uint8Array, start: number, end: number) {
     array.fill(0, start, end);
 }
 
-export function createClipping(count: number, clippingData?: ClippingData): ClippingData {
+export function createClipping(count: number, type: ClippingType, clippingData?: ClippingData): ClippingData {
     const clipping = createTextureImage(Math.max(1, count), 1, Uint8Array, clippingData && clippingData.tClipping.ref.value.array);
     if (clippingData) {
         ValueCell.update(clippingData.tClipping, clipping);
         ValueCell.update(clippingData.uClippingTexDim, Vec2.create(clipping.width, clipping.height));
         ValueCell.updateIfChanged(clippingData.dClipping, count > 0);
+        ValueCell.updateIfChanged(clippingData.dClippingType, type);
         return clippingData;
     } else {
         return {
             tClipping: ValueCell.create(clipping),
             uClippingTexDim: ValueCell.create(Vec2.create(clipping.width, clipping.height)),
             dClipping: ValueCell.create(count > 0),
+            dClippingType: ValueCell.create(type),
         };
     }
 }
@@ -52,6 +57,7 @@ export function createEmptyClipping(clippingData?: ClippingData): ClippingData {
             tClipping: ValueCell.create(emptyClippingTexture),
             uClippingTexDim: ValueCell.create(Vec2.create(1, 1)),
             dClipping: ValueCell.create(false),
+            dClippingType: ValueCell.create('groupInstance'),
         };
     }
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 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 Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -11,11 +11,13 @@ import { Color } from '../../mol-util/color';
 import { Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
 import { LocationIterator } from '../util/location-iterator';
 import { NullLocation } from '../../mol-model/location';
-import { LocationColor, ColorTheme } from '../../mol-theme/color';
-import { Geometry } from './geometry';
+import { LocationColor, ColorTheme, ColorVolume } from '../../mol-theme/color';
 import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
 
-export type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance' | 'volume' | 'volumeInstance' | 'direct'
+export type ColorTypeLocation = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance';
+export type ColorTypeGrid = 'volume' | 'volumeInstance';
+export type ColorTypeDirect = 'direct';
+export type ColorType = ColorTypeLocation | ColorTypeGrid | ColorTypeDirect;
 
 export type ColorData = {
     uColor: ValueCell<Vec3>,
@@ -29,7 +31,7 @@ export type ColorData = {
     dUsePalette: ValueCell<boolean>,
 }
 
-export function createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any>, colorData?: ColorData): ColorData {
+export function createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any, any>, colorData?: ColorData): ColorData {
     const data = _createColors(locationIt, positionIt, colorTheme, colorData);
     if (colorTheme.palette) {
         ValueCell.updateIfChanged(data.dUsePalette, true);
@@ -40,16 +42,19 @@ export function createColors(locationIt: LocationIterator, positionIt: LocationI
     return data;
 }
 
-function _createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any>, colorData?: ColorData): ColorData {
-    switch (Geometry.getGranularity(locationIt, colorTheme.granularity)) {
+function _createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any, any>, colorData?: ColorData): ColorData {
+    switch (colorTheme.granularity) {
         case 'uniform': return createUniformColor(locationIt, colorTheme.color, colorData);
-        case 'instance': return createInstanceColor(locationIt, colorTheme.color, colorData);
+        case 'instance':
+            return locationIt.nonInstanceable
+                ? createGroupColor(locationIt, colorTheme.color, colorData)
+                : createInstanceColor(locationIt, colorTheme.color, colorData);
         case 'group': return createGroupColor(locationIt, colorTheme.color, colorData);
         case 'groupInstance': return createGroupInstanceColor(locationIt, colorTheme.color, colorData);
         case 'vertex': return createVertexColor(positionIt, colorTheme.color, colorData);
         case 'vertexInstance': return createVertexInstanceColor(positionIt, colorTheme.color, colorData);
-        case 'volume': return createGridColor((colorTheme as any).grid, 'volume', colorData);
-        case 'volumeInstance': return createGridColor((colorTheme as any).grid, 'volumeInstance', colorData);
+        case 'volume': return createGridColor(colorTheme.grid, 'volume', colorData);
+        case 'volumeInstance': return createGridColor(colorTheme.grid, 'volumeInstance', colorData);
         case 'direct': return createDirectColor(colorData);
     }
 }
@@ -207,12 +212,6 @@ function createVertexInstanceColor(locationIt: LocationIterator, color: Location
 
 //
 
-interface ColorVolume {
-    colors: Texture
-    dimension: Vec3
-    transform: Vec4
-}
-
 export function createGridColor(grid: ColorVolume, type: ColorType, colorData?: ColorData): ColorData {
     const { colors, dimension, transform } = grid;
     const width = colors.getWidth();

src/mol-geo/geometry/cylinders/cylinders.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -157,6 +157,7 @@ export namespace Cylinders {
         doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
+        transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
         bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
         bumpAmplitude: PD.Numeric(1, { min: 0, max: 5, step: 0.1 }, BaseGeometry.ShadingCategory),
     };
@@ -200,7 +201,9 @@ export namespace Cylinders {
 
         const color = createColors(locationIt, positionIt, theme.color);
         const size = createSizes(locationIt, theme.size);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();
@@ -241,6 +244,7 @@ export namespace Cylinders {
             uDoubleSided: ValueCell.create(props.doubleSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
+            dTransparentBackfaces: ValueCell.create(props.transparentBackfaces),
             uBumpFrequency: ValueCell.create(props.bumpFrequency),
             uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
         };
@@ -258,6 +262,7 @@ export namespace Cylinders {
         ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
         ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }

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

@@ -211,7 +211,9 @@ export namespace DirectVolume {
         const positionIt = Utils.createPositionIterator(directVolume, transform);
 
         const color = createColors(locationIt, positionIt, theme.color);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();

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

@@ -143,7 +143,9 @@ namespace Image {
         const positionIt = Utils.createPositionIterator(image, transform);
 
         const color = createColors(locationIt, positionIt, theme.color);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();

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

@@ -1,5 +1,5 @@
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -165,7 +165,7 @@ export namespace Lines {
 
     export const Params = {
         ...BaseGeometry.Params,
-        sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
+        sizeFactor: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }),
         lineSizeAttenuation: PD.Boolean(false),
     };
     export type Params = typeof Params
@@ -208,7 +208,9 @@ export namespace Lines {
 
         const color = createColors(locationIt, positionIt, theme.color);
         const size = createSizes(locationIt, theme.size);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,12 +8,15 @@ import { ValueCell } from '../../mol-util/value-cell';
 import { Vec2 } from '../../mol-math/linear-algebra';
 import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
 
+export type MarkerType = 'instance' | 'groupInstance';
+
 export type MarkerData = {
-    uMarker: ValueCell<number>,
+    uMarker: ValueCell<number>
     tMarker: ValueCell<TextureImage<Uint8Array>>
     uMarkerTexDim: ValueCell<Vec2>
     markerAverage: ValueCell<number>
     markerStatus: ValueCell<number>
+    dMarkerType: ValueCell<string>
 }
 
 const MarkerCountLut = new Uint8Array(0x0303 + 1);
@@ -64,7 +67,7 @@ export function getMarkersAverage(array: Uint8Array, count: number): number {
     return sum / count;
 }
 
-export function createMarkers(count: number, markerData?: MarkerData): MarkerData {
+export function createMarkers(count: number, type: MarkerType, markerData?: MarkerData): MarkerData {
     const markers = createTextureImage(Math.max(1, count), 1, Uint8Array, markerData && markerData.tMarker.ref.value.array);
     const average = getMarkersAverage(markers.array, count);
     const status = average === 0 ? 0 : -1;
@@ -74,6 +77,7 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
         ValueCell.update(markerData.uMarkerTexDim, Vec2.create(markers.width, markers.height));
         ValueCell.updateIfChanged(markerData.markerAverage, average);
         ValueCell.updateIfChanged(markerData.markerStatus, status);
+        ValueCell.updateIfChanged(markerData.dMarkerType, type);
         return markerData;
     } else {
         return {
@@ -82,6 +86,7 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
             uMarkerTexDim: ValueCell.create(Vec2.create(markers.width, markers.height)),
             markerAverage: ValueCell.create(average),
             markerStatus: ValueCell.create(status),
+            dMarkerType: ValueCell.create(type),
         };
     }
 }
@@ -102,6 +107,7 @@ export function createEmptyMarkers(markerData?: MarkerData): MarkerData {
             uMarkerTexDim: ValueCell.create(Vec2.create(1, 1)),
             markerAverage: ValueCell.create(0),
             markerStatus: ValueCell.create(0),
+            dMarkerType: ValueCell.create('groupInstance'),
         };
     }
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -34,13 +34,15 @@ export function calcMeshColorSmoothing(input: ColorSmoothingInput, resolution: n
 
     const isInstanceType = colorType.endsWith('Instance');
     const box = Box3D.fromSphere3D(Box3D(), isInstanceType ? input.boundingSphere : input.invariantBoundingSphere);
+    const pad = 1 + resolution;
+    const expandedBox = Box3D.expand(Box3D(), box, Vec3.create(pad, pad, pad));
 
     const scaleFactor = 1 / resolution;
-    const scaledBox = Box3D.scale(Box3D(), box, scaleFactor);
+    const scaledBox = Box3D.scale(Box3D(), expandedBox, scaleFactor);
     const gridDim = Box3D.size(Vec3(), scaledBox);
     Vec3.ceil(gridDim, gridDim);
     Vec3.add(gridDim, gridDim, Vec3.create(2, 2, 2));
-    const { min } = box;
+    const { min } = expandedBox;
 
     const [xn, yn] = gridDim;
     const { width, height } = getVolumeTexture2dLayout(gridDim);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 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 Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -45,6 +45,8 @@ export interface Mesh {
     readonly normalBuffer: ValueCell<Float32Array>,
     /** Group buffer as array of group ids for each vertex wrapped in a value cell */
     readonly groupBuffer: ValueCell<Float32Array>,
+    /** Indicates that group may vary within a triangle, wrapped in a value cell */
+    readonly varyingGroup: ValueCell<boolean>,
 
     /** Bounding sphere of the mesh */
     readonly boundingSphere: Sphere3D
@@ -95,6 +97,7 @@ export namespace Mesh {
             indexBuffer: ValueCell.create(indices),
             normalBuffer: ValueCell.create(normals),
             groupBuffer: ValueCell.create(groups),
+            varyingGroup: ValueCell.create(false),
             get boundingSphere() {
                 const newHash = hashCode(mesh);
                 if (newHash !== currentHash) {
@@ -625,6 +628,7 @@ export namespace Mesh {
         flatShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
+        transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
         bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
         bumpAmplitude: PD.Numeric(1, { min: 0, max: 5, step: 0.1 }, BaseGeometry.ShadingCategory),
     };
@@ -665,7 +669,9 @@ export namespace Mesh {
         const positionIt = createPositionIterator(mesh, transform);
 
         const color = createColors(locationIt, positionIt, theme.color);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();
@@ -683,6 +689,7 @@ export namespace Mesh {
             aNormal: mesh.normalBuffer,
             aGroup: mesh.groupBuffer,
             elements: mesh.indexBuffer,
+            dVaryingGroup: mesh.varyingGroup,
             boundingSphere: ValueCell.create(boundingSphere),
             invariantBoundingSphere: ValueCell.create(invariantBoundingSphere),
             uInvariantBoundingSphere: ValueCell.create(Vec4.ofSphere(invariantBoundingSphere)),
@@ -700,6 +707,7 @@ export namespace Mesh {
             dFlipSided: ValueCell.create(props.flipSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
+            dTransparentBackfaces: ValueCell.create(props.transparentBackfaces),
             uBumpFrequency: ValueCell.create(props.bumpFrequency),
             uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
 
@@ -720,6 +728,7 @@ export namespace Mesh {
         ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
         ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,6 +10,8 @@ import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
 import { Color } from '../../mol-util/color';
 import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
 
+export type OverpaintType = 'instance' | 'groupInstance' | 'volumeInstance';
+
 export type OverpaintData = {
     tOverpaint: ValueCell<TextureImage<Uint8Array>>
     uOverpaintTexDim: ValueCell<Vec2>
@@ -19,6 +21,7 @@ export type OverpaintData = {
     uOverpaintGridDim: ValueCell<Vec3>,
     uOverpaintGridTransform: ValueCell<Vec4>,
     dOverpaintType: ValueCell<string>,
+    uOverpaintStrength: ValueCell<number>,
 }
 
 export function applyOverpaintColor(array: Uint8Array, start: number, end: number, color: Color) {
@@ -34,12 +37,13 @@ export function clearOverpaint(array: Uint8Array, start: number, end: number) {
     return true;
 }
 
-export function createOverpaint(count: number, overpaintData?: OverpaintData): OverpaintData {
+export function createOverpaint(count: number, type: OverpaintType, overpaintData?: OverpaintData): OverpaintData {
     const overpaint = createTextureImage(Math.max(1, count), 4, Uint8Array, overpaintData && overpaintData.tOverpaint.ref.value.array);
     if (overpaintData) {
         ValueCell.update(overpaintData.tOverpaint, overpaint);
         ValueCell.update(overpaintData.uOverpaintTexDim, Vec2.create(overpaint.width, overpaint.height));
         ValueCell.updateIfChanged(overpaintData.dOverpaint, count > 0);
+        ValueCell.updateIfChanged(overpaintData.dOverpaintType, type);
         return overpaintData;
     } else {
         return {
@@ -50,7 +54,8 @@ export function createOverpaint(count: number, overpaintData?: OverpaintData): O
             tOverpaintGrid: ValueCell.create(createNullTexture()),
             uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
-            dOverpaintType: ValueCell.create('groupInstance'),
+            dOverpaintType: ValueCell.create(type),
+            uOverpaintStrength: ValueCell.create(1),
         };
     }
 }
@@ -71,6 +76,7 @@ export function createEmptyOverpaint(overpaintData?: OverpaintData): OverpaintDa
             uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dOverpaintType: ValueCell.create('groupInstance'),
+            uOverpaintStrength: ValueCell.create(1),
         };
     }
 }

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

@@ -170,7 +170,9 @@ export namespace Points {
 
         const color = createColors(locationIt, positionIt, theme.color);
         const size = createSizes(locationIt, theme.size);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 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>
  */
@@ -129,6 +129,7 @@ export namespace Spheres {
         doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
+        transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
         bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
         bumpAmplitude: PD.Numeric(1, { min: 0, max: 5, step: 0.1 }, BaseGeometry.ShadingCategory),
     };
@@ -170,7 +171,9 @@ export namespace Spheres {
 
         const color = createColors(locationIt, positionIt, theme.color);
         const size = createSizes(locationIt, theme.size);
-        const marker = createMarkers(instanceCount * groupCount);
+        const marker = props.instanceGranularity
+            ? createMarkers(instanceCount, 'instance')
+            : createMarkers(instanceCount * groupCount, 'groupInstance');
         const overpaint = createEmptyOverpaint();
         const transparency = createEmptyTransparency();
         const material = createEmptySubstance();
@@ -208,6 +211,7 @@ export namespace Spheres {
             uDoubleSided: ValueCell.create(props.doubleSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
+            dTransparentBackfaces: ValueCell.create(props.transparentBackfaces),
             uBumpFrequency: ValueCell.create(props.bumpFrequency),
             uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
         };
@@ -225,6 +229,7 @@ export namespace Spheres {
         ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
         ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,6 +10,8 @@ import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
 import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
 import { Material } from '../../mol-util/material';
 
+export type SubstanceType = 'instance' | 'groupInstance' | 'volumeInstance';
+
 export type SubstanceData = {
     tSubstance: ValueCell<TextureImage<Uint8Array>>
     uSubstanceTexDim: ValueCell<Vec2>
@@ -19,6 +21,7 @@ export type SubstanceData = {
     uSubstanceGridDim: ValueCell<Vec3>,
     uSubstanceGridTransform: ValueCell<Vec4>,
     dSubstanceType: ValueCell<string>,
+    uSubstanceStrength: ValueCell<number>,
 }
 
 export function applySubstanceMaterial(array: Uint8Array, start: number, end: number, material: Material) {
@@ -34,12 +37,13 @@ export function clearSubstance(array: Uint8Array, start: number, end: number) {
     return true;
 }
 
-export function createSubstance(count: number, substanceData?: SubstanceData): SubstanceData {
+export function createSubstance(count: number, type: SubstanceType, substanceData?: SubstanceData): SubstanceData {
     const substance = createTextureImage(Math.max(1, count), 4, Uint8Array, substanceData && substanceData.tSubstance.ref.value.array);
     if (substanceData) {
         ValueCell.update(substanceData.tSubstance, substance);
         ValueCell.update(substanceData.uSubstanceTexDim, Vec2.create(substance.width, substance.height));
         ValueCell.updateIfChanged(substanceData.dSubstance, count > 0);
+        ValueCell.updateIfChanged(substanceData.dSubstanceType, type);
         return substanceData;
     } else {
         return {
@@ -50,7 +54,8 @@ export function createSubstance(count: number, substanceData?: SubstanceData): S
             tSubstanceGrid: ValueCell.create(createNullTexture()),
             uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
-            dSubstanceType: ValueCell.create('groupInstance'),
+            dSubstanceType: ValueCell.create(type),
+            uSubstanceStrength: ValueCell.create(1),
         };
     }
 }
@@ -71,6 +76,7 @@ export function createEmptySubstance(substanceData?: SubstanceData): SubstanceDa
             uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
             uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
             dSubstanceType: ValueCell.create('groupInstance'),
+            uSubstanceStrength: ValueCell.create(1),
         };
     }
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 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>
  */
@@ -88,7 +88,7 @@ export class FontAtlas {
         this.scratchCanvas.width = this.maxWidth;
         this.scratchCanvas.height = this.lineHeight;
 
-        this.scratchContext = this.scratchCanvas.getContext('2d')!;
+        this.scratchContext = this.scratchCanvas.getContext('2d', { willReadFrequently: true })!;
         this.scratchContext.font = `${p.fontStyle} ${p.fontVariant} ${p.fontWeight} ${fontSize}px ${p.fontFamily}`;
         this.scratchContext.fillStyle = 'black';
         this.scratchContext.textBaseline = 'middle';

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

@@ -8,6 +8,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { ChunkedArray } from '../../../mol-data/util';
 import { Text } from './text';
 import { getFontAtlas } from './font-atlas';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
 
 const quadIndices = new Uint16Array([
     0, 1, 2,
@@ -237,7 +238,7 @@ export namespace TextBuilder {
                             yBaseCenter = yTop;
                             break;
                         default:
-                            throw new Error('unsupported attachment');
+                            assertUnreachable(attachment);
                     }
                     caAdd2(mappings, xTip, yTip); // tip
                     caAdd2(mappings, xBaseA, yBaseA); // base A