3.2.0

Add TraceOnly option for Structure Superposition

.github/workflows/node.yml

@@ -9,7 +9,7 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-node@v2
       with:
-        node-version: 14
+        node-version: 17
     - run: npm ci
     - run: sudo apt-get install xvfb
     - name: Lint

.npmignore

@@ -1 +1,5 @@
-lib/tsconfig.commonjs.tsbuildinfo
+tests
+perf-tests
+_spec
+*.tsbuildinfo
+*.js.map

.vscode/settings.json

@@ -7,6 +7,8 @@
         "*.gql.ts": "graphql"
     },
     "eslint.options": {
-        "ignorePattern": ["webpack.config.js", "scripts/*"],
+        "overrideConfig": {
+            "ignorePatterns": ["webpack.config.js", "scripts/*"],
+        },
     }
 }

CHANGELOG.md

@@ -6,11 +6,175 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [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``
+- Pass animation info (current frame & count) to state animations
+    - Fix camera stutter for "camera spin" animation
+- Add formal charge parsing support for MOL/SDF files (thanks @ptourlas)
+- [Breaking] Cleaner looking ``MembraneOrientationVisuals`` defaults
+- [Breaking] Add rock animation to trackball controls
+    - Add ``animate`` to ``TrackballControlsParams``, remove ``spin`` and ``spinSpeed``
+    - Add ``animate`` to ``SimpleSettingsParams``, remove ``spin``
+- 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 instead of "chain-id"
+- Add "illustrative" representation preset
+
+## [v3.0.0-dev.9] - 2022-01-09
+
+- Add PDBj as a ``pdb-provider`` option
+- Move Viewer APP to a separate file to allow use without importing light theme & index.html
+- Add symmetry support for mol2 files (only spacegroup setting 1)
+- Fix mol2 files element symbol assignment
+- Improve bond assignment from ``IndexPairBonds``
+    - Add ``key`` field for mapping to source data
+    - Fix assignment of bonds with unphysical length
+- Fix label/stats of single atom selection in multi-chain units
+
+## [v3.0.0-dev.8] - 2021-12-31
+
+- Add ``PluginFeatureDetection`` and disable WBOIT in Safari 15.
+- Add ``disable-wboit`` Viewer GET param
+- Add ``prefer-webgl1`` Viewer GET param
+- [Breaking] Refactor direct-volume rendering
+    - Remove isosurface render-mode (use GPU MC instead)
+    - Move coloring into theme (like for other geometries/renderables)
+        - Add ``direct`` color type
+        - Remove color from transfer-function (now only alpha)
+        - Add direct-volume color theme support
+        - Add volume-value color theme
+- [Breaking] Use size theme in molecular/gaussian surface & label representations
+    - This is breaking because it was hardcoded to ``physical`` internally but the repr size theme default was ``uniform`` (now ``physical``)
+
+## [v3.0.0-dev.7] - 2021-12-20
+
+- Reduce number of created programs/shaders
+    - Support specifying variants when creating graphics render-items
+    - Change double-side shader param from define to uniform
+    - Remove dMarkerType shader define (use uMarker as needed)
+    - Support to ignore defines depending on the shader variant
+    - Combine pickObject/pickInstance/pickGroup shader variants into one
+    - Combine markingDepth/markingMask shader variants into one
+    - Correctly set shader define flags for overpaint, transparency, substance, clipping
+- [Breaking] Add per-object clip rendering properties (variant/objects)
+    - ``SimpleSettingsParams.clipping.variant/objects`` and ``RendererParams.clip`` were removed
+
+## [v3.0.0-dev.6] - 2021-12-19
+
+- Enable temporal multi-sampling by default
+    - Fix flickering during marking with camera at rest
+- Enable ``aromaticBonds`` in structure representations by default
+- Add ``PluginConfig.Structure.DefaultRepresentationPreset``
+- Add ModelArchive support
+    - schema extensions (e.g., AlphaFold uses it for the pLDDT score)
+    - ModelArchive option in DownloadStructure action
+    - ``model-archive`` GET parameter for Viewer app
+    - ``Viewer.loadModelArchive`` method
+- Improve support for loading AlphaFold structures
+    - Automatic coloring by pLDDT
+    - AlphaFold DB option in DownloadStructure action
+    - ``afdb`` GET parameter for Viewer app
+    - ``Viewer.loadAlphaFoldDb`` method
+- Add QualityAssessment extension (using data from ma_qa_metric_local mmcif category)
+    - pLDDT & qmean score: coloring, repr presets, molql symbol, loci labels (including avg for mutli-residue selections)
+    - pLDDT: selection query
+- Warn about erroneous symmetry operator matrix (instead of throwing an error)
+- Added ``createPluginUI`` to ``mol-plugin-ui``
+    - Support ``onBeforeUIRender`` to make sure initial UI works with custom presets and similar features.
+- [Breaking] Removed ``createPlugin`` and ``createPluginAsync`` from ``mol-plugin-ui``
+    - Please use ``createPluginUI`` instead
+- Improve aromatic bonds handling
+    - Don't detect aromatic bonds for rings < 5 atoms based on planarity
+    - Prefer atoms in aromatic rings as bond reference positions
+
+## [v3.0.0-dev.5] - 2021-12-16
+
+- Fix initial camera reset not triggering for some entries.
+
+## [v3.0.0-dev.4] - 2021-12-14
+
+- Add ``bumpiness`` (per-object and per-group), ``bumpFrequency`` & ``bumpAmplitude`` (per-object) render parameters (#299)
+- Change ``label`` representation defaults: Use text border instead of rectangle background
+- Add outline color option to renderer
+- Fix false positives in Model.isFromPdbArchive
+- Add drag and drop support for loading any file, including multiple at once
+    - If there are session files (.molx or .molj) among the dropped files, only the first session will be loaded
+- Add drag and drop overlay
+- Safari 15.1 - 15.3 WebGL 2 support workaround
+- [Breaking] Move ``react`` and ``react-dom`` to ``peerDependencies``. This might break some builds.
+
+## [v3.0.0-dev.3] - 2021-12-4
+
+- Fix OBJ and USDZ export
+
+## [v3.0.0-dev.2] - 2021-12-1
+
+- Do not include tests and source maps in NPM package
+
 ## [v3.0.0-dev.0] - 2021-11-28
 
 - Add multiple lights support (with color, intensity, and direction parameters)
 - [Breaking] Add per-object material rendering properties
+    - ``SimpleSettingsParams.lighting.renderStyle`` and ``RendererParams.style`` were removed
 - Add substance theme with per-group material rendering properties
+- ``StructureComponentManager.Options`` state saving support
+- ``ParamDefinition.Group.presets`` support
 
 ## [v2.4.1] - 2021-11-28
 

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

@@ -11,6 +11,13 @@ When using Mol*, please cite:
 
 David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
 
+### Protein Data Bank Integrations
+
+- The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
+
+- [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
+
+
 ## Project Structure Overview
 
 The core of Mol* consists of these modules (see under `src/`):
@@ -68,6 +75,17 @@ If working on just the viewer, ``npm run watch-viewer`` will provide shorter com
 
 Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
 
+### Cleaning and forcing a full rebuild
+    npm run clean
+
+Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
+
+    npm run rebuild
+
+Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
+
+Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
+
 ### Build for production:
     NODE_ENV=production npm run build
 

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
@@ -246,6 +251,14 @@ citation_author.ordinal
 exptl.entry_id
 exptl.method
 
+software.classification
+software.date
+software.description
+software.name
+software.pdbx_ordinal
+software.type
+software.version
+
 struct.entry_id
 struct.title
 struct.pdbx_descriptor
@@ -802,4 +815,58 @@ ihm_multi_state_modeling.population_fraction_sd
 ihm_multi_state_modeling.state_type
 ihm_multi_state_modeling.state_name
 ihm_multi_state_modeling.experiment_type
-ihm_multi_state_modeling.details
+ihm_multi_state_modeling.details
+
+ma_data.content_type
+ma_data.content_type_other_details
+ma_data.id
+ma_data.name
+
+ma_model_list.data_id
+ma_model_list.model_group_id
+ma_model_list.model_group_name
+ma_model_list.model_id
+ma_model_list.model_name
+ma_model_list.model_type
+ma_model_list.ordinal_id
+
+ma_qa_metric.id
+ma_qa_metric.mode
+ma_qa_metric.name
+ma_qa_metric.software_group_id
+ma_qa_metric.type
+
+ma_qa_metric_global.metric_id
+ma_qa_metric_global.metric_value
+ma_qa_metric_global.model_id
+ma_qa_metric_global.ordinal_id
+
+ma_qa_metric_local.label_asym_id
+ma_qa_metric_local.label_comp_id
+ma_qa_metric_local.label_seq_id
+ma_qa_metric_local.metric_id
+ma_qa_metric_local.metric_value
+ma_qa_metric_local.model_id
+ma_qa_metric_local.ordinal_id
+
+ma_software_group.group_id
+ma_software_group.ordinal_id
+ma_software_group.software_id
+
+ma_target_entity.data_id
+ma_target_entity.entity_id
+ma_target_entity.origin
+
+ma_target_entity_instance.asym_id
+ma_target_entity_instance.details
+ma_target_entity_instance.entity_id
+
+ma_target_ref_db_details.db_accession
+ma_target_ref_db_details.db_code
+ma_target_ref_db_details.db_name
+ma_target_ref_db_details.ncbi_taxonomy_id
+ma_target_ref_db_details.organism_scientific
+ma_target_ref_db_details.seq_db_align_begin
+ma_target_ref_db_details.seq_db_align_end
+ma_target_ref_db_details.seq_db_isoform
+ma_target_ref_db_details.target_entity_id

docs/interesting-pdb-entries.md

@@ -29,6 +29,11 @@
 * Long linear sugar chain (4HG6)
 * Anisotropic B-factors/Ellipsoids (1EJG)
 * NOS bridges (LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
+* Non-polymer components in polymer entities
+    * PN2 in 1F80
+    * ACE (many, e.g. 5AGU, 1E1X)
+    * ACY in 7ABY
+    * NH2 (many, e.g. 6Y13)
 
 Assembly symmetries
 * 5M30 (Assembly 1, C3 local and pseudo)

examples/ace2-hit.mol2

@@ -0,0 +1,86 @@
+@<TRIPOS>MOLECULE
+ace2_r_r2.top2000.poses.plain/3_Z1137565832_1_T2.pdb
+ 37 41 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1  C         64.7720   85.9180   38.1090 C.3     1  LIG1        0.0799
+      2  C         64.6440   84.6900   37.1570 C.3     1  LIG1        0.0306
+      3  C         65.2660   83.4260   37.8080 C.3     1  LIG1        0.0927
+      4  N         66.6560   83.6710   38.1790 N.pl3   1  LIG1       -0.2919
+      5  C         67.7080   82.9280   37.6260 C.ar    1  LIG1        0.1520
+      6  C         69.0970   83.1860   37.8250 C.ar    1  LIG1        0.0393
+      7  C         70.0830   82.4100   37.1810 C.ar    1  LIG1        0.0436
+      8  C         69.6450   81.3740   36.3510 C.ar    1  LIG1        0.1867
+      9  N         70.3370   80.5030   35.6050 N.ar    1  LIG1       -0.1270
+     10  N         69.4700   79.7480   35.0040 N.ar    1  LIG1       -0.1228
+     11  C         68.2200   80.1120   35.3570 C.ar    1  LIG1        0.2583
+     12  N         68.3350   81.1470   36.2040 N.ar    1  LIG1       -0.1866
+     13  N         67.4230   81.8700   36.8030 N.ar    1  LIG1       -0.1473
+     14  C         66.8190   84.7600   39.1350 C.3     1  LIG1        0.0927
+     15  C         66.2560   86.0870   38.5570 C.3     1  LIG1        0.0306
+     16  N         64.4520   87.4670   36.2150 N.am    1  LIG1       -0.2979
+     17  H         64.9740   86.7650   35.7110 H       1  LIG1        0.1498
+     18  C         64.2290   87.1720   37.5220 C.2     1  LIG1        0.2224
+     19  O         63.5690   87.9550   38.2480 O.2     1  LIG1       -0.2751
+     20  C         64.0160   88.6470   35.5420 C.3     1  LIG1        0.1559
+     21  C         65.9650   88.2170   32.5700 C.ar    1  LIG1        0.1629
+     22  N         65.8040   88.0390   33.8860 N.ar    1  LIG1       -0.3232
+     23  H         66.4190   87.5270   34.5040 H       1  LIG1        0.1686
+     24  C         64.6770   88.6690   34.2330 C.ar    1  LIG1        0.1601
+     25  N         64.1890   89.2810   33.1430 N.ar    1  LIG1       -0.1318
+     26  N         64.9640   89.0070   32.1450 N.ar    1  LIG1       -0.1293
+     27  F         69.9260   86.0280   29.3520 F       1  LIG1       -0.2042
+     28  C         68.9880   86.5420   30.0990 C.ar    1  LIG1        0.1401
+     29  C         67.6590   86.0900   29.9830 C.ar    1  LIG1        0.0297
+     30  C         66.6500   86.6450   30.7950 C.ar    1  LIG1        0.0053
+     31  C         66.9590   87.6470   31.7450 C.ar    1  LIG1        0.0359
+     32  C         68.2970   88.0990   31.8400 C.ar    1  LIG1        0.0053
+     33  C         69.3030   87.5560   31.0230 C.ar    1  LIG1        0.0297
+     34  C         66.9850   79.4910   34.8440 C.3     1  LIG1        0.4541
+     35  F         67.3150   78.4110   34.0640 F       1  LIG1       -0.1631
+     36  F         66.2460   80.3690   34.0910 F       1  LIG1       -0.1631
+     37  F         66.1920   79.0650   35.8800 F       1  LIG1       -0.1631
+@<TRIPOS>BOND
+     1     1     2    1
+     2     1    18    1
+     3     1    15    1
+     4     2     3    1
+     5     3     4    1
+     6     4     5    1
+     7     4    14    1
+     8     5    13   ar
+     9     5     6   ar
+    10     6     7   ar
+    11     7     8   ar
+    12     8     9   ar
+    13     8    12   ar
+    14     9    10   ar
+    15    10    11   ar
+    16    11    34    1
+    17    11    12   ar
+    18    12    13   ar
+    19    14    15    1
+    20    16    20    1
+    21    16    17    1
+    22    16    18   am
+    23    18    19    2
+    24    20    24    1
+    25    21    31    1
+    26    21    26   ar
+    27    21    22   ar
+    28    22    24   ar
+    29    22    23    1
+    30    24    25   ar
+    31    25    26   ar
+    32    27    28    1
+    33    28    29   ar
+    34    28    33   ar
+    35    29    30   ar
+    36    30    31   ar
+    37    31    32   ar
+    38    32    33   ar
+    39    34    35    1
+    40    34    36    1
+    41    34    37    1

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.0-dev.0",
+  "version": "3.2.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -13,9 +13,11 @@
   "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/",
@@ -36,7 +38,7 @@
     "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
     "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
     "preversion": "npm run test",
-    "version": "npm run build",
+    "version": "npm run rebuild && cpx .npmignore lib/",
     "postversion": "git push && git push --tags"
   },
   "files": [
@@ -84,75 +86,75 @@
     "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
     "Ludovic Autin <autin@scripps.edu>",
     "Michal Malý <michal.maly@ibt.cas.cz>",
-    "Jiří Černý <jiri.cerny@ibt.cas.cz>"
+    "Jiří Černý <jiri.cerny@ibt.cas.cz>",
+    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.1.0",
-    "@graphql-codegen/cli": "^2.3.0",
-    "@graphql-codegen/time": "^3.1.0",
-    "@graphql-codegen/typescript": "^2.4.1",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.1",
-    "@graphql-codegen/typescript-operations": "^2.2.1",
+    "@graphql-codegen/add": "^3.1.1",
+    "@graphql-codegen/cli": "^2.5.0",
+    "@graphql-codegen/time": "^3.1.1",
+    "@graphql-codegen/typescript": "^2.4.3",
+    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
+    "@graphql-codegen/typescript-graphql-request": "^4.3.4",
+    "@graphql-codegen/typescript-operations": "^2.2.4",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
-    "@types/jest": "^27.0.3",
-    "@typescript-eslint/eslint-plugin": "^5.4.0",
-    "@typescript-eslint/parser": "^5.4.0",
+    "@types/jest": "^27.4.0",
+    "@typescript-eslint/eslint-plugin": "^5.10.2",
+    "@typescript-eslint/parser": "^5.10.2",
     "benchmark": "^2.1.4",
-    "concurrently": "^6.4.0",
-    "cpx2": "^4.0.0",
+    "concurrently": "^7.0.0",
+    "cpx2": "^4.1.2",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.5.1",
-    "eslint": "^8.3.0",
+    "css-loader": "^6.6.0",
+    "eslint": "^8.8.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.0.0",
-    "graphql": "^15.7.2",
-    "http-server": "^14.0.0",
-    "jest": "^27.3.1",
-    "mini-css-extract-plugin": "^2.4.5",
+    "graphql": "^16.3.0",
+    "http-server": "^14.1.0",
+    "jest": "^27.5.0",
+    "mini-css-extract-plugin": "^2.5.3",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass": "^1.43.5",
-    "sass-loader": "^12.3.0",
-    "simple-git": "^2.47.0",
+    "sass": "^1.49.7",
+    "sass-loader": "^12.4.0",
+    "simple-git": "^3.1.1",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^27.0.7",
-    "typescript": "^4.5.2",
-    "webpack": "^5.64.4",
-    "webpack-cli": "^4.9.1"
+    "ts-jest": "^27.1.3",
+    "typescript": "^4.5.5",
+    "webpack": "^5.68.0",
+    "webpack-cli": "^4.9.2"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.10",
+    "@types/node": "^16.11.22",
     "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.37",
+    "@types/react": "^17.0.39",
     "@types/react-dom": "^17.0.11",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
-    "body-parser": "^1.19.0",
+    "body-parser": "^1.19.1",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.17.1",
+    "express": "^4.17.2",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.7",
-    "immutable": "^3.8.2",
-    "node-fetch": "^2.6.2",
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2",
-    "rxjs": "^7.4.0",
-    "swagger-ui-dist": "^4.1.1",
+    "immer": "^9.0.12",
+    "immutable": "^4.0.0",
+    "node-fetch": "^2.6.7",
+    "rxjs": "^7.5.2",
+    "swagger-ui-dist": "^4.5.0",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"
   },
-  "optionalDependencies": {
-    "gl": "^4.9.2"
+  "peerDependencies": {
+    "react": "^17.0.2",
+    "react-dom": "^17.0.2"
   }
 }

scripts/clean.js

@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <malym@ibt.cas.cz>
+ */
+
+const fs = require('fs');
+const path = require('path');
+
+function removeDir(dirPath) {
+    for (const ent of fs.readdirSync(dirPath)) {
+        const entryPath = path.join(dirPath, ent);
+        remove(entryPath);
+    }
+
+    fs.rmdirSync(dirPath);
+}
+
+function remove(entryPath) {
+    const st = fs.statSync(entryPath);
+    if (st.isDirectory())
+        removeDir(entryPath);
+    else
+        fs.unlinkSync(entryPath);
+}
+
+const toClean = [
+    path.resolve(__dirname, '../build'),
+    path.resolve(__dirname, '../lib'),
+    path.resolve(__dirname, '../tsconfig.tsbuildinfo'),
+];
+
+toClean.forEach(ph => {
+    if (fs.existsSync(ph)) {
+        try {
+            remove(ph);
+        } catch (err) {
+            console.warn(`Cleanup failed: ${err}`);
+        }
+    }
+});

scripts/deploy.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,6 +14,9 @@ const buildDir = path.resolve(__dirname, '../build/');
 const deployDir = path.resolve(buildDir, 'deploy/');
 const localPath = path.resolve(deployDir, 'molstar.github.io/');
 
+const analyticsTag = /<!-- __MOLSTAR_ANALYTICS__ -->/g;
+const analyticsCode = `<!-- Cloudflare Web Analytics --><script defer src='https://static.cloudflareinsights.com/beacon.min.js' data-cf-beacon='{"token": "c414cbae2d284ea995171a81e4a3e721"}'></script><!-- End Cloudflare Web Analytics -->`;
+
 function log(command, stdout, stderr) {
     if (command) {
         console.log('\n###', command);
@@ -22,11 +25,36 @@ function log(command, stdout, stderr) {
     }
 }
 
+function addAnalytics(path) {
+    const data = fs.readFileSync(path, 'utf8');
+    const result = data.replace(analyticsTag, analyticsCode);
+    fs.writeFileSync(path, result, 'utf8');
+}
+
 function copyViewer() {
     console.log('\n###', 'copy viewer files');
     const viewerBuildPath = path.resolve(buildDir, '../build/viewer/');
     const viewerDeployPath = path.resolve(localPath, 'viewer/');
     fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(viewerDeployPath, 'index.html'));
+}
+
+function copyDemos() {
+    console.log('\n###', 'copy demos files');
+    const lightingBuildPath = path.resolve(buildDir, '../build/examples/lighting/');
+    const lightingDeployPath = path.resolve(localPath, 'demos/lighting/');
+    fse.copySync(lightingBuildPath, lightingDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(lightingDeployPath, 'index.html'));
+
+    const orbitalsBuildPath = path.resolve(buildDir, '../build/examples/alpha-orbitals/');
+    const orbitalsDeployPath = path.resolve(localPath, 'demos/alpha-orbitals/');
+    fse.copySync(orbitalsBuildPath, orbitalsDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(orbitalsDeployPath, 'index.html'));
+}
+
+function copyFiles() {
+    copyViewer();
+    copyDemos();
 }
 
 if (!fs.existsSync(localPath)) {
@@ -42,9 +70,9 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .outputHandler(log)
         .clone(remoteUrl, localPath)
         .fetch(['--all'])
-        .exec(copyViewer)
+        .exec(copyFiles)
         .add(['-A'])
-        .commit('updated viewer')
+        .commit('updated viewer & demos')
         .push();
 } else {
     console.log('\n###', 'update repository');
@@ -52,8 +80,8 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .outputHandler(log)
         .fetch(['--all'])
         .reset(['--hard', 'origin/master'])
-        .exec(copyViewer)
+        .exec(copyFiles)
         .add(['-A'])
-        .commit('updated viewer')
+        .commit('updated viewer & demos')
         .push();
 }

src/apps/docking-viewer/index.html

@@ -19,19 +19,19 @@
         <div id="app"></div>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
-            var viewer = new DockingViewer('app', [0x33DD22, 0x1133EE], true);
-
             function getParam(name, regex) {
                 var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
                 return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
             }
-            var pdbqt = getParam('pdbqt', '[^&]+').trim();
-            var mol2 = getParam('mol2', '[^&]+').trim();
+            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
+            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
 
-            viewer.loadStructuresFromUrlsAndMerge([
-                { url: pdbqt, format: 'pdbqt' },
-                { url: mol2, format: 'mol2' }
-            ]);
+            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
+                viewer.loadStructuresFromUrlsAndMerge([
+                    { url: pdbqt, format: 'pdbqt' },
+                    { url: mol2, format: 'mol2' }
+                ]);
+            });
         </script>
     </body>
 </html>

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 { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
@@ -54,9 +54,10 @@ const DefaultViewerOptions = {
 };
 
 class Viewer {
-    plugin: PluginUIContext
+    constructor(public plugin: PluginUIContext) {
+    }
 
-    constructor(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
+    static async create(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
         const o = { ...DefaultViewerOptions, ...{
             layoutIsExpanded: false,
             layoutShowControls: false,
@@ -125,29 +126,31 @@ class Viewer {
             ? document.getElementById(elementOrId)
             : elementOrId;
         if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        this.plugin = createPlugin(element, spec);
+        const plugin = await createPluginUI(element, spec);
 
-        (this.plugin.customState as any) = {
+        (plugin.customState as any) = {
             colorPalette: {
                 name: 'colors',
                 params: { list: { colors } }
             }
         };
 
-        this.plugin.behaviors.canvas3d.initialized.subscribe(v => {
+        plugin.behaviors.canvas3d.initialized.subscribe(v => {
             if (v) {
-                PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
+                PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
                     renderer: {
-                        ...this.plugin.canvas3d!.props.renderer,
+                        ...plugin.canvas3d!.props.renderer,
                         backgroundColor: ColorNames.white,
                     },
                     camera: {
-                        ...this.plugin.canvas3d!.props.camera,
+                        ...plugin.canvas3d!.props.camera,
                         helper: { axes: { name: 'off', params: {} } }
                     }
                 } });
             }
         });
+
+        return new Viewer(plugin);
     }
 
     async loadStructuresFromUrlsAndMerge(sources: { url: string, format: BuiltInTrajectoryFormat, isBinary?: boolean }[]) {

src/apps/docking-viewer/viewport.tsx

@@ -21,6 +21,7 @@ import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { StateObjectRef } from '../../mol-state';
 import { Color } from '../../mol-util/color';
+import { Material } from '../../mol-util/material';
 
 function shinyStyle(plugin: PluginContext) {
     return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
@@ -50,7 +51,8 @@ function occlusionStyle(plugin: PluginContext) {
             } },
             outline: { name: 'on', params: {
                 scale: 1.0,
-                threshold: 0.33
+                threshold: 0.33,
+                color: Color(0x0000),
             } }
         }
     } });
@@ -75,7 +77,7 @@ const PresetParams = {
     ...StructureRepresentationPresetProvider.CommonParams,
 };
 
-
+const CustomMaterial = Material({ roughness: 0.2, metalness: 0 });
 
 export const StructurePreset = StructureRepresentationPresetProvider({
     id: 'preset-structure',
@@ -92,8 +94,8 @@ export const StructurePreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, roughness: 0.2, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, roughness: 0.2 }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, material: CustomMaterial }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -147,8 +149,8 @@ const SurfacePreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, roughness: 0.2, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, roughness: 0.2, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, material: CustomMaterial, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -175,8 +177,8 @@ const PocketPreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, roughness: 0.2, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, roughness: 0.2, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, material: CustomMaterial, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -204,10 +206,10 @@ const InteractionsPreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, roughness: 0.2, 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, roughness: 0.2, 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, roughness: 0.2 }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
-            label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, roughness: 0.2, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
+            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' }),
+            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' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -228,7 +230,7 @@ export class ViewportComponent extends PluginUIComponent {
 
     set = async (preset: StructureRepresentationPresetProvider) => {
         await this._set(this.plugin.managers.structure.hierarchy.selection.structures, preset);
-    }
+    };
 
     structurePreset = () => this.set(StructurePreset);
     illustrativePreset = () => this.set(IllustrativePreset);

src/apps/viewer/app.ts

@@ -0,0 +1,491 @@
+/**
+ * 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>
+ */
+
+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { CellPack } from '../../extensions/cellpack';
+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+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 { 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 { 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 { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectRef, StateObjectSelector } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+
+const CustomFormats = [
+    ['g3d', G3dProvider] as const
+];
+
+const Extensions = {
+    'cellpack': PluginSpec.Behavior(CellPack),
+    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    '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),
+};
+
+const DefaultViewerOptions = {
+    customFormats: CustomFormats as [string, DataFormatProvider][],
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
+    collapseRightPanel: false,
+    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: PluginConfig.General.PixelScale.defaultValue,
+    pickScale: PluginConfig.General.PickScale.defaultValue,
+    pickPadding: PluginConfig.General.PickPadding.defaultValue,
+    enableWboit: PluginConfig.General.EnableWboit.defaultValue,
+    preferWebgl1: PluginConfig.General.PreferWebGl1.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,
+    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,
+};
+type ViewerOptions = typeof DefaultViewerOptions;
+
+export class Viewer {
+    constructor(public plugin: PluginUIContext) {
+    }
+
+    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
+        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 = {
+            actions: defaultSpec.actions,
+            behaviors: [
+                ...defaultSpec.behaviors,
+                ...o.extensions.map(e => Extensions[e]),
+            ],
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
+            customFormats: o?.customFormats,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: o.collapseRightPanel ? 'hidden' : 'full',
+                        top: 'full',
+                    }
+                },
+            },
+            components: {
+                ...defaultSpec.components,
+                controls: {
+                    ...defaultSpec.components?.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                },
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+            },
+            config: [
+                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.PickScale, o.pickScale],
+                [PluginConfig.General.PickPadding, o.pickPadding],
+                [PluginConfig.General.EnableWboit, o.enableWboit],
+                [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+                [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.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
+            ]
+        };
+
+        const element = typeof elementOrId === 'string'
+            ? document.getElementById(elementOrId)
+            : elementOrId;
+        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
+        const plugin = await createPluginUI(element, spec, {
+            onBeforeUIRender: plugin => {
+                // the preset needs to be added before the UI renders otherwise
+                // "Download Structure" wont be able to pick it up
+                plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
+            }
+        });
+        return new Viewer(plugin);
+    }
+
+    setRemoteSnapshot(id: string) {
+        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
+        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
+    }
+
+    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
+        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
+    }
+
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'url',
+                params: {
+                    url: Asset.Url(url),
+                    format: format as any,
+                    isBinary,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const plugin = this.plugin;
+
+        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
+    }
+
+    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
+        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    }
+
+    loadPdb(pdb: string, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb' as const,
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue as any
+                        }
+                    },
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    loadPdbDev(pdbDev: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev' as const,
+                params: {
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    loadEmdb(emdb: string, options?: { detail?: number }) {
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds' as const,
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: options?.detail ?? 3,
+                }
+            }
+        }));
+    }
+
+    loadAlphaFoldDb(afdb: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'alphafolddb' as const,
+                params: {
+                    id: afdb,
+                    options: {
+                        ...params.source.params.options,
+                        representation: 'preset-structure-representation-ma-quality-assessment-plddt'
+                    },
+                }
+            }
+        }));
+    }
+
+    loadModelArchive(id: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'modelarchive' as const,
+                params: {
+                    id,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
+        const plugin = this.plugin;
+
+        if (!plugin.dataFormats.get(format)) {
+            throw new Error(`Unknown density format: ${format}`);
+        }
+
+        if (options?.isLazy) {
+            const update = this.plugin.build();
+            update.toRoot().apply(StateTransforms.Data.LazyVolume, {
+                url,
+                format,
+                entryId: options?.entryId,
+                isBinary,
+                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
+            });
+            return update.commit();
+        }
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+
+            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
+
+            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(volume)
+                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                        type: 'isosurface',
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
+                        color: 'uniform',
+                        colorParams: { value: iso.color }
+                    }));
+            }
+
+            await repr.commit();
+        });
+    }
+
+    /**
+     * @example
+     *  viewer.loadTrajectory({
+     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+     *      preset: 'all-models' // or 'default'
+     *  });
+     */
+    async loadTrajectory(params: LoadTrajectoryParams) {
+        const plugin = this.plugin;
+
+        let model: StateObjectSelector, coords: StateObjectSelector;
+
+        if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
+            const data = params.model.kind === 'model-data'
+                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+            const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
+            model = await plugin.builders.structure.createModel(trajectory);
+        } else {
+            const data = params.model.kind === 'topology-data'
+                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+            const provider = plugin.dataFormats.get(params.model.format);
+            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 provider = plugin.dataFormats.get(params.coordinates.format);
+            coords = await provider!.parse(plugin, data);
+        }
+
+        const trajectory = await plugin.build().toRoot()
+            .apply(TrajectoryFromModelAndCoordinates, {
+                modelRef: model.ref,
+                coordinatesRef: coords.ref
+            }, { dependsOn: [model.ref, coords.ref] })
+            .commit();
+
+        const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
+
+        return { model, coords, preset };
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next(void 0);
+    }
+}
+
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams
+}
+
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative',
+    value: number,
+    color: Color,
+    alpha?: number,
+    volumeIndex?: number
+}
+
+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 },
+    modelLabel?: string,
+    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
+    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    coordinatesLabel?: string,
+    preset?: keyof PresetTrajectoryHierarchy
+}
+
+export const ViewerAutoPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-viewer-auto',
+    display: {
+        name: 'Automatic (w/ Annotation)', group: 'Annotation',
+        description: 'Show standard automatic representation but colored by quality assessment (if available in the model).'
+    },
+    isApplicable(a) {
+        return (
+            !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')) ||
+            !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))
+        );
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT'))) {
+            return await QualityAssessmentPLDDTPreset.apply(ref, params, plugin);
+        } else if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))) {
+            return await QualityAssessmentQmeanPreset.apply(ref, params, plugin);
+        } else {
+            return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
+        }
+    }
+});

src/apps/viewer/embedded.html

@@ -20,7 +20,7 @@
         <div id="app"></div>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
-            var viewer = new molstar.Viewer('app', {
+            molstar.Viewer.create('app', {
                 layoutIsExpanded: true,
                 layoutShowControls: false,
                 layoutShowRemoteState: false,
@@ -34,11 +34,11 @@
 
                 pdbProvider: 'rcsb',
                 emdbProvider: 'rcsb',
+            }).then(viewer => {
+                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.loadPdb('7bv2');
-            viewer.loadEmdb('EMD-30210', { detail: 6 });            
-
-            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>
 </html>

src/apps/viewer/index.html

@@ -56,7 +56,10 @@
             var pixelScale = getParam('pixel-scale', '[^&]+').trim();
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
-            var viewer = new molstar.Viewer('app', {
+            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+
+            molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
                 collapseLeftPanel: collapseLeftPanel,
@@ -68,28 +71,37 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
+                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
+                preferWebgl1: preferWebgl1,
+            }).then(viewer => {
+                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+
+                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+
+                var structureUrl = getParam('structure-url', '[^&]+').trim();
+                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+
+                var pdb = getParam('pdb', '[^&]+').trim();
+                if (pdb) viewer.loadPdb(pdb);
+
+                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+                if (pdbDev) viewer.loadPdbDev(pdbDev);
+
+                var emdb = getParam('emdb', '[^&]+').trim();
+                if (emdb) viewer.loadEmdb(emdb);
+
+                var afdb = getParam('afdb', '[^&]+').trim();
+                if (afdb) viewer.loadAlphaFoldDb(afdb);
+
+                var modelArchive = getParam('model-archive', '[^&]+').trim();
+                if (modelArchive) viewer.loadModelArchive(modelArchive);
             });
-
-            var snapshotId = getParam('snapshot-id', '[^&]+').trim();
-            if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
-
-            var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
-            if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
-
-            var structureUrl = getParam('structure-url', '[^&]+').trim();
-            var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
-            var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
-            if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
-
-            var pdb = getParam('pdb', '[^&]+').trim();
-            if (pdb) viewer.loadPdb(pdb);
-
-            var pdbDev = getParam('pdb-dev', '[^&]+').trim();
-            if (pdbDev) viewer.loadPdbDev(pdbDev);
-
-            var emdb = getParam('emdb', '[^&]+').trim();
-            if (emdb) viewer.loadEmdb(emdb);
         </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
 </html>

src/apps/viewer/index.ts

@@ -1,412 +1,12 @@
 /**
- * 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>
  */
 
-import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
-import { CellPack } from '../../extensions/cellpack';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
-import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { GeometryExport } from '../../extensions/geo-export';
-import { Mp4Export } from '../../extensions/mp4-export';
-import { PDBeStructureQualityReport } from '../../extensions/pdbe';
-import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
-import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
-import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
-import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
-import { 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 { 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 { createPlugin } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginConfig } from '../../mol-plugin/config';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { PluginState } from '../../mol-plugin/state';
-import { StateObjectSelector } from '../../mol-state';
-import { Asset } from '../../mol-util/assets';
-import { Color } from '../../mol-util/color';
-import '../../mol-util/polyfill';
-import { ObjectKeys } from '../../mol-util/type-helpers';
 import './embedded.html';
 import './favicon.ico';
 import './index.html';
-
 require('mol-plugin-ui/skin/light.scss');
-
-export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
-
-const CustomFormats = [
-    ['g3d', G3dProvider] as const
-];
-
-const Extensions = {
-    'cellpack': PluginSpec.Behavior(CellPack),
-    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
-    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
-    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
-    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
-    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
-    'g3d': PluginSpec.Behavior(G3DFormat),
-    'mp4-export': PluginSpec.Behavior(Mp4Export),
-    'geo-export': PluginSpec.Behavior(GeometryExport)
-};
-
-const DefaultViewerOptions = {
-    customFormats: CustomFormats as [string, DataFormatProvider][],
-    extensions: ObjectKeys(Extensions),
-    layoutIsExpanded: true,
-    layoutShowControls: true,
-    layoutShowRemoteState: true,
-    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
-    layoutShowSequence: true,
-    layoutShowLog: true,
-    layoutShowLeftPanel: true,
-    collapseLeftPanel: false,
-    collapseRightPanel: false,
-    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
-    pixelScale: PluginConfig.General.PixelScale.defaultValue,
-    pickScale: PluginConfig.General.PickScale.defaultValue,
-    pickPadding: PluginConfig.General.PickPadding.defaultValue,
-    enableWboit: PluginConfig.General.EnableWboit.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,
-    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,
-};
-type ViewerOptions = typeof DefaultViewerOptions;
-
-export class Viewer {
-    plugin: PluginUIContext
-
-    constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
-        const defaultSpec = DefaultPluginUISpec();
-
-        const spec: PluginUISpec = {
-            actions: defaultSpec.actions,
-            behaviors: [
-                ...defaultSpec.behaviors,
-                ...o.extensions.map(e => Extensions[e]),
-            ],
-            animations: [...defaultSpec.animations || []],
-            customParamEditors: defaultSpec.customParamEditors,
-            customFormats: o?.customFormats,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    controlsDisplay: o.layoutControlsDisplay,
-                    regionState: {
-                        bottom: 'full',
-                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
-                        right: o.collapseRightPanel ? 'hidden' : 'full',
-                        top: 'full',
-                    }
-                },
-            },
-            components: {
-                ...defaultSpec.components,
-                controls: {
-                    ...defaultSpec.components?.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                },
-                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
-            },
-            config: [
-                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
-                [PluginConfig.General.PixelScale, o.pixelScale],
-                [PluginConfig.General.PickScale, o.pickScale],
-                [PluginConfig.General.PickPadding, o.pickPadding],
-                [PluginConfig.General.EnableWboit, o.enableWboit],
-                [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.State.DefaultServer, o.pluginStateServer],
-                [PluginConfig.State.CurrentServer, o.pluginStateServer],
-                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
-                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
-                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
-            ]
-        };
-
-        const element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        this.plugin = createPlugin(element, spec);
-    }
-
-    setRemoteSnapshot(id: string) {
-        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
-        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
-    }
-
-    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
-        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
-    }
-
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'url',
-                params: {
-                    url: Asset.Url(url),
-                    format: format as any,
-                    isBinary,
-                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const plugin = this.plugin;
-
-        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
-        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
-
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
-    }
-
-    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
-        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
-        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
-    }
-
-    loadPdb(pdb: string, options?: LoadStructureOptions) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'pdb' as const,
-                params: {
-                    provider: {
-                        id: pdb,
-                        server: {
-                            name: provider,
-                            params: PdbDownloadProvider[provider].defaultValue as any
-                        }
-                    },
-                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    loadPdbDev(pdbDev: string) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'pdb-dev' as const,
-                params: {
-                    provider: {
-                        id: pdbDev,
-                        encoding: 'bcif',
-                    },
-                    options: params.source.params.options,
-                }
-            }
-        }));
-    }
-
-    loadEmdb(emdb: string, options?: { detail?: number }) {
-        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
-            source: {
-                name: 'pdb-emd-ds' as const,
-                params: {
-                    provider: {
-                        id: emdb,
-                        server: provider,
-                    },
-                    detail: options?.detail ?? 3,
-                }
-            }
-        }));
-    }
-
-    /**
-     * @example Load X-ray density from volume server
-        viewer.loadVolumeFromUrl({
-            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
-            format: 'dscif',
-            isBinary: true
-        }, [{
-            type: 'relative',
-            value: 1.5,
-            color: 0x3362B2
-        }, {
-            type: 'relative',
-            value: 3,
-            color: 0x33BB33,
-            volumeIndex: 1
-        }, {
-            type: 'relative',
-            value: -3,
-            color: 0xBB3333,
-            volumeIndex: 1
-        }], {
-            entryId: ['2FO-FC', 'FO-FC'],
-            isLazy: true
-        });
-     * *********************
-     * @example Load EM density from volume server
-        viewer.loadVolumeFromUrl({
-            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
-            format: 'dscif',
-            isBinary: true
-        }, [{
-            type: 'relative',
-            value: 1,
-            color: 0x3377aa
-        }], {
-            entryId: 'EMD-30210',
-            isLazy: true
-        });
-     */
-    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
-        const plugin = this.plugin;
-
-        if (!plugin.dataFormats.get(format)) {
-            throw new Error(`Unknown density format: ${format}`);
-        }
-
-        if (options?.isLazy) {
-            const update = this.plugin.build();
-            update.toRoot().apply(StateTransforms.Data.LazyVolume, {
-                url,
-                format,
-                entryId: options?.entryId,
-                isBinary,
-                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
-            });
-            return update.commit();
-        }
-
-        return plugin.dataTransaction(async () => {
-            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
-
-            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
-            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
-
-            const repr = plugin.build();
-            for (const iso of isovalues) {
-                repr
-                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.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 } },
-                        color: 'uniform',
-                        colorParams: { value: iso.color }
-                    }));
-            }
-
-            await repr.commit();
-        });
-    }
-
-    /**
-     * @example
-     *  viewer.loadTrajectory({
-     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
-     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
-     *      preset: 'all-models' // or 'default'
-     *  });
-     */
-    async loadTrajectory(params: LoadTrajectoryParams) {
-        const plugin = this.plugin;
-
-        let model: StateObjectSelector, coords: StateObjectSelector;
-
-        if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
-            const data = params.model.kind === 'model-data'
-                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
-                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
-
-            const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
-            model = await plugin.builders.structure.createModel(trajectory);
-        } else {
-            const data = params.model.kind === 'topology-data'
-                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
-                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
-
-            const provider = plugin.dataFormats.get(params.model.format);
-            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 provider = plugin.dataFormats.get(params.coordinates.format);
-            coords = await provider!.parse(plugin, data);
-        }
-
-        const trajectory = await plugin.build().toRoot()
-            .apply(TrajectoryFromModelAndCoordinates, {
-                modelRef: model.ref,
-                coordinatesRef: coords.ref
-            }, { dependsOn: [model.ref, coords.ref] })
-            .commit();
-
-        const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
-
-        return { model, coords, preset };
-    }
-
-    handleResize() {
-        this.plugin.layout.events.updated.next(void 0);
-    }
-}
-
-export interface LoadStructureOptions {
-    representationParams?: StructureRepresentationPresetProvider.CommonParams
-}
-
-export interface VolumeIsovalueInfo {
-    type: 'absolute' | 'relative',
-    value: number,
-    color: Color,
-    alpha?: number,
-    volumeIndex?: number
-}
-
-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 },
-    modelLabel?: string,
-    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
-    coordinatesLabel?: string,
-    preset?: keyof PresetTrajectoryHierarchy
-}
+export * from './app';

src/cli/cifschema/index.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -35,20 +35,16 @@ async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, type
     const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
     if (ihmDic.isError) throw ihmDic;
 
-    await ensureCarbBranchDicAvailable();
-    const carbBranchDic = await parseCifText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
-    if (carbBranchDic.isError) throw carbBranchDic;
-
-    await ensureCarbCompDicAvailable();
-    const carbCompDic = await parseCifText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
-    if (carbCompDic.isError) throw carbCompDic;
+    await ensureMaDicAvailable();
+    const maDic = await parseCifText(fs.readFileSync(MA_DIC_PATH, 'utf8')).run();
+    if (maDic.isError) throw maDic;
 
     const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
     const ihmDicVersion = getDicVersion(ihmDic.result.blocks[0]);
-    const carbDicVersion = 'draft';
-    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}, CARB ${carbDicVersion}.`;
+    const maDicVersion = getDicVersion(maDic.result.blocks[0]);
+    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}, MA ${maDicVersion}.`;
 
-    const frames: CifFrame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames, ...carbBranchDic.result.blocks[0].saveFrames, ...carbCompDic.result.blocks[0].saveFrames];
+    const frames: CifFrame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames, ...maDic.result.blocks[0].saveFrames];
     const schema = generateSchema(frames);
 
     await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases);
@@ -139,8 +135,7 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
 
 async function ensureMmcifDicAvailable() { await ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL); }
 async function ensureIhmDicAvailable() { await ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL); }
-async function ensureCarbBranchDicAvailable() { await ensureDicAvailable(CARB_BRANCH_DIC_PATH, CARB_BRANCH_DIC_URL); }
-async function ensureCarbCompDicAvailable() { await ensureDicAvailable(CARB_COMP_DIC_PATH, CARB_COMP_DIC_URL); }
+async function ensureMaDicAvailable() { await ensureDicAvailable(MA_DIC_PATH, MA_DIC_URL); }
 async function ensureCifCoreDicAvailable() {
     await ensureDicAvailable(CIF_CORE_DIC_PATH, CIF_CORE_DIC_URL);
     await ensureDicAvailable(CIF_CORE_ENUM_PATH, CIF_CORE_ENUM_URL);
@@ -165,10 +160,8 @@ const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`;
 const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic';
 const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`;
 const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
-const CARB_BRANCH_DIC_PATH = `${DIC_DIR}/entity_branch-extension.dic`;
-const CARB_BRANCH_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/entity_branch-extension.dic';
-const CARB_COMP_DIC_PATH = `${DIC_DIR}/chem_comp-extension.dic`;
-const CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-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 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/examples/alpha-orbitals/index.html

@@ -57,5 +57,6 @@
         <script>
             AlphaOrbitalsExample.init('app')
         </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
 </html>

src/examples/alpha-orbitals/index.ts

@@ -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 { createPluginAsync } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -54,7 +54,7 @@ export class AlphaOrbitalsExample {
 
     async init(target: string | HTMLElement) {
         const defaultSpec = DefaultPluginUISpec();
-        this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
+        this.plugin = await createPluginUI(typeof target === 'string' ? document.getElementById(target)! : target, {
             ...defaultSpec,
             layout: {
                 initial: {
@@ -67,7 +67,7 @@ export class AlphaOrbitalsExample {
             },
             canvas3d: {
                 camera: {
-                    helper: { axes: { name: 'off', params: { } } }
+                    helper: { axes: { name: 'off', params: {} } }
                 }
             },
             config: [
@@ -97,7 +97,7 @@ export class AlphaOrbitalsExample {
     }
 
     readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
-    readonly state = new BehaviorSubject<Params>({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
+    readonly state = new BehaviorSubject<Params>({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: true });
 
     private selectors?: Selectors = void 0;
     private basis?: StateObjectSelector<BasisAndOrbitals> = void 0;
@@ -170,12 +170,11 @@ export class AlphaOrbitalsExample {
         return {
             alpha: 0.85,
             color,
-            directVolume: this.state.value.gpuSurface,
             kind,
             relativeIsovalue: this.state.value.isoValue,
             pickable: false,
             xrayShaded: true,
-            tryUseGpu: false
+            tryUseGpu: true
         };
     }
 

src/examples/basic-wrapper/index.html

@@ -69,8 +69,9 @@
             $('format').value = format;
             $('format').onchange = function (e) { format = e.target.value; }
 
-            BasicMolStarWrapper.init('app' /** or document.getElementById('app') */);
-            BasicMolStarWrapper.setBackground(0xffffff);
+            BasicMolStarWrapper.init('app' /** or document.getElementById('app') */).then(() => {
+                BasicMolStarWrapper.setBackground(0xffffff);
+            });
 
             addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
             addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));

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 { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -28,8 +28,8 @@ type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: bo
 class BasicWrapper {
     plugin: PluginUIContext;
 
-    init(target: string | HTMLElement) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+    async init(target: string | HTMLElement) {
+        this.plugin = await createPluginUI(typeof target === 'string' ? document.getElementById(target)! : target, {
             ...DefaultPluginUISpec(),
             layout: {
                 initial: {
@@ -60,7 +60,7 @@ class BasicWrapper {
                 params: { id: assemblyId }
             } : {
                 name: 'model',
-                params: { }
+                params: {}
             },
             showUnitcell: false,
             representationPreset: 'auto'
@@ -74,12 +74,20 @@ class BasicWrapper {
     toggleSpin() {
         if (!this.plugin.canvas3d) return;
 
+        const trackball = this.plugin.canvas3d.props.trackball;
         PluginCommands.Canvas3D.SetSettings(this.plugin, {
-            settings: props => {
-                props.trackball.spin = !props.trackball.spin;
+            settings: {
+                trackball: {
+                    ...trackball,
+                    animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } }
+                }
             }
         });
-        if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
+        if (this.plugin.canvas3d.props.trackball.animate.name !== 'spin') {
+            PluginCommands.Camera.Reset(this.plugin, {});
+        }
     }
 
     private animateModelIndexTargetFps() {
@@ -95,7 +103,7 @@ class BasicWrapper {
             loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: { direction: 'forward' } } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
-    }
+    };
 
     coloring = {
         applyStripes: async () => {
@@ -119,7 +127,7 @@ class BasicWrapper {
                 }
             });
         }
-    }
+    };
 
     interactivity = {
         highlightOn: () => {
@@ -137,7 +145,7 @@ class BasicWrapper {
         clearHighlight: () => {
             this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
         }
-    }
+    };
 
     tests = {
         staticSuperposition: async () => {
@@ -168,7 +176,7 @@ class BasicWrapper {
             PluginCommands.Toast.Hide(this.plugin, { key: 'toast-1' });
             PluginCommands.Toast.Hide(this.plugin, { key: 'toast-2' });
         }
-    }
+    };
 }
 
 (window as any).BasicMolStarWrapper = new BasicWrapper();

src/examples/lighting/index.html

@@ -45,8 +45,9 @@
         <div id='controls'></div>
         <div id="app"></div>
         <script>
-            LightingDemo.init('app')
-            LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3)
+            LightingDemo.init('app').then(() => {
+                LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3);
+            });
 
             addHeader('Example PDB IDs');
             addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
@@ -83,5 +84,6 @@
                 $('controls').appendChild(h);
             }
         </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
 </html>

src/examples/lighting/index.ts

@@ -1,59 +1,62 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
 
 type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
 
-type _Preset = Pick<Canvas3DProps, 'multiSample' | 'postprocessing' | 'renderer'>
+type _Preset = Pick<Canvas3DProps, 'postprocessing' | 'renderer'>
 type Preset = { [K in keyof _Preset]: Partial<_Preset[K]> }
 
 const Canvas3DPresets = {
-    illustrative: <Preset> {
-        multiSample: {
-            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
-            outline: { name: 'on', params: { scale: 1, threshold: 0.1 } }
-        },
-        renderer: {
-            style: { name: 'flat', params: {} }
+    illustrative: {
+        canvas3d: <Preset>{
+            postprocessing: {
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000) } }
+            },
+            renderer: {
+                ambientIntensity: 1.0,
+                light: []
+            }
         }
     },
-    occlusion: <Preset> {
-        multiSample: {
-            mode: 'temporal' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
-            outline: { name: 'off', params: { } }
-        },
-        renderer: {
-            style: { name: 'matte', params: {} }
+    occlusion: {
+        canvas3d: <Preset>{
+            postprocessing: {
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                outline: { name: 'off', params: {} }
+            },
+            renderer: {
+                ambientIntensity: 0.4,
+                light: [{ inclination: 180, azimuth: 0, color: Color.fromNormalizedRgb(1.0, 1.0, 1.0),
+                    intensity: 0.6 }]
+            }
         }
     },
-    standard: <Preset> {
-        multiSample: {
-            mode: 'off' as Canvas3DProps['multiSample']['mode']
-        },
-        postprocessing: {
-            occlusion: { name: 'off', params: { } },
-            outline: { name: 'off', params: { } }
-        },
-        renderer: {
-            style: { name: 'matte', params: {} }
+    standard: {
+        canvas3d: <Preset>{
+            postprocessing: {
+                occlusion: { name: 'off', params: {} },
+                outline: { name: 'off', params: {} }
+            },
+            renderer: {
+                ambientIntensity: 0.4,
+                light: [{ inclination: 180, azimuth: 0, color: Color.fromNormalizedRgb(1.0, 1.0, 1.0),
+                    intensity: 0.6 }]
+            }
         }
     }
 };
@@ -68,8 +71,8 @@ class LightingDemo {
     private bias = 1.1;
     private preset: Canvas3DPreset = 'illustrative';
 
-    init(target: string | HTMLElement) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+    async init(target: string | HTMLElement) {
+        this.plugin = await createPluginUI(typeof target === 'string' ? document.getElementById(target)! : target, {
             ...DefaultPluginUISpec(),
             layout: {
                 initial: {
@@ -87,25 +90,23 @@ class LightingDemo {
 
     setPreset(preset: Canvas3DPreset) {
         const props = Canvas3DPresets[preset];
-        if (props.postprocessing.occlusion?.name === 'on') {
-            props.postprocessing.occlusion.params.radius = this.radius;
-            props.postprocessing.occlusion.params.bias = this.bias;
+        if (props.canvas3d.postprocessing.occlusion?.name === 'on') {
+            props.canvas3d.postprocessing.occlusion.params.radius = this.radius;
+            props.canvas3d.postprocessing.occlusion.params.bias = this.bias;
         }
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
-            ...props,
-            multiSample: {
-                ...this.plugin.canvas3d!.props.multiSample,
-                ...props.multiSample
-            },
-            renderer: {
-                ...this.plugin.canvas3d!.props.renderer,
-                ...props.renderer
-            },
-            postprocessing: {
-                ...this.plugin.canvas3d!.props.postprocessing,
-                ...props.postprocessing
-            },
-        } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: {
+                ...props,
+                renderer: {
+                    ...this.plugin.canvas3d!.props.renderer,
+                    ...props.canvas3d.renderer
+                },
+                postprocessing: {
+                    ...this.plugin.canvas3d!.props.postprocessing,
+                    ...props.canvas3d.postprocessing
+                },
+            }
+        });
     }
 
     async load({ url, format = 'mmcif', isBinary = true, assemblyId = '' }: LoadParams, radius: number, bias: number) {
@@ -114,7 +115,7 @@ class LightingDemo {
         const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
         const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
         const model = await this.plugin.builders.structure.createModel(trajectory);
-        const structure = await this.plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'model', params: { } });
+        const structure = await this.plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'model', params: {} });
 
         const polymer = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'polymer');
         if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });

src/examples/proteopedia-wrapper/index.html

@@ -103,10 +103,11 @@
 
             PluginWrapper.init('app' /** or document.getElementById('app') */, {
                 customColorList: CustomColors
+            }).then(() => {
+                PluginWrapper.setBackground(0xffffff);
+                loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
+                PluginWrapper.toggleSpin();
             });
-            PluginWrapper.setBackground(0xffffff);
-            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
-            PluginWrapper.toggleSpin();
 
             PluginWrapper.events.modelInfo.subscribe(function (info) {
                 console.log('Model Info', info);

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 { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
@@ -43,10 +43,10 @@ class MolStarProteopediaWrapper {
 
     plugin: PluginUIContext;
 
-    init(target: string | HTMLElement, options?: {
+    async init(target: string | HTMLElement, options?: {
         customColorList?: number[]
     }) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
+        this.plugin = await createPluginUI(typeof target === 'string' ? document.getElementById(target)! : target, {
             ...DefaultPluginUISpec(),
             animations: [
                 AnimateModelIndex
@@ -95,7 +95,7 @@ class MolStarProteopediaWrapper {
                 params: { id: assemblyId }
             } : {
                 name: 'model' as const,
-                params: { }
+                params: {}
             }
         };
 
@@ -113,7 +113,7 @@ class MolStarProteopediaWrapper {
         const structure = this.getObj<PluginStateObject.Molecule.Structure>(StateElements.Assembly);
         if (!structure) return;
 
-        const style = _style || { };
+        const style = _style || {};
 
         const update = this.state.build();
 
@@ -229,7 +229,7 @@ class MolStarProteopediaWrapper {
                     params: { id: asmId }
                 } : {
                     name: 'model' as const,
-                    params: { }
+                    params: {}
                 }
             };
             tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
@@ -256,7 +256,16 @@ class MolStarProteopediaWrapper {
     toggleSpin() {
         if (!this.plugin.canvas3d) return;
         const trackball = this.plugin.canvas3d.props.trackball;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: {
+                trackball: {
+                    ...trackball,
+                    animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } }
+                }
+            }
+        });
     }
 
     viewport = {
@@ -269,8 +278,8 @@ class MolStarProteopediaWrapper {
 
     camera = {
         toggleSpin: () => this.toggleSpin(),
-        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
-    }
+        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, {})
+    };
 
     private animateModelIndexTargetFps() {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);
@@ -285,7 +294,7 @@ class MolStarProteopediaWrapper {
             loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: { direction: 'forward' } } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
-    }
+    };
 
     coloring = {
         evolutionaryConservation: async (params?: { sequence?: boolean, het?: boolean, keepStyle?: boolean }) => {
@@ -306,7 +315,7 @@ class MolStarProteopediaWrapper {
 
             await PluginCommands.State.Update(this.plugin, { state, tree });
         }
-    }
+    };
 
     private experimentalDataElement?: Element = void 0;
     experimentalData = {
@@ -330,17 +339,17 @@ class MolStarProteopediaWrapper {
                 this.experimentalDataElement = void 0;
             }
         }
-    }
+    };
 
     hetGroups = {
         reset: () => {
             const update = this.state.build().delete(StateElements.HetGroupFocusGroup);
             PluginCommands.State.Update(this.plugin, { state: this.state, tree: update });
-            PluginCommands.Camera.Reset(this.plugin, { });
+            PluginCommands.Camera.Reset(this.plugin, {});
         },
         focusFirst: async (compId: string, options?: { hideLabels: boolean, doNotLabelWaters: boolean }) => {
             if (!this.state.transforms.has(StateElements.Assembly)) return;
-            await PluginCommands.Camera.Reset(this.plugin, { });
+            await PluginCommands.Camera.Reset(this.plugin, {});
 
             const update = this.state.build();
 
@@ -397,7 +406,7 @@ class MolStarProteopediaWrapper {
             const snapshot = this.plugin.canvas3d!.camera.getFocus(sphere.center, radius);
             PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: 250 });
         }
-    }
+    };
 
     snapshot = {
         get: (params?: PluginState.SnapshotParams) => {
@@ -420,7 +429,7 @@ class MolStarProteopediaWrapper {
             }
         }
 
-    }
+    };
 }
 
 (window as any).MolStarProteopediaWrapper = MolStarProteopediaWrapper;

src/extensions/alpha-orbitals/transforms.ts

@@ -166,7 +166,6 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
     from: PluginStateObject.Volume.Data,
     to: PluginStateObject.Volume.Representation3D,
     params: {
-        directVolume: PD.Boolean(false),
         relativeIsovalue: PD.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
         kind: PD.Select<'positive' | 'negative'>('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
         color: PD.Color(ColorNames.blue),
@@ -217,19 +216,7 @@ function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Da
 
     const value = isovalues[params.kind];
 
-    return createVolumeRepresentationParams(plugin, volume.data, params.directVolume ? {
-        type: 'direct-volume',
-        typeParams: {
-            alpha: params.alpha,
-            renderMode: {
-                name: 'isosurface',
-                params: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, singleLayer: false }
-            },
-            xrayShaded: params.xrayShaded
-        },
-        color: 'uniform',
-        colorParams: { value: params.color }
-    } : {
+    return createVolumeRepresentationParams(plugin, volume.data, {
         type: 'isosurface',
         typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded, tryUseGpu: params.tryUseGpu },
         color: 'uniform',

src/extensions/anvil/behavior.ts

@@ -30,7 +30,7 @@ export const ANVILMembraneOrientation = PluginBehavior.create<{ autoAttach: bool
         description: 'Data calculated with ANVIL algorithm.'
     },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
-        private provider = MembraneOrientationProvider
+        private provider = MembraneOrientationProvider;
 
         register(): void {
             DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);

src/extensions/anvil/representation.ts

@@ -43,9 +43,9 @@ export type BilayerPlanesProps = PD.Values<BilayerPlanesParams>
 const BilayerRimsParams = {
     ...Lines.Params,
     ...SharedParams,
-    lineSizeAttenuation: PD.Boolean(true),
-    linesSize: PD.Numeric(0.3, { min: 0.01, max: 50, step: 0.01 }),
-    dashedLines: PD.Boolean(true),
+    lineSizeAttenuation: PD.Boolean(false),
+    linesSize: PD.Numeric(0.5, { min: 0.01, max: 50, step: 0.01 }),
+    dashedLines: PD.Boolean(false),
 };
 export type BilayerRimsParams = typeof BilayerRimsParams
 export type BilayerRimsProps = PD.Values<BilayerRimsParams>

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

@@ -66,7 +66,7 @@ export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean,
                 /* TODO: Implement this */
                 return void 0;
             }
-        }
+        };
 
         register(): void {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);

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

@@ -114,7 +114,7 @@ export namespace ConfalPyramidsUtil {
             this.modelNum = unit.model.modelNum;
         }
 
-        protected readonly data: CPT.PyramidsData
+        protected readonly data: CPT.PyramidsData;
         protected readonly hasMultipleModels: boolean;
         protected readonly entryId: string;
         protected readonly modelNum: number;

src/extensions/geo-export/controls.ts

@@ -29,7 +29,7 @@ export const GeometryParams = {
 export class GeometryControls extends PluginComponent {
     readonly behaviors = {
         params: this.ev.behavior<PD.Values<typeof GeometryParams>>(PD.getDefaultValues(GeometryParams))
-    }
+    };
 
     private getFilename() {
         const models = this.plugin.state.data.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Model)).map(s => s.obj!.data);

src/extensions/geo-export/mesh-exporter.ts

@@ -25,7 +25,7 @@ import { sizeDataFactor } from '../../mol-geo/geometry/size-data';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { RuntimeContext } from '../../mol-task';
 import { Color } from '../../mol-util/color/color';
-import { decodeFloatRGB } from '../../mol-util/float-packing';
+import { unpackRGBToInt } from '../../mol-util/number-packing';
 import { RenderObjectExporter, RenderObjectExportData } from './render-object-exporter';
 import { readAlphaTexture, readTexture } from '../../mol-gl/compute/util';
 
@@ -65,7 +65,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
         const r = tSize.array[i * 3];
         const g = tSize.array[i * 3 + 1];
         const b = tSize.array[i * 3 + 2];
-        return decodeFloatRGB(r, g, b) / sizeDataFactor;
+        return unpackRGBToInt(r, g, b) / sizeDataFactor;
     }
 
     private static getSize(values: BaseValues & SizeValues, instanceIndex: number, group: number): number {
@@ -95,9 +95,9 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
         const g = groups[i4 + 1];
         const b = groups[i4 + 2];
         if (groups instanceof Float32Array) {
-            return decodeFloatRGB(r * 255 + 0.5, g * 255 + 0.5, b * 255 + 0.5);
+            return unpackRGBToInt(r * 255 + 0.5, g * 255 + 0.5, b * 255 + 0.5);
         }
-        return decodeFloatRGB(r, g, b);
+        return unpackRGBToInt(r, g, b);
     }
 
     protected static getInterpolatedColors(webgl: WebGLContext, input: { vertices: Float32Array, vertexCount: number, values: BaseValues, stride: 3 | 4, colorType: 'volume' | 'volumeInstance' }) {

src/extensions/geo-export/obj-exporter.ts

@@ -145,7 +145,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
                 const color = ObjExporter.getColor(v, geoData, interpolatedColors, interpolatedOverpaint);
                 Color.toArray(color, quantizedColors, i);
             }
-            ObjExporter.quantizeColors(quantizedColors, mesh!.vertexCount);
+            ObjExporter.quantizeColors(quantizedColors, vertexCount);
 
             // face
             for (let i = 0; i < drawCount; i += 3) {

src/extensions/geo-export/ui.tsx

@@ -85,7 +85,7 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
         } finally {
             this.setState({ busy: false });
         }
-    }
+    };
 
     viewInAR = async () => {
         try {
@@ -104,5 +104,5 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
         } finally {
             this.setState({ busy: false });
         }
-    }
+    };
 }

src/extensions/geo-export/usdz-exporter.ts

@@ -149,7 +149,7 @@ def Material "material${materialKey}"
                 const color = UsdzExporter.getColor(v, geoData, interpolatedColors, interpolatedOverpaint);
                 Color.toArray(color, quantizedColors, i);
             }
-            UsdzExporter.quantizeColors(quantizedColors, mesh!.vertexCount);
+            UsdzExporter.quantizeColors(quantizedColors, vertexCount);
 
             // material
             const faceIndicesByMaterial = new Map<number, number[]>();

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

@@ -0,0 +1,212 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { Loci } from '../../../mol-model/loci';
+import { DefaultQueryRuntimeTable } from '../../../mol-script/runtime/query/compiler';
+import { PLDDTConfidenceColorThemeProvider } from './color/plddt';
+import { QualityAssessment, QualityAssessmentProvider } from './prop';
+import { StructureSelectionCategory, StructureSelectionQuery } from '../../../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
+import { OrderedSet } from '../../../mol-data/int';
+import { cantorPairing } from '../../../mol-data/util';
+import { QmeanScoreColorThemeProvider } from './color/qmean';
+import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
+import { StateObjectRef } from '../../../mol-state';
+
+export const MAQualityAssessment = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'ma-quality-assessment-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Quality Assessment',
+        description: 'Data included in Model Archive files.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+        private provider = QualityAssessmentProvider;
+
+        private labelProvider = {
+            label: (loci: Loci): string | undefined => {
+                if (!this.params.showTooltip) return;
+                return [
+                    plddtLabel(loci),
+                    qmeanLabel(loci),
+                ].filter(l => !!l).join('</br>');
+            }
+        };
+
+        register(): void {
+            DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
+
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+
+            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(PLDDTConfidenceColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(QmeanScoreColorThemeProvider);
+
+            this.ctx.query.structure.registry.add(confidentPLDDT);
+
+            this.ctx.builders.structure.representation.registerPreset(QualityAssessmentPLDDTPreset);
+            this.ctx.builders.structure.representation.registerPreset(QualityAssessmentQmeanPreset);
+        }
+
+        update(p: { autoAttach: boolean, showTooltip: boolean }) {
+            const updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+
+            this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
+
+            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(PLDDTConfidenceColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(QmeanScoreColorThemeProvider);
+
+            this.ctx.query.structure.registry.remove(confidentPLDDT);
+
+            this.ctx.builders.structure.representation.unregisterPreset(QualityAssessmentPLDDTPreset);
+            this.ctx.builders.structure.representation.unregisterPreset(QualityAssessmentQmeanPreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false),
+        showTooltip: PD.Boolean(true),
+    })
+});
+
+//
+
+function plddtCategory(score: number) {
+    if (score > 50 && score <= 70) return 'Low';
+    if (score > 70 && score <= 90) return 'Confident';
+    if (score > 90) return 'Very high';
+    return 'Very low';
+}
+
+function plddtLabel(loci: Loci): string | undefined {
+    return metricLabel(loci, 'pLDDT', (scoreAvg: number, countInfo: string) => `pLDDT Score ${countInfo}: ${scoreAvg.toFixed(2)} <small>(${plddtCategory(scoreAvg)})</small>`);
+}
+
+function qmeanLabel(loci: Loci): string | undefined {
+    return metricLabel(loci, 'qmean', (scoreAvg: number, countInfo: string) => `QMEAN Score ${countInfo}: ${scoreAvg.toFixed(2)}`);
+}
+
+function metricLabel(loci: Loci, name: 'qmean' | 'pLDDT', label: (scoreAvg: number, countInfo: string) => string): string | undefined {
+    if (loci.kind === 'element-loci') {
+        if (loci.elements.length === 0) return;
+
+        const seen = new Set<number>();
+        const scoreSeen = new Set<number>();
+        let scoreSum = 0;
+
+        for (const { indices, unit } of loci.elements) {
+            const metric = QualityAssessmentProvider.get(unit.model).value?.[name];
+            if (!metric) continue;
+
+            const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index;
+            const { elements } = unit;
+
+            OrderedSet.forEach(indices, idx => {
+                const eI = elements[idx];
+                const rI = residueIndex[eI];
+
+                const residueKey = cantorPairing(rI, unit.id);
+                if (!seen.has(residueKey)) {
+                    const score = metric.get(residueIndex[eI]) ?? -1;
+                    if (score !== -1) {
+                        scoreSum += score;
+                        scoreSeen.add(residueKey);
+                    }
+                    seen.add(residueKey);
+                }
+            });
+        }
+
+        if (seen.size === 0) return;
+
+        const summary: string[] = [];
+
+        if (scoreSeen.size) {
+            const countInfo = `<small>(${scoreSeen.size} ${scoreSeen.size > 1 ? 'Residues avg.' : 'Residue'})</small>`;
+            const scoreAvg = scoreSum / scoreSeen.size;
+            summary.push(label(scoreAvg, countInfo));
+        }
+
+        if (summary.length) {
+            return summary.join('</br>');
+        }
+    }
+}
+
+//
+
+const confidentPLDDT = StructureSelectionQuery('Confident pLDDT (> 70)', MS.struct.modifier.union([
+    MS.struct.modifier.wholeResidues([
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.rel.gr([QualityAssessment.symbols.pLDDT.symbol(), 70]),
+            })
+        ])
+    ])
+]), {
+    description: 'Select residues with a pLDDT > 70 (confident).',
+    category: StructureSelectionCategory.Validation,
+    ensureCustomProperties: async (ctx, structure) => {
+        for (const m of structure.models) {
+            await QualityAssessmentProvider.attach(ctx, m, void 0, true);
+        }
+    }
+});
+
+//
+
+export const QualityAssessmentPLDDTPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-ma-quality-assessment-plddt',
+    display: {
+        name: 'Quality Assessment (pLDDT)', group: 'Annotation',
+        description: 'Color structure based on pLDDT Confidence.'
+    },
+    isApplicable(a) {
+        return !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT'));
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        const colorTheme = PLDDTConfidenceColorThemeProvider.name as any;
+        return await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
+    }
+});
+
+export const QualityAssessmentQmeanPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-ma-quality-assessment-qmean',
+    display: {
+        name: 'Quality Assessment (QMEAN)', group: 'Annotation',
+        description: 'Color structure based on QMEAN Score.'
+    },
+    isApplicable(a) {
+        return !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'qmean'));
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        const colorTheme = QmeanScoreColorThemeProvider.name as any;
+        return await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
+    }
+});

src/extensions/model-archive/quality-assessment/color/plddt.ts

@@ -0,0 +1,106 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Mandar Deshpande <mandar@ebi.ac.uk>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QualityAssessment, QualityAssessmentProvider } from '../prop';
+import { Location } from '../../../../mol-model/location';
+import { Bond, StructureElement, Unit } from '../../../../mol-model/structure';
+import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { Color } from '../../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
+import { TableLegend } from '../../../../mol-util/legend';
+
+const DefaultColor = Color(0xaaaaaa);
+const ConfidenceColors = {
+    'No Score': DefaultColor,
+    'Very Low': Color(0xff7d45),
+    'Low': Color(0xffdb13),
+    'Confident': Color(0x65cbf3),
+    'Very High': Color(0x0053d6)
+};
+
+const ConfidenceColorLegend = TableLegend(Object.entries(ConfidenceColors));
+
+export function getPLDDTConfidenceColorThemeParams(ctx: ThemeDataContext) {
+    return {};
+}
+export type PLDDTConfidenceColorThemeParams = ReturnType<typeof getPLDDTConfidenceColorThemeParams>
+
+export function PLDDTConfidenceColorTheme(ctx: ThemeDataContext, props: PD.Values<PLDDTConfidenceColorThemeParams>): ColorTheme<PLDDTConfidenceColorThemeParams> {
+    let color: LocationColor = () => DefaultColor;
+
+    if (ctx.structure) {
+        const l = StructureElement.Location.create(ctx.structure.root);
+
+        const getColor = (location: StructureElement.Location): Color => {
+            const { unit, element } = location;
+            if (!Unit.isAtomic(unit)) return DefaultColor;
+            const qualityAssessment = QualityAssessmentProvider.get(unit.model).value;
+            const score = qualityAssessment?.pLDDT?.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]) ?? -1;
+            if (score < 0) {
+                return DefaultColor;
+            } else if (score <= 50) {
+                return Color(0xff7d45);
+            } else if (score <= 70) {
+                return Color(0xffdb13);
+            } else if (score <= 90) {
+                return Color(0x65cbf3);
+            } else {
+                return Color(0x0053d6);
+            }
+        };
+
+        color = (location: Location) => {
+            if (StructureElement.Location.is(location)) {
+                return getColor(location);
+            } else if (Bond.isLocation(location)) {
+                l.unit = location.aUnit;
+                l.element = location.aUnit.elements[location.aIndex];
+                return getColor(l);
+            }
+            return DefaultColor;
+        };
+    }
+
+    return {
+        factory: PLDDTConfidenceColorTheme,
+        granularity: 'group',
+        preferSmoothing: true,
+        color,
+        props,
+        description: 'Assigns residue colors according to the pLDDT Confidence score.',
+        legend: ConfidenceColorLegend
+    };
+}
+
+export const PLDDTConfidenceColorThemeProvider: ColorTheme.Provider<PLDDTConfidenceColorThemeParams, 'plddt-confidence'> = {
+    name: 'plddt-confidence',
+    label: 'pLDDT Confidence',
+    category: ColorTheme.Category.Validation,
+    factory: PLDDTConfidenceColorTheme,
+    getParams: getPLDDTConfidenceColorThemeParams,
+    defaultValues: PD.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')),
+    ensureCustomProperties: {
+        attach: async (ctx: CustomProperty.Context, data: ThemeDataContext) => {
+            if (data.structure) {
+                for (const m of data.structure.models) {
+                    await QualityAssessmentProvider.attach(ctx, m, void 0, true);
+                }
+            }
+        },
+        detach: async (data: ThemeDataContext) => {
+            if (data.structure) {
+                for (const m of data.structure.models) {
+                    QualityAssessmentProvider.ref(m, false);
+                }
+            }
+        }
+    }
+};

src/extensions/model-archive/quality-assessment/color/qmean.ts

@@ -0,0 +1,95 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QualityAssessment, QualityAssessmentProvider } from '../prop';
+import { Location } from '../../../../mol-model/location';
+import { Bond, StructureElement, Unit } from '../../../../mol-model/structure';
+import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
+import { ThemeDataContext } from '../../../../mol-theme/theme';
+import { Color, ColorScale } from '../../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
+
+const DefaultColor = Color(0xaaaaaa);
+
+export function getQmeanScoreColorThemeParams(ctx: ThemeDataContext) {
+    return {};
+}
+export type QmeanScoreColorThemeParams = ReturnType<typeof getQmeanScoreColorThemeParams>
+
+export function QmeanScoreColorTheme(ctx: ThemeDataContext, props: PD.Values<QmeanScoreColorThemeParams>): ColorTheme<QmeanScoreColorThemeParams> {
+    let color: LocationColor = () => DefaultColor;
+
+    const scale = ColorScale.create({
+        domain: [0, 1],
+        listOrName: [
+            [Color(0xFF5000), 0.5], [Color(0x025AFD), 1.0]
+        ]
+    });
+
+    if (ctx.structure) {
+        const l = StructureElement.Location.create(ctx.structure.root);
+
+        const getColor = (location: StructureElement.Location): Color => {
+            const { unit, element } = location;
+            if (!Unit.isAtomic(unit)) return DefaultColor;
+            const qualityAssessment = QualityAssessmentProvider.get(unit.model).value;
+            const score = qualityAssessment?.qmean?.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]) ?? -1;
+            if (score < 0) {
+                return DefaultColor;
+            } else {
+                return scale.color(score);
+            }
+        };
+
+        color = (location: Location) => {
+            if (StructureElement.Location.is(location)) {
+                return getColor(location);
+            } else if (Bond.isLocation(location)) {
+                l.unit = location.aUnit;
+                l.element = location.aUnit.elements[location.aIndex];
+                return getColor(l);
+            }
+            return DefaultColor;
+        };
+    }
+
+    return {
+        factory: QmeanScoreColorTheme,
+        granularity: 'group',
+        preferSmoothing: true,
+        color,
+        props,
+        description: 'Assigns residue colors according to the QMEAN score.',
+        legend: scale.legend
+    };
+}
+
+export const QmeanScoreColorThemeProvider: ColorTheme.Provider<QmeanScoreColorThemeParams, 'qmean-score'> = {
+    name: 'qmean-score',
+    label: 'QMEAN Score',
+    category: ColorTheme.Category.Validation,
+    factory: QmeanScoreColorTheme,
+    getParams: getQmeanScoreColorThemeParams,
+    defaultValues: PD.getDefaultValues(getQmeanScoreColorThemeParams({})),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => QualityAssessment.isApplicable(m, 'qmean')),
+    ensureCustomProperties: {
+        attach: async (ctx: CustomProperty.Context, data: ThemeDataContext) => {
+            if (data.structure) {
+                for (const m of data.structure.models) {
+                    await QualityAssessmentProvider.attach(ctx, m, void 0, true);
+                }
+            }
+        },
+        detach: async (data: ThemeDataContext) => {
+            if (data.structure) {
+                for (const m of data.structure.models) {
+                    QualityAssessmentProvider.ref(m, false);
+                }
+            }
+        }
+    }
+};

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

@@ -0,0 +1,131 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Unit } from '../../../mol-model/structure';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Model, ResidueIndex } from '../../../mol-model/structure/model';
+import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+import { CustomPropSymbol } from '../../../mol-script/language/symbol';
+import { Type } from '../../../mol-script/language/type';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+
+export { QualityAssessment };
+
+interface QualityAssessment {
+    localMetrics: Map<string, Map<ResidueIndex, number>>
+    pLDDT?: Map<ResidueIndex, number>
+    qmean?: Map<ResidueIndex, number>
+}
+
+namespace QualityAssessment {
+    const Empty = {
+        value: {
+            localMetrics: new Map()
+        }
+    };
+
+    export function isApplicable(model?: Model, localMetricName?: 'pLDDT' | 'qmean'): boolean {
+        if (!model || !MmcifFormat.is(model.sourceData)) return false;
+        const { db } = model.sourceData.data;
+        const hasLocalMetric = (
+            db.ma_qa_metric.id.isDefined &&
+            db.ma_qa_metric_local.ordinal_id.isDefined
+        );
+        if (localMetricName && hasLocalMetric) {
+            for (let i = 0, il = db.ma_qa_metric._rowCount; i < il; i++) {
+                if (db.ma_qa_metric.mode.value(i) !== 'local') continue;
+                if (localMetricName === db.ma_qa_metric.name.value(i)) return true;
+            }
+            return false;
+        } else {
+            return hasLocalMetric;
+        }
+    }
+
+    export async function obtain(ctx: CustomProperty.Context, model: Model, props: QualityAssessmentProps): Promise<CustomProperty.Data<QualityAssessment>> {
+        if (!model || !MmcifFormat.is(model.sourceData)) return Empty;
+        const { ma_qa_metric, ma_qa_metric_local } = model.sourceData.data.db;
+        const { model_id, label_asym_id, label_seq_id, metric_id, metric_value } = ma_qa_metric_local;
+        const { index } = model.atomicHierarchy;
+
+        // for simplicity we assume names in ma_qa_metric for mode 'local' are unique
+        const localMetrics = new Map<string, Map<ResidueIndex, number>>();
+        const localNames = new Map<number, string>();
+
+        for (let i = 0, il = ma_qa_metric._rowCount; i < il; i++) {
+            if (ma_qa_metric.mode.value(i) !== 'local') continue;
+
+            const name = ma_qa_metric.name.value(i);
+            if (localMetrics.has(name)) {
+                console.warn(`local ma_qa_metric with name '${name}' already added`);
+                continue;
+            }
+
+            localMetrics.set(name, new Map());
+            localNames.set(ma_qa_metric.id.value(i), name);
+        }
+
+        for (let i = 0, il = ma_qa_metric_local._rowCount; i < il; i++) {
+            if (model_id.value(i) !== model.modelNum) continue;
+
+            const labelAsymId = label_asym_id.value(i);
+            const entityIndex = index.findEntity(labelAsymId);
+            const rI = index.findResidue(model.entities.data.id.value(entityIndex), labelAsymId, label_seq_id.value(i));
+            const name = localNames.get(metric_id.value(i))!;
+            localMetrics.get(name)!.set(rI, metric_value.value(i));
+        }
+
+        return {
+            value: {
+                localMetrics,
+                pLDDT: localMetrics.get('pLDDT'),
+                qmean: localMetrics.get('qmean'),
+            }
+        };
+    }
+
+    export const symbols = {
+        pLDDT: QuerySymbolRuntime.Dynamic(CustomPropSymbol('ma', 'quality-assessment.pLDDT', Type.Num),
+            ctx => {
+                const { unit, element } = ctx.element;
+                if (!Unit.isAtomic(unit)) return -1;
+                const qualityAssessment = QualityAssessmentProvider.get(unit.model).value;
+                return qualityAssessment?.pLDDT?.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]) ?? -1;
+            }
+        ),
+        qmean: QuerySymbolRuntime.Dynamic(CustomPropSymbol('ma', 'quality-assessment.qmean', Type.Num),
+            ctx => {
+                const { unit, element } = ctx.element;
+                if (!Unit.isAtomic(unit)) return -1;
+                const qualityAssessment = QualityAssessmentProvider.get(unit.model).value;
+                return qualityAssessment?.qmean?.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]) ?? -1;
+            }
+        ),
+    };
+}
+
+export const QualityAssessmentParams = { };
+export type QualityAssessmentParams = typeof QualityAssessmentParams
+export type QualityAssessmentProps = PD.Values<QualityAssessmentParams>
+
+export const QualityAssessmentProvider: CustomModelProperty.Provider<QualityAssessmentParams, QualityAssessment> = CustomModelProperty.createProvider({
+    label: 'QualityAssessment',
+    descriptor: CustomPropertyDescriptor({
+        name: 'ma_quality_assessment',
+        symbols: QualityAssessment.symbols
+    }),
+    type: 'static',
+    defaultParams: QualityAssessmentParams,
+    getParams: (data: Model) => QualityAssessmentParams,
+    isApplicable: (data: Model) => QualityAssessment.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<QualityAssessmentProps>) => {
+        const p = { ...PD.getDefaultValues(QualityAssessmentParams), ...props };
+        return await QualityAssessment.obtain(ctx, data, p);
+    }
+});

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

@@ -31,7 +31,7 @@ export class Mp4Controls extends PluginComponent {
         canApply: this.ev.behavior<PluginStateAnimation.CanApply>({ canApply: false }),
         info: this.ev.behavior<Mp4AnimationInfo>({ width: 0, height: 0 }),
         params: this.ev.behavior<PD.Values<typeof Mp4AnimationParams>>(PD.getDefaultValues(Mp4AnimationParams))
-    }
+    };
 
     setCurrent(name?: string) {
         const anim = this.animations.find(a => a.name === name);
@@ -125,17 +125,20 @@ export class Mp4Controls extends PluginComponent {
         this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
         this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
 
-        this.subscribe(this.plugin.behaviors.state.isBusy, b => {
-            const anim = this.current;
-            if (!b && anim) {
-                this.behaviors.canApply.next(anim.anim.canApply?.(this.plugin) ?? { canApply: true });
-            }
-        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, b => this.updateCanApply(b));
+        this.subscribe(this.plugin.managers.snapshot.events.changed, b => this.updateCanApply(b));
 
         this.sync();
         this.syncInfo();
     }
 
+    private updateCanApply(b?: any) {
+        const anim = this.current;
+        if (!b && anim) {
+            this.behaviors.canApply.next(anim.anim.canApply?.(this.plugin) ?? { canApply: true });
+        }
+    }
+
     constructor(private plugin: PluginContext) {
         super();
 

src/extensions/mp4-export/encoder.ts

@@ -73,7 +73,7 @@ export async function encodeMp4Animation<A extends PluginStateAnimation>(plugin:
         await plugin.managers.animation.play(params.animation.definition, params.animation.params);
         stoppedAnimation = false;
         for (let i = 0; i <= N; i++) {
-            await loop.tick(i * dt, { isSynchronous: true, manualDraw: true });
+            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true });
 
             const image = params.pass.getImageData(width, height, normalizedViewport);
             encoder.addFrameRgba(image.data);

src/extensions/mp4-export/ui.tsx

@@ -108,7 +108,7 @@ export class Mp4EncoderUI extends CollapsableControls<{}, State> {
 
     save = () => {
         download(new Blob([this.state.data!.movie]), this.state.data!.filename);
-    }
+    };
 
     generate = async () => {
         try {
@@ -119,5 +119,5 @@ export class Mp4EncoderUI extends CollapsableControls<{}, State> {
             console.error(e);
             this.setState({ busy: false });
         }
-    }
+    };
 }

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

@@ -21,7 +21,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
     },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
 
-        private provider = StructureQualityReportProvider
+        private provider = StructureQualityReportProvider;
 
         private labelPDBeValidation = {
             label: (loci: Loci): string | undefined => {
@@ -42,7 +42,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
                     default: return void 0;
                 }
             }
-        }
+        };
 
         register(): void {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);

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

@@ -38,7 +38,7 @@ namespace StructureQualityReport {
     }
 
     export function isApplicable(model?: Model): boolean {
-        return !!model && Model.isFromPdbArchive(model);
+        return !!model && Model.hasPdbId(model);
     }
 
     export const Schema = {

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

@@ -27,7 +27,7 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
         description: 'Assembly Symmetry data calculated with BioJava, obtained via RCSB PDB.'
     },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
-        private provider = AssemblySymmetryProvider
+        private provider = AssemblySymmetryProvider;
 
         register(): void {
             this.ctx.state.data.actions.add(InitAssemblySymmetry3D);

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

@@ -53,7 +53,7 @@ export namespace AssemblySymmetry {
     export function isApplicable(structure?: Structure): boolean {
         return (
             !!structure && structure.models.length === 1 &&
-            Model.isFromPdbArchive(structure.models[0]) &&
+            Model.hasPdbId(structure.models[0]) &&
             isBiologicalAssembly(structure)
         );
     }

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

@@ -118,7 +118,7 @@ export class AssemblySymmetryControls extends CollapsableControls<{}, AssemblySy
 
     paramsOnChange = (options: AssemblySymmetryProps) => {
         this.updateAssemblySymmetry(options);
-    }
+    };
 
     get hasAssemblySymmetry3D() {
         return !this.pivot.cell.parent || !!StateSelection.findTagInSubtree(this.pivot.cell.parent.tree, this.pivot.cell.transform.ref, AssemblySymmetry.Tag.Representation);

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 2021-11-25T14:34:23-08:00
+// Generated on 2022-02-06T15:40:15-08:00
 
 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -11113,11 +11113,11 @@ export type RcsbUniprotAlignments = {
 
 export type RcsbUniprotAlignmentsCoreEntityAlignments = {
   /** Aligned region */
-  readonly aligned_regions?: Maybe<ReadonlyArray<Maybe<CoreEntityAlignmentsAlignedRegions>>>;
+  readonly aligned_regions: ReadonlyArray<Maybe<CoreEntityAlignmentsAlignedRegions>>;
   /** core_entity identifiers */
   readonly core_entity_identifiers?: Maybe<CoreEntityAlignmentsCoreEntityIdentifiers>;
   /** Alignment scores */
-  readonly scores?: Maybe<CoreEntityAlignmentsScores>;
+  readonly scores: CoreEntityAlignmentsScores;
 };
 
 export type RcsbUniprotAnnotation = {
@@ -13145,4 +13145,4 @@ 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/behavior.ts

@@ -30,7 +30,7 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
         description: 'Data from wwPDB Validation Report, obtained via RCSB PDB.'
     },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
-        private provider = ValidationReportProvider
+        private provider = ValidationReportProvider;
 
         private labelProvider = {
             label: (loci: Loci): string | undefined => {
@@ -41,7 +41,7 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
                     randomCoilIndexLabel(loci)
                 ].filter(l => !!l).join('</br>');
             }
-        }
+        };
 
         register(): void {
             DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);

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

@@ -92,7 +92,7 @@ namespace ValidationReport {
     }
 
     export function isApplicable(model?: Model): boolean {
-        return !!model && Model.isFromPdbArchive(model);
+        return !!model && Model.hasPdbId(model);
     }
 
     export function fromXml(xml: XMLDocument, model: Model): ValidationReport {

src/mol-canvas3d/camera.ts

@@ -37,7 +37,7 @@ class Camera implements ICamera {
     readonly projectionView: Mat4 = Mat4.identity();
     readonly inverseProjectionView: Mat4 = Mat4.identity();
 
-    private pixelScale: number
+    private pixelScale: number;
     get pixelRatio() {
         const dpr = (typeof window !== 'undefined') ? window.devicePixelRatio : 1;
         return dpr * this.pixelScale;
@@ -47,11 +47,11 @@ class Camera implements ICamera {
     readonly state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
     readonly viewOffset = Camera.ViewOffset();
 
-    near = 1
-    far = 10000
-    fogNear = 5000
-    fogFar = 10000
-    zoom = 1
+    near = 1;
+    far = 10000;
+    fogNear = 5000;
+    fogFar = 10000;
+    zoom = 1;
 
     readonly transition: CameraTransitionManager = new CameraTransitionManager(this);
     readonly stateChanged = new BehaviorSubject<Partial<Camera.Snapshot>>(this.state);

src/mol-canvas3d/camera/stereo.ts

@@ -33,7 +33,7 @@ class StereoCamera {
         return this.parent.viewOffset;
     }
 
-    private props: StereoCameraProps
+    private props: StereoCameraProps;
 
     constructor(private parent: Camera, props: Partial<StereoCameraProps> = {}) {
         this.props = { ...DefaultStereoCameraProps, ...props };

src/mol-canvas3d/canvas3d.ts

@@ -39,6 +39,7 @@ 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';
 
 export const Canvas3DParams = {
     camera: PD.Group({
@@ -222,7 +223,7 @@ interface Canvas3D {
     clear(): void
     syncVisibility(): void
 
-    requestDraw(force?: boolean): void
+    requestDraw(): void
 
     /** Reset the timers, used by "animate" */
     resetTime(t: number): void
@@ -296,7 +297,7 @@ namespace Canvas3D {
         let height = 128;
         updateViewport();
 
-        const scene = Scene.create(webgl);
+        const scene = Scene.create(webgl, passes.draw.wboitEnabled ? GraphicsRenderVariantsWboit : GraphicsRenderVariantsBlended);
 
         const camera = new Camera({
             position: Vec3.create(0, 0, 100),
@@ -354,17 +355,24 @@ namespace Canvas3D {
                 changed = helper.camera.mark(loci, action) || changed;
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
-            if (changed && !noDraw) {
-                scene.update(void 0, true);
-                helper.handle.scene.update(void 0, true);
-                helper.camera.scene.update(void 0, true);
-                const prevPickDirty = pickHelper.dirty;
-                draw(true);
-                pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
+            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
+                }
             }
         }
 
-        function render(force: boolean) {
+        function render(force: boolean, allowMulti: boolean) {
             if (webgl.isContextLost) return false;
 
             let resized = false;
@@ -394,10 +402,12 @@ namespace Canvas3D {
                     cam = stereoCamera;
                 }
 
+                const ctx = { renderer, camera: cam, scene, helper };
                 if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                    const forceOn = !cameraChanged && allowMulti && !controls.isAnimating;
+                    multiSampleHelper.render(ctx, p, true, forceOn);
                 } else {
-                    passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing, p.marking);
+                    passes.draw.render(ctx, p, true);
                 }
                 pickHelper.dirty = true;
                 didRender = true;
@@ -411,15 +421,15 @@ namespace Canvas3D {
         let currentTime = 0;
         let drawPaused = false;
 
-        function draw(force?: boolean) {
+        function draw(options?: { force?: boolean, allowMulti?: boolean }) {
             if (drawPaused) return;
-            if (render(!!force) && notifyDidDraw) {
+            if (render(!!options?.force, !!options?.allowMulti) && notifyDidDraw) {
                 didDraw.next(now() - startTime as now.Timestamp);
             }
         }
 
-        function requestDraw(force?: boolean) {
-            forceNextRender = forceNextRender || !!force;
+        function requestDraw() {
+            forceNextRender = true;
         }
 
         let animationFrameHandle = 0;
@@ -433,7 +443,7 @@ namespace Canvas3D {
                 return;
             }
 
-            draw(false);
+            draw();
             if (!camera.transition.inTransition && !webgl.isContextLost) {
                 interactionHelper.tick(currentTime);
             }
@@ -473,7 +483,7 @@ namespace Canvas3D {
                 resolveCameraReset();
                 if (forceDrawAfterAllCommited) {
                     if (helper.debug.isEnabled) helper.debug.update();
-                    draw(true);
+                    draw({ force: true });
                     forceDrawAfterAllCommited = false;
                 }
                 commited.next(now());
@@ -514,7 +524,7 @@ namespace Canvas3D {
 
             if (camera.transition.inTransition || nextCameraResetSnapshot) return false;
 
-            let cameraSphereOverlapsNone = true;
+            let cameraSphereOverlapsNone = true, isEmpty = true;
             Sphere3D.set(cameraSphere, camera.state.target, camera.state.radius);
 
             // check if any renderable has moved outside of the old bounding sphere
@@ -525,12 +535,13 @@ namespace Canvas3D {
                 const b = r.values.boundingSphere.ref.value;
                 if (!b.radius) continue;
 
+                isEmpty = false;
                 const cameraDist = Vec3.distance(cameraSphere.center, b.center);
                 if ((cameraDist > cameraSphere.radius || cameraDist > b.radius || b.radius > camera.state.radiusMax) && !Sphere3D.includes(oldBoundingSphereVisible, b)) return true;
                 if (Sphere3D.overlaps(cameraSphere, b)) cameraSphereOverlapsNone = false;
             }
 
-            return cameraSphereOverlapsNone;
+            return cameraSphereOverlapsNone || (!isEmpty && cameraSphere.radius <= 0.1);
         }
 
         const sceneCommitTimeoutMs = 250;
@@ -655,11 +666,11 @@ namespace Canvas3D {
 
         const contextRestoredSub = contextRestored.subscribe(() => {
             pickHelper.dirty = true;
-            draw(true);
+            draw({ force: true });
             // Unclear why, but in Chrome with wboit enabled the first `draw` only clears
             // the drawingBuffer. Note that in Firefox the drawingBuffer is preserved after
             // context loss so it is unclear if it behaves the same.
-            draw(true);
+            draw({ force: true });
         });
 
         const resized = new BehaviorSubject<any>(0);
@@ -668,7 +679,7 @@ namespace Canvas3D {
             passes.updateSize();
             updateViewport();
             syncViewport();
-            if (draw) requestDraw(true);
+            if (draw) requestDraw();
             resized.next(+new Date());
         }
 
@@ -693,7 +704,7 @@ namespace Canvas3D {
                 reprRenderObjects.clear();
                 scene.clear();
                 helper.debug.clear();
-                requestDraw(true);
+                requestDraw();
                 reprCount.next(reprRenderObjects.size);
             },
             syncVisibility: () => {
@@ -705,7 +716,7 @@ namespace Canvas3D {
                 if (scene.syncVisibility()) {
                     if (helper.debug.isEnabled) helper.debug.update();
                 }
-                requestDraw(true);
+                requestDraw();
             },
 
             requestDraw,
@@ -793,7 +804,7 @@ namespace Canvas3D {
                 }
 
                 if (!doNotRequestDraw) {
-                    requestDraw(true);
+                    requestDraw();
                 }
             },
             getImagePass: (props: Partial<ImageProps> = {}) => {

src/mol-canvas3d/controls/trackball.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>
@@ -13,7 +13,7 @@ import { Viewport } from '../camera/util';
 import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys, GestureInput } from '../../mol-util/input/input-observer';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera } from '../camera';
-import { absMax } from '../../mol-math/misc';
+import { absMax, degToRad } from '../../mol-math/misc';
 import { Binding } from '../../mol-util/binding';
 
 const B = ButtonsType;
@@ -40,8 +40,16 @@ export const TrackballControlsParams = {
     zoomSpeed: PD.Numeric(7.0, { min: 1, max: 15, step: 1 }),
     panSpeed: PD.Numeric(1.0, { min: 0.1, max: 5, step: 0.1 }),
 
-    spin: PD.Boolean(false, { description: 'Spin the 3D scene around the x-axis in view space' }),
-    spinSpeed: PD.Numeric(1, { min: -20, max: 20, step: 1 }),
+    animate: PD.MappedStatic('off', {
+        off: PD.EmptyGroup(),
+        spin: PD.Group({
+            speed: PD.Numeric(1, { min: -20, max: 20, step: 1 }),
+        }, { description: 'Spin the 3D scene around the x-axis in view space' }),
+        rock: PD.Group({
+            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }),
+            angle: PD.Numeric(10, { min: 0, max: 90, step: 1 }, { description: 'How many degrees to rotate in each direction.' }),
+        }, { description: 'Rock the 3D scene around the x-axis in view space' })
+    }),
 
     staticMoving: PD.Boolean(true, { isHidden: true }),
     dynamicDampingFactor: PD.Numeric(0.2, {}, { isHidden: true }),
@@ -72,7 +80,8 @@ export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 
 export { TrackballControls };
 interface TrackballControls {
-    viewport: Viewport
+    readonly viewport: Viewport
+    readonly isAnimating: boolean
 
     readonly props: Readonly<TrackballControlsProps>
     setProps: (props: Partial<TrackballControlsProps>) => void
@@ -144,6 +153,11 @@ namespace TrackballControls {
             );
         }
 
+        function getRotateFactor() {
+            const aspectRatio = input.width / input.height;
+            return p.rotateSpeed * input.pixelRatio * aspectRatio;
+        }
+
         const rotAxis = Vec3();
         const rotQuat = Quat();
         const rotEyeDir = Vec3();
@@ -156,8 +170,7 @@ namespace TrackballControls {
             const dy = _rotCurr[1] - _rotPrev[1];
             Vec3.set(rotMoveDir, dx, dy, 0);
 
-            const aspectRatio = input.width / input.height;
-            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed * input.pixelRatio * aspectRatio;
+            const angle = Vec3.magnitude(rotMoveDir) * getRotateFactor();
 
             if (angle) {
                 Vec3.sub(_eye, camera.position, camera.target);
@@ -306,7 +319,10 @@ namespace TrackballControls {
         /** Update the object's position, direction and up vectors */
         function update(t: number) {
             if (lastUpdated === t) return;
-            if (p.spin && lastUpdated > 0) spin(t - lastUpdated);
+            if (lastUpdated > 0) {
+                if (p.animate.name === 'spin') spin(t - lastUpdated);
+                else if (p.animate.name === 'rock') rock(t - lastUpdated);
+            }
 
             Vec3.sub(_eye, camera.position, camera.target);
 
@@ -345,6 +361,7 @@ namespace TrackballControls {
             if (!isStart && !_isInteracting) return;
 
             _isInteracting = true;
+            resetRock(); // start rocking from the center after interactions
 
             const dragRotate = Binding.match(p.bindings.dragRotate, buttons, modifiers);
             const dragRotateZ = Binding.match(p.bindings.dragRotateZ, buttons, modifiers);
@@ -434,11 +451,34 @@ namespace TrackballControls {
 
         const _spinSpeed = Vec2.create(0.005, 0);
         function spin(deltaT: number) {
-            if (p.spinSpeed === 0) return;
+            if (p.animate.name !== 'spin' || p.animate.params.speed === 0 || _isInteracting) return;
 
-            const frameSpeed = (p.spinSpeed || 0) / 1000;
+            const frameSpeed = p.animate.params.speed / 1000;
             _spinSpeed[0] = 60 * Math.min(Math.abs(deltaT), 1000 / 8) / 1000 * frameSpeed;
-            if (!_isInteracting) Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
+            Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
+        }
+
+        let _rockPhase = 0;
+        const _rockSpeed = Vec2.create(0.005, 0);
+        function rock(deltaT: number) {
+            if (p.animate.name !== 'rock' || p.animate.params.speed === 0 || _isInteracting) return;
+
+            const dt = deltaT / 1000 * p.animate.params.speed;
+            const maxAngle = degToRad(p.animate.params.angle) / getRotateFactor();
+            const angleA = Math.sin(_rockPhase * Math.PI * 2) * maxAngle;
+            const angleB = Math.sin((_rockPhase + dt) * Math.PI * 2) * maxAngle;
+
+            _rockSpeed[0] = angleB - angleA;
+            Vec2.add(_rotCurr, _rotPrev, _rockSpeed);
+
+            _rockPhase += dt;
+            if (_rockPhase >= 1) {
+                _rockPhase = 0;
+            }
+        }
+
+        function resetRock() {
+            _rockPhase = 0;
         }
 
         function start(t: number) {
@@ -448,9 +488,13 @@ namespace TrackballControls {
 
         return {
             viewport,
+            get isAnimating() { return p.animate.name !== 'off'; },
 
             get props() { return p as Readonly<TrackballControlsProps>; },
             setProps: (props: Partial<TrackballControlsProps>) => {
+                if (props.animate?.name === 'rock' && p.animate.name !== 'rock') {
+                    resetRock(); // start rocking from the center
+                }
                 Object.assign(p, props);
             },
 

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

@@ -18,6 +18,7 @@ import { TransformData } from '../../mol-geo/geometry/transform-data';
 import { sphereVertexCount } from '../../mol-geo/primitive/sphere';
 import { ValueCell } from '../../mol-util';
 import { Geometry } from '../../mol-geo/geometry/geometry';
+import { GraphicsRenderVariantsBlended } from '../../mol-gl/webgl/render-item';
 
 export const DebugHelperParams = {
     sceneBoundingSpheres: PD.Boolean(false, { description: 'Show full scene bounding spheres.' }),
@@ -31,17 +32,17 @@ export type DebugHelperProps = PD.Values<DebugHelperParams>
 type BoundingSphereData = { boundingSphere: Sphere3D, renderObject: GraphicsRenderObject, mesh: Mesh }
 
 export class BoundingSphereHelper {
-    readonly scene: Scene
+    readonly scene: Scene;
 
-    private readonly parent: Scene
-    private _props: DebugHelperProps
-    private objectsData = new Map<GraphicsRenderObject, BoundingSphereData>()
-    private instancesData = new Map<GraphicsRenderObject, BoundingSphereData>()
-    private sceneData: BoundingSphereData | undefined
-    private visibleSceneData: BoundingSphereData | undefined
+    private readonly parent: Scene;
+    private _props: DebugHelperProps;
+    private objectsData = new Map<GraphicsRenderObject, BoundingSphereData>();
+    private instancesData = new Map<GraphicsRenderObject, BoundingSphereData>();
+    private sceneData: BoundingSphereData | undefined;
+    private visibleSceneData: BoundingSphereData | undefined;
 
     constructor(ctx: WebGLContext, parent: Scene, props: Partial<DebugHelperProps>) {
-        this.scene = Scene.create(ctx);
+        this.scene = Scene.create(ctx, GraphicsRenderVariantsBlended);
         this.parent = parent;
         this._props = { ...PD.getDefaultValues(DebugHelperParams), ...props };
     }
@@ -160,5 +161,5 @@ const instanceMaterialId = getNextMaterialId();
 
 function createBoundingSphereRenderObject(mesh: Mesh, color: Color, materialId: number, transform?: TransformData) {
     const values = Mesh.Utils.createValuesSimple(mesh, { alpha: 0.1, doubleSided: false }, color, 1, transform);
-    return createRenderObject('mesh', values, { disposed: false, visible: true, alphaFactor: 1, pickable: false, colorOnly: false, opaque: false, writeDepth: false, noClip: false }, materialId);
+    return createRenderObject('mesh', values, { disposed: false, visible: true, alphaFactor: 1, pickable: false, colorOnly: false, opaque: false, writeDepth: false }, materialId);
 }

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

@@ -14,6 +14,7 @@ import { PickingId } from '../../mol-geo/geometry/picking';
 import { GraphicsRenderObject } from '../../mol-gl/render-object';
 import { Scene } from '../../mol-gl/scene';
 import { WebGLContext } from '../../mol-gl/webgl/context';
+import { 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';
@@ -49,16 +50,16 @@ export type CameraHelperParams = typeof CameraHelperParams
 export type CameraHelperProps = PD.Values<CameraHelperParams>
 
 export class CameraHelper {
-    scene: Scene
-    camera: Camera
+    scene: Scene;
+    camera: Camera;
     props: CameraHelperProps = {
         axes: { name: 'off', params: {} }
-    }
+    };
 
-    private renderObject: GraphicsRenderObject | undefined
+    private renderObject: GraphicsRenderObject | undefined;
 
     constructor(private webgl: WebGLContext, props: Partial<CameraHelperProps> = {}) {
-        this.scene = Scene.create(webgl);
+        this.scene = Scene.create(webgl, GraphicsRenderVariantsBlended);
 
         this.camera = new Camera();
         Vec3.set(this.camera.up, 0, 1, 0);
@@ -75,7 +76,6 @@ export class CameraHelper {
                     this.scene.clear();
                     const params = { ...props.axes.params, scale: props.axes.params.scale * this.webgl.pixelRatio };
                     this.renderObject = createAxesRenderObject(params);
-                    this.renderObject.state.noClip = true;
                     this.scene.add(this.renderObject);
                     this.scene.commit();
 
@@ -109,7 +109,7 @@ export class CameraHelper {
             if (apply(Interval.ofSingleton(idx))) changed = true;
         }
         return changed;
-    }
+    };
 
     mark(loci: Loci, action: MarkerAction) {
         if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
@@ -201,7 +201,7 @@ function createAxesMesh(scale: number, mesh?: Mesh) {
     const x = Vec3.scale(Vec3(), Vec3.unitX, scale);
     const y = Vec3.scale(Vec3(), Vec3.unitY, scale);
     const z = Vec3.scale(Vec3(), Vec3.unitZ, scale);
-    const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments: 32 };
+    const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments: 32 };
 
     state.currentGroup = CameraHelperAxis.None;
     addSphere(state, Vec3.origin, radius, 2);

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

@@ -24,6 +24,7 @@ import { DataLoci, EmptyLoci, 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';
+import { GraphicsRenderVariantsBlended } from '../../mol-gl/webgl/render-item';
 
 const HandleParams = {
     ...Mesh.Params,
@@ -47,12 +48,12 @@ export type HandleHelperParams = typeof HandleHelperParams
 export type HandleHelperProps = PD.Values<HandleHelperParams>
 
 export class HandleHelper {
-    scene: Scene
+    scene: Scene;
     props: HandleHelperProps = {
         handle: { name: 'off', params: {} }
-    }
+    };
 
-    private renderObject: GraphicsRenderObject | undefined
+    private renderObject: GraphicsRenderObject | undefined;
 
     private _transform = Mat4();
     getBoundingSphere(out: Sphere3D, instanceId: number) {
@@ -72,7 +73,6 @@ export class HandleHelper {
                     this.scene.clear();
                     const params = { ...props.handle.params, scale: props.handle.params.scale * this.webgl.pixelRatio };
                     this.renderObject = createHandleRenderObject(params);
-                    this.renderObject.state.noClip = true;
                     this.scene.add(this.renderObject);
                     this.scene.commit();
 
@@ -117,7 +117,7 @@ export class HandleHelper {
             if (apply(Interval.ofSingleton(idx))) changed = true;
         }
         return changed;
-    }
+    };
 
     mark(loci: Loci, action: MarkerAction) {
         if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
@@ -127,7 +127,7 @@ export class HandleHelper {
     }
 
     constructor(private webgl: WebGLContext, props: Partial<HandleHelperProps> = {}) {
-        this.scene = Scene.create(webgl);
+        this.scene = Scene.create(webgl, GraphicsRenderVariantsBlended);
         this.setProps(props);
     }
 }

src/mol-canvas3d/helper/helper.ts

@@ -23,9 +23,9 @@ export type HelperProps = PD.Values<typeof HelperParams>
 
 
 export class Helper {
-    readonly debug: BoundingSphereHelper
-    readonly camera: CameraHelper
-    readonly handle: HandleHelper
+    readonly debug: BoundingSphereHelper;
+    readonly camera: CameraHelper;
+    readonly handle: HandleHelper;
 
     constructor(webgl: WebGLContext, scene: Scene, props: Partial<HelperProps> = {}) {
         const p = { ...DefaultHelperProps, ...props };

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/draw.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 Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -53,28 +53,41 @@ function getDepthMergeRenderable(ctx: WebGLContext, depthTexturePrimitives: Text
     return createComputeRenderable(renderItem, values);
 }
 
+type Props = {
+    postprocessing: PostprocessingProps
+    marking: MarkingProps
+    transparentBackground: boolean;
+}
+
+type RenderContext = {
+    renderer: Renderer;
+    camera: Camera | StereoCamera;
+    scene: Scene;
+    helper: Helper;
+}
+
 export class DrawPass {
-    private readonly drawTarget: RenderTarget
+    private readonly drawTarget: RenderTarget;
 
-    readonly colorTarget: RenderTarget
-    readonly depthTexture: Texture
-    readonly depthTexturePrimitives: Texture
+    readonly colorTarget: RenderTarget;
+    readonly depthTexture: Texture;
+    readonly depthTexturePrimitives: Texture;
 
-    readonly packedDepth: boolean
+    readonly packedDepth: boolean;
 
-    private depthTarget: RenderTarget
-    private depthTargetPrimitives: RenderTarget | null
-    private depthTargetVolumes: RenderTarget | null
-    private depthTextureVolumes: Texture
-    private depthMerge: DepthMergeRenderable
+    private depthTarget: RenderTarget;
+    private depthTargetPrimitives: RenderTarget | null;
+    private depthTargetVolumes: RenderTarget | null;
+    private depthTextureVolumes: Texture;
+    private depthMerge: DepthMergeRenderable;
 
-    private copyFboTarget: CopyRenderable
-    private copyFboPostprocessing: CopyRenderable
+    private copyFboTarget: CopyRenderable;
+    private copyFboPostprocessing: CopyRenderable;
 
-    private wboit: WboitPass | undefined
-    private readonly marking: MarkingPass
-    readonly postprocessing: PostprocessingPass
-    private readonly antialiasing: AntialiasingPass
+    private wboit: WboitPass | undefined;
+    private readonly marking: MarkingPass;
+    readonly postprocessing: PostprocessingPass;
+    private readonly antialiasing: AntialiasingPass;
 
     get wboitEnabled() {
         return !!this.wboit?.supported;
@@ -264,25 +277,25 @@ export class DrawPass {
         renderer.renderBlendedTransparent(scene.primitives, camera, null);
     }
 
-    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps, markingProps: MarkingProps) {
+    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, props: Props) {
         const volumeRendering = scene.volumes.renderables.length > 0;
-        const postprocessingEnabled = PostprocessingPass.isEnabled(postprocessingProps);
-        const antialiasingEnabled = AntialiasingPass.isEnabled(postprocessingProps);
-        const markingEnabled = MarkingPass.isEnabled(markingProps);
+        const postprocessingEnabled = PostprocessingPass.isEnabled(props.postprocessing);
+        const antialiasingEnabled = AntialiasingPass.isEnabled(props.postprocessing);
+        const markingEnabled = MarkingPass.isEnabled(props.marking);
 
         const { x, y, width, height } = camera.viewport;
         renderer.setViewport(x, y, width, height);
         renderer.update(camera);
 
-        if (transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
+        if (props.transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
             this.drawTarget.bind();
             renderer.clear(false);
         }
 
         if (this.wboitEnabled) {
-            this._renderWboit(renderer, camera, scene, transparentBackground, postprocessingProps);
+            this._renderWboit(renderer, camera, scene, props.transparentBackground, props.postprocessing);
         } else {
-            this._renderBlended(renderer, camera, scene, !volumeRendering && !postprocessingEnabled && !antialiasingEnabled && toDrawingBuffer, transparentBackground, postprocessingProps);
+            this._renderBlended(renderer, camera, scene, !volumeRendering && !postprocessingEnabled && !antialiasingEnabled && toDrawingBuffer, props.transparentBackground, props.postprocessing);
         }
 
         if (postprocessingEnabled) {
@@ -294,18 +307,18 @@ export class DrawPass {
         }
 
         if (markingEnabled) {
-            const markingDepthTest = markingProps.ghostEdgeStrength < 1;
+            const markingDepthTest = props.marking.ghostEdgeStrength < 1;
             if (markingDepthTest) {
                 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(markingProps);
+            this.marking.update(props.marking);
             this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
         }
 
@@ -323,7 +336,7 @@ export class DrawPass {
         }
 
         if (antialiasingEnabled) {
-            this.antialiasing.render(camera, toDrawingBuffer, postprocessingProps);
+            this.antialiasing.render(camera, toDrawingBuffer, props.postprocessing);
         } else if (toDrawingBuffer) {
             this.drawTarget.bind();
 
@@ -338,16 +351,17 @@ export class DrawPass {
         this.webgl.gl.flush();
     }
 
-    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps, markingProps: MarkingProps) {
-        renderer.setTransparentBackground(transparentBackground);
+    render(ctx: RenderContext, props: Props, toDrawingBuffer: boolean) {
+        const { renderer, camera, scene, helper } = ctx;
+        renderer.setTransparentBackground(props.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, transparentBackground, postprocessingProps, markingProps);
-            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps, markingProps);
+            this._render(renderer, camera.left, scene, helper, toDrawingBuffer, props);
+            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, props);
         } else {
-            this._render(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps, markingProps);
+            this._render(renderer, camera, scene, helper, toDrawingBuffer, props);
         }
     }
 

src/mol-canvas3d/passes/fxaa.ts

@@ -28,7 +28,7 @@ export const FxaaParams = {
 export type FxaaProps = PD.Values<typeof FxaaParams>
 
 export class FxaaPass {
-    private readonly renderable: FxaaRenderable
+    private readonly renderable: FxaaRenderable;
 
     constructor(private webgl: WebGLContext, input: Texture) {
         this.renderable = getFxaaRenderable(webgl, input);

src/mol-canvas3d/passes/image.ts

@@ -30,19 +30,19 @@ export const ImageParams = {
 export type ImageProps = PD.Values<typeof ImageParams>
 
 export class ImagePass {
-    private _width = 0
-    private _height = 0
-    private _camera = new Camera()
+    private _width = 0;
+    private _height = 0;
+    private _camera = new Camera();
 
-    readonly props: ImageProps
+    readonly props: ImageProps;
 
-    private _colorTarget: RenderTarget
+    private _colorTarget: RenderTarget;
     get colorTarget() { return this._colorTarget; }
 
-    private readonly drawPass: DrawPass
-    private readonly multiSamplePass: MultiSamplePass
-    private readonly multiSampleHelper: MultiSampleHelper
-    private readonly helper: Helper
+    private readonly drawPass: DrawPass;
+    private readonly multiSamplePass: MultiSamplePass;
+    private readonly multiSampleHelper: MultiSampleHelper;
+    private readonly helper: Helper;
 
     get width() { return this._width; }
     get height() { return this._height; }
@@ -83,11 +83,12 @@ export class ImagePass {
         Viewport.set(this._camera.viewport, 0, 0, this._width, this._height);
         this._camera.update();
 
+        const ctx = { renderer: this.renderer, camera: this._camera, scene: this.scene, helper: this.helper };
         if (MultiSamplePass.isEnabled(this.props.multiSample)) {
-            this.multiSampleHelper.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props);
+            this.multiSampleHelper.render(ctx, this.props, false);
             this._colorTarget = this.multiSamplePass.colorTarget;
         } else {
-            this.drawPass.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props.postprocessing, this.props.marking);
+            this.drawPass.render(ctx, this.props, false);
             this._colorTarget = this.drawPass.getColorTarget(this.props.postprocessing);
         }
     }

src/mol-canvas3d/passes/marking.ts

@@ -22,7 +22,7 @@ import { Color } from '../../mol-util/color';
 import { edge_frag } from '../../mol-gl/shader/marking/edge.frag';
 
 export const MarkingParams = {
-    enabled: PD.Boolean(false),
+    enabled: PD.Boolean(true),
     highlightEdgeColor: PD.Color(Color.darken(Color.fromNormalizedRgb(1.0, 0.4, 0.6), 1.0)),
     selectEdgeColor: PD.Color(Color.darken(Color.fromNormalizedRgb(0.2, 1.0, 0.1), 1.0)),
     edgeScale: PD.Numeric(1, { min: 1, max: 3, step: 1 }, { description: 'Thickness of the edge.' }),
@@ -36,12 +36,12 @@ export class MarkingPass {
         return props.enabled;
     }
 
-    readonly depthTarget: RenderTarget
-    readonly maskTarget: RenderTarget
-    private readonly edgesTarget: RenderTarget
+    readonly depthTarget: RenderTarget;
+    readonly maskTarget: RenderTarget;
+    private readonly edgesTarget: RenderTarget;
 
-    private readonly edge: EdgeRenderable
-    private readonly overlay: OverlayRenderable
+    private readonly edge: EdgeRenderable;
+    private readonly overlay: OverlayRenderable;
 
     constructor(private webgl: WebGLContext, width: number, height: number) {
         this.depthTarget = webgl.createRenderTarget(width, height);

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

@@ -50,8 +50,8 @@ function getComposeRenderable(ctx: WebGLContext, colorTexture: Texture): Compose
 }
 
 export const MultiSampleParams = {
-    mode: PD.Select('off', [['off', 'Off'], ['on', 'On'], ['temporal', 'Temporal']]),
-    sampleLevel: PD.Numeric(2, { min: 0, max: 5, step: 1 }),
+    mode: PD.Select('temporal', [['off', 'Off'], ['on', 'On'], ['temporal', 'Temporal']]),
+    sampleLevel: PD.Numeric(2, { min: 0, max: 5, step: 1 }, { description: 'Take level^2 samples.' }),
 };
 export type MultiSampleProps = PD.Values<typeof MultiSampleParams>
 
@@ -59,6 +59,14 @@ type Props = {
     multiSample: MultiSampleProps
     postprocessing: PostprocessingProps
     marking: MarkingProps
+    transparentBackground: boolean;
+}
+
+type RenderContext = {
+    renderer: Renderer;
+    camera: Camera | StereoCamera;
+    scene: Scene;
+    helper: Helper;
 }
 
 export class MultiSamplePass {
@@ -66,11 +74,11 @@ export class MultiSamplePass {
         return props.mode !== 'off';
     }
 
-    colorTarget: RenderTarget
+    colorTarget: RenderTarget;
 
-    private composeTarget: RenderTarget
-    private holdTarget: RenderTarget
-    private compose: ComposeRenderable
+    private composeTarget: RenderTarget;
+    private holdTarget: RenderTarget;
+    private compose: ComposeRenderable;
 
     constructor(private webgl: WebGLContext, private drawPass: DrawPass) {
         const { colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat } = webgl.extensions;
@@ -97,12 +105,12 @@ export class MultiSamplePass {
         }
     }
 
-    render(sampleIndex: number, renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
-        if (props.multiSample.mode === 'temporal') {
-            return this.renderTemporalMultiSample(sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+    render(sampleIndex: number, ctx: RenderContext, props: Props, toDrawingBuffer: boolean, forceOn: boolean) {
+        if (props.multiSample.mode === 'temporal' && !forceOn) {
+            return this.renderTemporalMultiSample(sampleIndex, ctx, props, toDrawingBuffer);
         } else {
-            this.renderMultiSample(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
-            return sampleIndex;
+            this.renderMultiSample(ctx, toDrawingBuffer, props);
+            return -2;
         }
     }
 
@@ -114,7 +122,8 @@ export class MultiSamplePass {
         }
     }
 
-    private renderMultiSample(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
+    private renderMultiSample(ctx: RenderContext, toDrawingBuffer: boolean, props: Props) {
+        const { camera } = ctx;
         const { compose, composeTarget, drawPass, webgl } = this;
         const { gl, state } = webgl;
 
@@ -148,7 +157,7 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, sampleWeight);
 
             // render scene
-            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
+            drawPass.render(ctx, props, false);
 
             // compose rendered scene with compose target
             composeTarget.bind();
@@ -181,7 +190,8 @@ export class MultiSamplePass {
         camera.update();
     }
 
-    private renderTemporalMultiSample(sampleIndex: number, renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
+    private renderTemporalMultiSample(sampleIndex: number, ctx: RenderContext, props: Props, toDrawingBuffer: boolean) {
+        const { camera } = ctx;
         const { compose, composeTarget, holdTarget, drawPass, webgl } = this;
         const { gl, state } = webgl;
 
@@ -198,7 +208,7 @@ export class MultiSamplePass {
         const sampleWeight = 1.0 / offsetList.length;
 
         if (sampleIndex === -1) {
-            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
+            drawPass.render(ctx, props, false);
             ValueCell.update(compose.values.uWeight, 1.0);
             ValueCell.update(compose.values.tColor, drawPass.getColorTarget(props.postprocessing).texture);
             compose.update();
@@ -226,7 +236,7 @@ export class MultiSamplePass {
                 camera.update();
 
                 // render scene
-                drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
+                drawPass.render(ctx, props, false);
 
                 // compose rendered scene with compose target
                 composeTarget.bind();
@@ -317,15 +327,17 @@ JitterVectors.forEach(offsetList => {
 });
 
 export class MultiSampleHelper {
-    private sampleIndex = -2
+    private sampleIndex = -2;
 
     update(changed: boolean, props: MultiSampleProps) {
         if (changed) this.sampleIndex = -1;
         return props.mode === 'temporal' ? this.sampleIndex !== -2 : false;
     }
 
-    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props) {
-        this.sampleIndex = this.multiSamplePass.render(this.sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+    /** Return `true` while more samples are needed */
+    render(ctx: RenderContext, props: Props, toDrawingBuffer: boolean, forceOn?: boolean) {
+        this.sampleIndex = this.multiSamplePass.render(this.sampleIndex, ctx, props, toDrawingBuffer, !!forceOn);
+        return this.sampleIndex < 0;
     }
 
     constructor(private multiSamplePass: MultiSamplePass) {

src/mol-canvas3d/passes/passes.ts

@@ -10,9 +10,9 @@ import { MultiSamplePass } from './multi-sample';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 
 export class Passes {
-    readonly draw: DrawPass
-    readonly pick: PickPass
-    readonly multiSample: MultiSamplePass
+    readonly draw: DrawPass;
+    readonly pick: PickPass;
+    readonly multiSample: MultiSamplePass;
 
     constructor(private webgl: WebGLContext, attribs: Partial<{ pickScale: number, enableWboit: boolean }> = {}) {
         const { gl } = webgl;

src/mol-canvas3d/passes/pick.ts

@@ -5,14 +5,14 @@
  */
 
 import { PickingId } from '../../mol-geo/geometry/picking';
-import { Renderer } from '../../mol-gl/renderer';
+import { PickType, Renderer } from '../../mol-gl/renderer';
 import { Scene } from '../../mol-gl/scene';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { GraphicsRenderVariant } from '../../mol-gl/webgl/render-item';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { spiral2d } from '../../mol-math/misc';
-import { decodeFloatRGB, unpackRGBAToDepth } from '../../mol-util/float-packing';
+import { unpackRGBToInt, unpackRGBAToDepth } from '../../mol-util/number-packing';
 import { Camera, ICamera } from '../camera';
 import { StereoCamera } from '../camera/stereo';
 import { cameraUnproject } from '../camera/util';
@@ -25,13 +25,13 @@ 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
+    readonly objectPickTarget: RenderTarget;
+    readonly instancePickTarget: RenderTarget;
+    readonly groupPickTarget: RenderTarget;
+    readonly depthPickTarget: RenderTarget;
 
-    private pickWidth: number
-    private pickHeight: number
+    private pickWidth: number;
+    private pickHeight: number;
 
     constructor(private webgl: WebGLContext, private drawPass: DrawPass, readonly pickBaseScale: number) {
         const pickScale = pickBaseScale / webgl.pixelRatio;
@@ -64,56 +64,56 @@ export class PickPass {
         }
     }
 
-    private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: GraphicsRenderVariant) {
+    private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: GraphicsRenderVariant, pickType: number) {
         const depth = this.drawPass.depthTexturePrimitives;
         renderer.clear(false);
 
         renderer.update(camera);
-        renderer.renderPick(scene.primitives, camera, variant, null);
-        renderer.renderPick(scene.volumes, camera, variant, depth);
-        renderer.renderPick(helper.handle.scene, camera, variant, null);
+        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.camera.isEnabled) {
             helper.camera.update(camera);
             renderer.update(helper.camera.camera);
-            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null);
+            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null, pickType);
         }
     }
 
     render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper) {
         this.objectPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pickObject');
+        this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Object);
 
         this.instancePickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pickInstance');
+        this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Instance);
 
         this.groupPickTarget.bind();
-        this.renderVariant(renderer, camera, scene, helper, 'pickGroup');
+        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');
+        this.renderVariant(renderer, camera, scene, helper, 'depth', PickType.None);
     }
 }
 
 export class PickHelper {
-    dirty = true
+    dirty = true;
 
-    private objectBuffer: Uint8Array
-    private instanceBuffer: Uint8Array
-    private groupBuffer: Uint8Array
-    private depthBuffer: Uint8Array
+    private objectBuffer: Uint8Array;
+    private instanceBuffer: Uint8Array;
+    private groupBuffer: Uint8Array;
+    private depthBuffer: Uint8Array;
 
-    private viewport = Viewport()
+    private viewport = Viewport();
 
-    private pickScale: number
-    private pickX: number
-    private pickY: number
-    private pickWidth: number
-    private pickHeight: number
-    private halfPickWidth: number
+    private pickScale: number;
+    private pickX: number;
+    private pickY: number;
+    private pickWidth: number;
+    private pickHeight: number;
+    private halfPickWidth: number;
 
-    private spiral: [number, number][]
+    private spiral: [number, number][];
 
     private setupBuffers() {
         const bufferSize = this.pickWidth * this.pickHeight * 4;
@@ -174,7 +174,7 @@ export class PickHelper {
 
     private getId(x: number, y: number, buffer: Uint8Array) {
         const idx = this.getBufferIdx(x, y);
-        return decodeFloatRGB(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
+        return unpackRGBToInt(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
     }
 
     private render(camera: Camera | StereoCamera) {

src/mol-canvas3d/passes/postprocessing.ts

@@ -86,7 +86,7 @@ function getSsaoRenderable(ctx: WebGLContext, depthTexture: Texture): SsaoRender
         tDepth: ValueCell.create(depthTexture),
 
         uSamples: ValueCell.create([0.0, 0.0, 1.0]),
-        dNSamples: ValueCell.create(1),
+        dNSamples: ValueCell.create(32),
 
         uProjection: ValueCell.create(Mat4.identity()),
         uInvProjection: ValueCell.create(Mat4.identity()),
@@ -133,7 +133,7 @@ function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, dir
         uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())),
 
         uKernel: ValueCell.create([0.0]),
-        dOcclusionKernelSize: ValueCell.create(1),
+        dOcclusionKernelSize: ValueCell.create(15),
 
         uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0),
         uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0),
@@ -193,6 +193,7 @@ const PostprocessingSchema = {
     uFogNear: UniformSpec('f'),
     uFogFar: UniformSpec('f'),
     uFogColor: UniformSpec('v3'),
+    uOutlineColor: UniformSpec('v3'),
     uTransparentBackground: UniformSpec('b'),
 
     uMaxPossibleViewZDiff: UniformSpec('f'),
@@ -220,11 +221,12 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
         uFogNear: ValueCell.create(10000),
         uFogFar: ValueCell.create(10000),
         uFogColor: ValueCell.create(Vec3.create(1, 1, 1)),
+        uOutlineColor: ValueCell.create(Vec3.create(0, 0, 0)),
         uTransparentBackground: ValueCell.create(false),
 
         uMaxPossibleViewZDiff: ValueCell.create(0.5),
 
-        dOcclusionEnable: ValueCell.create(false),
+        dOcclusionEnable: ValueCell.create(true),
 
         dOutlineEnable: ValueCell.create(false),
         dOutlineScale: ValueCell.create(1),
@@ -252,6 +254,7 @@ export const PostprocessingParams = {
         on: PD.Group({
             scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
             threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
+            color: PD.Color(Color(0x000000)),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' }),
@@ -268,29 +271,29 @@ export class PostprocessingPass {
         return props.occlusion.name === 'on' || props.outline.name === 'on';
     }
 
-    readonly target: RenderTarget
+    readonly target: RenderTarget;
 
-    private readonly outlinesTarget: RenderTarget
-    private readonly outlinesRenderable: OutlinesRenderable
+    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 randomHemisphereVector: Vec3[];
+    private readonly ssaoFramebuffer: Framebuffer;
+    private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
+    private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;
 
-    private readonly ssaoDepthTexture: Texture
-    private readonly ssaoDepthBlurProxyTexture: Texture
+    private readonly ssaoDepthTexture: Texture;
+    private readonly ssaoDepthBlurProxyTexture: Texture;
 
-    private readonly ssaoRenderable: SsaoRenderable
-    private readonly ssaoBlurFirstPassRenderable: SsaoBlurRenderable
-    private readonly ssaoBlurSecondPassRenderable: SsaoBlurRenderable
+    private readonly ssaoRenderable: SsaoRenderable;
+    private readonly ssaoBlurFirstPassRenderable: SsaoBlurRenderable;
+    private readonly ssaoBlurSecondPassRenderable: SsaoBlurRenderable;
 
-    private nSamples: number
-    private blurKernelSize: number
+    private nSamples: number;
+    private blurKernelSize: number;
 
-    private readonly renderable: PostprocessingRenderable
+    private readonly renderable: PostprocessingRenderable;
 
-    private ssaoScale: number
+    private ssaoScale: number;
     private calcSsaoScale() {
         // downscale ssao for high pixel-ratios
         return Math.min(1, 1 / this.webgl.pixelRatio);
@@ -446,6 +449,8 @@ export class PostprocessingPass {
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
 
+            ValueCell.update(this.renderable.values.uOutlineColor, Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, props.outline.params.color));
+
             ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) { needsUpdateMain = true; }
             ValueCell.updateIfChanged(this.renderable.values.dOutlineScale, outlineScale);
@@ -538,9 +543,9 @@ export class AntialiasingPass {
         return props.antialiasing.name !== 'off';
     }
 
-    readonly target: RenderTarget
-    private readonly fxaa: FxaaPass
-    private readonly smaa: SmaaPass
+    readonly target: RenderTarget;
+    private readonly fxaa: FxaaPass;
+    private readonly smaa: SmaaPass;
 
     constructor(webgl: WebGLContext, private drawPass: DrawPass) {
         const { colorTarget } = drawPass;

src/mol-canvas3d/passes/smaa.ts

@@ -31,12 +31,12 @@ export const SmaaParams = {
 export type SmaaProps = PD.Values<typeof SmaaParams>
 
 export class SmaaPass {
-    private readonly edgesTarget: RenderTarget
-    private readonly weightsTarget: RenderTarget
+    private readonly edgesTarget: RenderTarget;
+    private readonly weightsTarget: RenderTarget;
 
-    private readonly edgesRenderable: EdgesRenderable
-    private readonly weightsRenderable: WeightsRenderable
-    private readonly blendRenderable: BlendRenderable
+    private readonly edgesRenderable: EdgesRenderable;
+    private readonly weightsRenderable: WeightsRenderable;
+    private readonly blendRenderable: BlendRenderable;
 
     private _supported = false;
     get supported() {
@@ -201,7 +201,7 @@ function getWeightsRenderable(ctx: WebGLContext, edgesTexture: Texture): Weights
         uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)),
         uViewport: ValueCell.create(Vec4()),
 
-        dMaxSearchSteps: ValueCell.create(8),
+        dMaxSearchSteps: ValueCell.create(16),
     };
 
     // Note: loading image textures requires `HTMLImageElement` to be available

src/mol-canvas3d/passes/wboit.ts

@@ -45,11 +45,11 @@ function getEvaluateWboitRenderable(ctx: WebGLContext, wboitATexture: Texture, w
 //
 
 export class WboitPass {
-    private readonly renderable: EvaluateWboitRenderable
+    private readonly renderable: EvaluateWboitRenderable;
 
-    private readonly framebuffer: Framebuffer
-    private readonly textureA: Texture
-    private readonly textureB: Texture
+    private readonly framebuffer: Framebuffer;
+    private readonly textureA: Texture;
+    private readonly textureB: Texture;
 
     private _supported = false;
     get supported() {

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

@@ -87,9 +87,9 @@ namespace SortedRanges {
     }
 
     export class Iterator<T extends number = number, I extends number = number> implements _Iterator<Segmentation.Segment<I>> {
-        private value: Segmentation.Segment<I> = { index: 0 as I, start: 0 as T, end: 0 as T }
+        private value: Segmentation.Segment<I> = { index: 0 as I, start: 0 as T, end: 0 as T };
 
-        private curIndex = 0
+        private curIndex = 0;
 
         hasNext: boolean = false;
 

src/mol-data/util/combination.ts

@@ -28,11 +28,11 @@ function nextIndex(n: number) {
 };
 
 export class CombinationIterator<T> implements Iterator<ReadonlyArray<T>> {
-    private value: T[]
-    private index: number
-    private maxIndex: number
+    private value: T[];
+    private index: number;
+    private maxIndex: number;
 
-    size: number
+    size: number;
     hasNext: boolean = false;
 
     move() {

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

@@ -9,10 +9,10 @@ import { OrderedSet, Interval, Segmentation } from '../int';
 
 /** Emits a segment of length one for each element in the interval that is also in the set */
 export class IntervalIterator<I extends number = number> implements Iterator<Segmentation.Segment<I>> {
-    private value: Segmentation.Segment<I> = { index: 0 as I, start: 0, end: 0 }
+    private value: Segmentation.Segment<I> = { index: 0 as I, start: 0, end: 0 };
 
-    private curIndex = 0
-    private maxIndex = 0
+    private curIndex = 0;
+    private maxIndex = 0;
 
     hasNext: boolean = false;
 

src/mol-geo/geometry/_spec/marker.spec.ts

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { getMarkersAverage } from '../marker-data';
+
+describe('marker-data', () => {
+    it('getMarkersAverage', () => {
+        expect(getMarkersAverage(new Uint8Array([0, 0, 0, 0]), 3)).toBe(0);
+        expect(getMarkersAverage(new Uint8Array([0, 0, 1, 0]), 3)).toBe(1 / 3);
+        expect(getMarkersAverage(new Uint8Array([0, 0, 0, 0]), 4)).toBe(0);
+        expect(getMarkersAverage(new Uint8Array([0, 0, 1, 0]), 4)).toBe(1 / 4);
+    });
+});

src/mol-geo/geometry/base.ts

@@ -17,6 +17,7 @@ import { UniformColorTheme } from '../../mol-theme/color/uniform';
 import { UniformSizeTheme } from '../../mol-theme/size/uniform';
 import { smoothstep } from '../../mol-math/interpolate';
 import { Material } from '../../mol-util/material';
+import { Clip } from '../../mol-util/clip';
 
 export const VisualQualityInfo = {
     'custom': {},
@@ -81,6 +82,7 @@ export namespace BaseGeometry {
         alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity', isEssential: true, description: 'How opaque/transparent the representation is rendered.' }),
         quality: PD.Select<VisualQuality>('auto', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }),
         material: Material.getParam(),
+        clip: PD.Group(Clip.Params),
     };
     export type Params = typeof Params
 
@@ -97,24 +99,42 @@ export namespace BaseGeometry {
     }
 
     export function createValues(props: PD.Values<Params>, counts: Counts) {
-        const { metalness, roughness } = Material.toObjectNormalized(props.material);
+        const clip = Clip.getClip(props.clip);
         return {
             alpha: ValueCell.create(props.alpha),
             uAlpha: ValueCell.create(props.alpha),
             uVertexCount: ValueCell.create(counts.vertexCount),
             uGroupCount: ValueCell.create(counts.groupCount),
             drawCount: ValueCell.create(counts.drawCount),
-            uMetalness: ValueCell.create(metalness),
-            uRoughness: ValueCell.create(roughness),
+            uMetalness: ValueCell.create(props.material.metalness),
+            uRoughness: ValueCell.create(props.material.roughness),
+            uBumpiness: ValueCell.create(props.material.bumpiness),
             dLightCount: ValueCell.create(1),
+
+            dClipObjectCount: ValueCell.create(clip.objects.count),
+            dClipVariant: ValueCell.create(clip.variant),
+            uClipObjectType: ValueCell.create(clip.objects.type),
+            uClipObjectInvert: ValueCell.create(clip.objects.invert),
+            uClipObjectPosition: ValueCell.create(clip.objects.position),
+            uClipObjectRotation: ValueCell.create(clip.objects.rotation),
+            uClipObjectScale: ValueCell.create(clip.objects.scale),
         };
     }
 
     export function updateValues(values: BaseValues, props: PD.Values<Params>) {
-        const { metalness, roughness } = Material.toObjectNormalized(props.material);
         ValueCell.updateIfChanged(values.alpha, props.alpha); // `uAlpha` is set in renderable.render
-        ValueCell.updateIfChanged(values.uMetalness, metalness);
-        ValueCell.updateIfChanged(values.uRoughness, roughness);
+        ValueCell.updateIfChanged(values.uMetalness, props.material.metalness);
+        ValueCell.updateIfChanged(values.uRoughness, props.material.roughness);
+        ValueCell.updateIfChanged(values.uBumpiness, props.material.bumpiness);
+
+        const clip = Clip.getClip(props.clip);
+        ValueCell.update(values.dClipObjectCount, clip.objects.count);
+        ValueCell.update(values.dClipVariant, clip.variant);
+        ValueCell.update(values.uClipObjectType, clip.objects.type);
+        ValueCell.update(values.uClipObjectInvert, clip.objects.invert);
+        ValueCell.update(values.uClipObjectPosition, clip.objects.position);
+        ValueCell.update(values.uClipObjectRotation, clip.objects.rotation);
+        ValueCell.update(values.uClipObjectScale, clip.objects.scale);
     }
 
     export function createRenderableState(props: Partial<PD.Values<Params>> = {}): RenderableState {
@@ -127,7 +147,6 @@ export namespace BaseGeometry {
             colorOnly: false,
             opaque,
             writeDepth: opaque,
-            noClip: false,
         };
     }
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,18 +10,13 @@ import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
 import { Clipping } from '../../mol-theme/clipping';
 
 export type ClippingData = {
-    dClipObjectCount: ValueCell<number>,
-    dClipVariant: ValueCell<string>,
-
     tClipping: ValueCell<TextureImage<Uint8Array>>
     uClippingTexDim: ValueCell<Vec2>
     dClipping: ValueCell<boolean>,
 }
 
 export function applyClippingGroups(array: Uint8Array, start: number, end: number, groups: Clipping.Groups) {
-    for (let i = start; i < end; ++i) {
-        array[i] = groups;
-    }
+    array.fill(groups, start, end);
     return true;
 }
 
@@ -38,9 +33,6 @@ export function createClipping(count: number, clippingData?: ClippingData): Clip
         return clippingData;
     } else {
         return {
-            dClipObjectCount: ValueCell.create(0),
-            dClipVariant: ValueCell.create('instance'),
-
             tClipping: ValueCell.create(clipping),
             uClippingTexDim: ValueCell.create(Vec2.create(clipping.width, clipping.height)),
             dClipping: ValueCell.create(count > 0),
@@ -53,12 +45,10 @@ export function createEmptyClipping(clippingData?: ClippingData): ClippingData {
     if (clippingData) {
         ValueCell.update(clippingData.tClipping, emptyClippingTexture);
         ValueCell.update(clippingData.uClippingTexDim, Vec2.create(1, 1));
+        ValueCell.updateIfChanged(clippingData.dClipping, false);
         return clippingData;
     } else {
         return {
-            dClipObjectCount: ValueCell.create(0),
-            dClipVariant: ValueCell.create('instance'),
-
             tClipping: ValueCell.create(emptyClippingTexture),
             uClippingTexDim: ValueCell.create(Vec2.create(1, 1)),
             dClipping: ValueCell.create(false),

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

@@ -15,7 +15,7 @@ import { LocationColor, ColorTheme } from '../../mol-theme/color';
 import { Geometry } from './geometry';
 import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
 
-export type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance' | 'volume' | 'volumeInstance'
+export type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 'vertex' | 'vertexInstance' | 'volume' | 'volumeInstance' | 'direct'
 
 export type ColorData = {
     uColor: ValueCell<Vec3>,
@@ -50,6 +50,7 @@ function _createColors(locationIt: LocationIterator, positionIt: LocationIterato
         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 'direct': return createDirectColor(colorData);
     }
 }
 
@@ -237,3 +238,25 @@ export function createGridColor(grid: ColorVolume, type: ColorType, colorData?:
         };
     }
 }
+
+//
+
+/** Creates direct color */
+function createDirectColor(colorData?: ColorData): ColorData {
+    if (colorData) {
+        ValueCell.updateIfChanged(colorData.dColorType, 'direct');
+        return colorData;
+    } else {
+        return {
+            uColor: ValueCell.create(Vec3()),
+            tColor: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            tColorGrid: ValueCell.create(createNullTexture()),
+            tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            uColorTexDim: ValueCell.create(Vec2.create(1, 1)),
+            uColorGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
+            uColorGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
+            dColorType: ValueCell.create('direct'),
+            dUsePalette: ValueCell.create(false),
+        };
+    }
+}

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

@@ -157,6 +157,8 @@ export namespace Cylinders {
         doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, 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),
     };
     export type Params = typeof Params
 
@@ -211,6 +213,8 @@ export namespace Cylinders {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('cylinders'),
+
             aMapping: cylinders.mappingBuffer,
             aGroup: cylinders.groupBuffer,
             aStart: cylinders.startBuffer,
@@ -234,9 +238,11 @@ export namespace Cylinders {
 
             ...BaseGeometry.createValues(props, counts),
             uSizeFactor: ValueCell.create(props.sizeFactor * props.sizeAspectRatio),
-            dDoubleSided: ValueCell.create(props.doubleSided),
+            uDoubleSided: ValueCell.create(props.doubleSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
+            uBumpFrequency: ValueCell.create(props.bumpFrequency),
+            uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
         };
     }
 
@@ -249,9 +255,11 @@ export namespace Cylinders {
     function updateValues(values: CylindersValues, props: PD.Values<Params>) {
         BaseGeometry.updateValues(values, props);
         ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor * props.sizeAspectRatio);
-        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
+        ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
 
     function updateBoundingSphere(values: CylindersValues, cylinders: Cylinders) {

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -26,8 +26,7 @@ import { TransformData } from '../transform-data';
 import { createEmptyTransparency } from '../transparency-data';
 import { createTransferFunctionTexture, getControlPointsFromVec2Array } from './transfer-function';
 import { createEmptyClipping } from '../clipping-data';
-import { Grid, Volume } from '../../../mol-model/volume';
-import { ColorNames } from '../../../mol-util/color/names';
+import { Grid } from '../../../mol-model/volume';
 import { createEmptySubstance } from '../substance-data';
 
 const VolumeBox = Box();
@@ -48,6 +47,7 @@ export interface DirectVolume {
     readonly unitToCartn: ValueCell<Mat4>
     readonly cartnToUnit: ValueCell<Mat4>
     readonly packedGroup: ValueCell<boolean>
+    readonly axisOrder: ValueCell<Vec3>
 
     /** Bounding sphere of the volume */
     readonly boundingSphere: Sphere3D
@@ -56,10 +56,10 @@ export interface DirectVolume {
 }
 
 export namespace DirectVolume {
-    export function create(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, directVolume?: DirectVolume): DirectVolume {
+    export function create(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, axisOrder: Vec3, directVolume?: DirectVolume): DirectVolume {
         return directVolume ?
-            update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) :
-            fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup);
+            update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, directVolume) :
+            fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder);
     }
 
     function hashCode(directVolume: DirectVolume) {
@@ -70,7 +70,7 @@ export namespace DirectVolume {
         ]);
     }
 
-    function fromData(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean): DirectVolume {
+    function fromData(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, axisOrder: Vec3): DirectVolume {
         const boundingSphere = Sphere3D();
         let currentHash = -1;
 
@@ -101,6 +101,7 @@ export namespace DirectVolume {
                 return boundingSphere;
             },
             packedGroup: ValueCell.create(packedGroup),
+            axisOrder: ValueCell.create(axisOrder),
             setBoundingSphere(sphere: Sphere3D) {
                 Sphere3D.copy(boundingSphere, sphere);
                 currentHash = hashCode(directVolume);
@@ -109,7 +110,7 @@ export namespace DirectVolume {
         return directVolume;
     }
 
-    function update(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, directVolume: DirectVolume): DirectVolume {
+    function update(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, axisOrder: Vec3, directVolume: DirectVolume): DirectVolume {
         const width = texture.getWidth();
         const height = texture.getHeight();
         const depth = texture.getDepth();
@@ -126,6 +127,7 @@ export namespace DirectVolume {
         ValueCell.update(directVolume.unitToCartn, unitToCartn);
         ValueCell.update(directVolume.cartnToUnit, Mat4.invert(Mat4(), unitToCartn));
         ValueCell.updateIfChanged(directVolume.packedGroup, packedGroup);
+        ValueCell.updateIfChanged(directVolume.axisOrder, Vec3.fromArray(directVolume.axisOrder.ref.value, axisOrder, 0));
         return directVolume;
     }
 
@@ -138,47 +140,19 @@ export namespace DirectVolume {
         const texture = createNullTexture();
         const stats = Grid.One.stats;
         const packedGroup = false;
-        return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume);
-    }
-
-    export function createRenderModeParam(stats?: Grid['stats']) {
-        const isoValueParam = stats
-            ? Volume.createIsoValueParam(Volume.IsoValue.relative(2), stats)
-            : Volume.IsoValueParam;
-
-        return PD.MappedStatic('volume', {
-            isosurface: PD.Group({
-                isoValue: isoValueParam,
-                singleLayer: PD.Boolean(false, { isEssential: true }),
-            }, { isFlat: true }),
-            volume: PD.Group({
-                controlPoints: PD.LineGraph([
-                    Vec2.create(0.19, 0.0), Vec2.create(0.2, 0.05), Vec2.create(0.25, 0.05), Vec2.create(0.26, 0.0),
-                    Vec2.create(0.79, 0.0), Vec2.create(0.8, 0.05), Vec2.create(0.85, 0.05), Vec2.create(0.86, 0.0),
-                ]),
-                list: PD.ColorList({
-                    kind: 'interpolate',
-                    colors: [
-                        [ColorNames.white, 0],
-                        [ColorNames.red, 0.25],
-                        [ColorNames.white, 0.5],
-                        [ColorNames.blue, 0.75],
-                        [ColorNames.white, 1]
-                    ]
-                }, { offsets: true }),
-            }, { isFlat: true })
-        }, { isEssential: true });
+        const axisOrder = Vec3.create(0, 1, 2);
+        return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, directVolume);
     }
 
     export const Params = {
         ...BaseGeometry.Params,
-        doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
-        flipSided: PD.Boolean(false, BaseGeometry.ShadingCategory),
-        flatShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
-        renderMode: createRenderModeParam(),
-        stepsPerCell: PD.Numeric(5, { min: 1, max: 20, step: 1 }),
+        controlPoints: PD.LineGraph([
+            Vec2.create(0.19, 0.0), Vec2.create(0.2, 0.05), Vec2.create(0.25, 0.05), Vec2.create(0.26, 0.0),
+            Vec2.create(0.79, 0.0), Vec2.create(0.8, 0.05), Vec2.create(0.85, 0.05), Vec2.create(0.86, 0.0),
+        ], { isEssential: true }),
+        stepsPerCell: PD.Numeric(3, { min: 1, max: 10, step: 1 }),
         jumpLength: PD.Numeric(0, { min: 0, max: 20, step: 0.1 }),
     };
     export type Params = typeof Params
@@ -217,13 +191,6 @@ export namespace DirectVolume {
         return LocationIterator(groupCount, instanceCount, 1, getLocation);
     }
 
-    function getNormalizedIsoValue(out: Vec2, isoValue: Volume.IsoValue, stats: Vec4) {
-        const [min, max, mean, sigma] = stats;
-        const value = Volume.IsoValue.toAbsolute(isoValue, { min, max, mean, sigma }).absoluteValue;
-        Vec2.set(out, (value - min) / (max - min), (0 - min) / (max - min));
-        return out;
-    }
-
     function getMaxSteps(gridDim: Vec3, stepsPerCell: number) {
         return Math.ceil(Vec3.magnitude(gridDim) * stepsPerCell);
     }
@@ -256,18 +223,12 @@ export namespace DirectVolume {
         const invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
-        const controlPoints = props.renderMode.name === 'volume' ? getControlPointsFromVec2Array(props.renderMode.params.controlPoints) : [];
-        const transferTex = createTransferFunctionTexture(controlPoints, props.renderMode.name === 'volume' ? props.renderMode.params.list.colors : []);
-
-        const isoValue = props.renderMode.name === 'isosurface'
-            ? props.renderMode.params.isoValue
-            : Volume.IsoValue.relative(2);
-
-        const singleLayer = props.renderMode.name === 'isosurface'
-            ? props.renderMode.params.singleLayer
-            : false;
+        const controlPoints = getControlPointsFromVec2Array(props.controlPoints);
+        const transferTex = createTransferFunctionTexture(controlPoints);
 
         return {
+            dGeometryType: ValueCell.create('directVolume'),
+
             ...color,
             ...marker,
             ...overpaint,
@@ -283,7 +244,6 @@ export namespace DirectVolume {
             invariantBoundingSphere: ValueCell.create(invariantBoundingSphere),
             uInvariantBoundingSphere: ValueCell.create(Vec4.ofSphere(invariantBoundingSphere)),
 
-            uIsoValue: ValueCell.create(getNormalizedIsoValue(Vec2(), isoValue, directVolume.gridStats.ref.value)),
             uBboxMin: bboxMin,
             uBboxMax: bboxMax,
             uBboxSize: bboxSize,
@@ -292,7 +252,6 @@ export namespace DirectVolume {
             uJumpLength: ValueCell.create(props.jumpLength),
             uTransform: gridTransform,
             uGridDim: gridDimension,
-            dRenderMode: ValueCell.create(props.renderMode.name),
             tTransferTex: transferTex,
             uTransferScale: ValueCell.create(getTransferScale(props.stepsPerCell)),
 
@@ -305,11 +264,8 @@ export namespace DirectVolume {
             uCartnToUnit: directVolume.cartnToUnit,
             uUnitToCartn: directVolume.unitToCartn,
             dPackedGroup: directVolume.packedGroup,
-            dSingleLayer: ValueCell.create(singleLayer),
+            dAxisOrder: ValueCell.create(directVolume.axisOrder.ref.value.join('')),
 
-            dDoubleSided: ValueCell.create(props.doubleSided),
-            dFlatShaded: ValueCell.create(props.flatShaded),
-            dFlipSided: ValueCell.create(props.flipSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
         };
@@ -323,20 +279,11 @@ export namespace DirectVolume {
 
     function updateValues(values: DirectVolumeValues, props: PD.Values<Params>) {
         BaseGeometry.updateValues(values, props);
-        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
-        ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded);
-        ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
-        ValueCell.updateIfChanged(values.dRenderMode, props.renderMode.name);
 
-        if (props.renderMode.name === 'isosurface') {
-            ValueCell.updateIfChanged(values.uIsoValue, getNormalizedIsoValue(values.uIsoValue.ref.value, props.renderMode.params.isoValue, values.uGridStats.ref.value));
-            ValueCell.updateIfChanged(values.dSingleLayer, props.renderMode.params.singleLayer);
-        } else if (props.renderMode.name === 'volume') {
-            const controlPoints = getControlPointsFromVec2Array(props.renderMode.params.controlPoints);
-            createTransferFunctionTexture(controlPoints, props.renderMode.params.list.colors, values.tTransferTex);
-        }
+        const controlPoints = getControlPointsFromVec2Array(props.controlPoints);
+        createTransferFunctionTexture(controlPoints, values.tTransferTex);
 
         ValueCell.updateIfChanged(values.uMaxSteps, getMaxSteps(values.uGridDim.ref.value, props.stepsPerCell));
         ValueCell.updateIfChanged(values.uStepScale, getStepScale(values.uCellDim.ref.value, props.stepsPerCell));
@@ -360,14 +307,14 @@ export namespace DirectVolume {
     function createRenderableState(props: PD.Values<Params>): RenderableState {
         const state = BaseGeometry.createRenderableState(props);
         state.opaque = false;
-        state.writeDepth = props.renderMode.name === 'isosurface';
+        state.writeDepth = false;
         return state;
     }
 
     function updateRenderableState(state: RenderableState, props: PD.Values<Params>) {
         BaseGeometry.updateRenderableState(state, props);
         state.opaque = false;
-        state.writeDepth = props.renderMode.name === 'isosurface';
+        state.writeDepth = false;
     }
 }
 

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

@@ -1,16 +1,13 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { TextureImage } from '../../../mol-gl/renderable/util';
 import { spline } from '../../../mol-math/interpolate';
-import { ColorScale } from '../../../mol-util/color';
 import { ValueCell } from '../../../mol-util';
 import { Vec2 } from '../../../mol-math/linear-algebra';
-import { ColorListName } from '../../../mol-util/color/lists';
-import { ColorListEntry } from '../../../mol-util/color/color';
 
 export interface ControlPoint { x: number, alpha: number }
 
@@ -25,7 +22,7 @@ export function getControlPointsFromVec2Array(array: Vec2[]): ControlPoint[] {
     return array.map(v => ({ x: v[0], alpha: v[1] }));
 }
 
-export function createTransferFunctionTexture(controlPoints: ControlPoint[], listOrName: ColorListEntry[] | ColorListName, texture?: ValueCell<TextureImage<Uint8Array>>): ValueCell<TextureImage<Uint8Array>> {
+export function createTransferFunctionTexture(controlPoints: ControlPoint[], texture?: ValueCell<TextureImage<Uint8Array>>): ValueCell<TextureImage<Uint8Array>> {
     const cp = [
         { x: 0, alpha: 0 },
         { x: 0, alpha: 0 },
@@ -33,10 +30,9 @@ export function createTransferFunctionTexture(controlPoints: ControlPoint[], lis
         { x: 1, alpha: 0 },
         { x: 1, alpha: 0 },
     ];
-    const scale = ColorScale.create({ domain: [0, 1], listOrName });
 
     const n = 256;
-    const array = texture ? texture.ref.value.array : new Uint8Array(n * 4);
+    const array = texture ? texture.ref.value.array : new Uint8Array(n);
 
     let k = 0;
     let x1: number, x2: number;
@@ -55,8 +51,7 @@ export function createTransferFunctionTexture(controlPoints: ControlPoint[], lis
         const jl = Math.round((x2 - x1) * n);
         for (let j = 0; j < jl; ++j) {
             const t = j / jl;
-            array[k * 4 + 3] = Math.max(0, spline(a0, a1, a2, a3, t, 0.5) * 255);
-            scale.colorToArray(k / 255, array, k * 4);
+            array[k] = Math.max(0, spline(a0, a1, a2, a3, t, 0.5) * 255);
             ++k;
         }
     }

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

@@ -155,6 +155,8 @@ namespace Image {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('image'),
+
             ...color,
             ...marker,
             ...overpaint,

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

@@ -220,6 +220,8 @@ export namespace Lines {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('lines'),
+
             aMapping: lines.mappingBuffer,
             aGroup: lines.groupBuffer,
             aStart: lines.startBuffer,
@@ -240,7 +242,7 @@ export namespace Lines {
             ...BaseGeometry.createValues(props, counts),
             uSizeFactor: ValueCell.create(props.sizeFactor),
             dLineSizeAttenuation: ValueCell.create(props.lineSizeAttenuation),
-            dDoubleSided: ValueCell.create(true),
+            uDoubleSided: ValueCell.create(true),
             dFlipSided: ValueCell.create(false),
         };
     }

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

@@ -12,7 +12,6 @@ export type MarkerData = {
     uMarker: ValueCell<number>,
     tMarker: ValueCell<TextureImage<Uint8Array>>
     uMarkerTexDim: ValueCell<Vec2>
-    dMarkerType: ValueCell<string>,
     markerAverage: ValueCell<number>
     markerStatus: ValueCell<number>
 }
@@ -48,12 +47,19 @@ export function getMarkersAverage(array: Uint8Array, count: number): number {
     const backStart = 4 * viewEnd;
 
     let sum = 0;
-    for (let i = 0; i < viewEnd; ++i) {
-        const v = view[i];
-        sum += MarkerCountLut[v & 0xFFFF] + MarkerCountLut[v >> 16];
-    }
-    for (let i = backStart; i < count; ++i) {
-        sum += array[i] && 1;
+    if (viewEnd < 0) {
+        // avoid edge cases with small arrays
+        for (let i = 0; i < count; ++i) {
+            sum += array[i] && 1;
+        }
+    } else {
+        for (let i = 0; i < viewEnd; ++i) {
+            const v = view[i];
+            sum += MarkerCountLut[v & 0xFFFF] + MarkerCountLut[v >> 16];
+        }
+        for (let i = backStart; i < count; ++i) {
+            sum += array[i] && 1;
+        }
     }
     return sum / count;
 }
@@ -66,7 +72,6 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
         ValueCell.updateIfChanged(markerData.uMarker, 0);
         ValueCell.update(markerData.tMarker, markers);
         ValueCell.update(markerData.uMarkerTexDim, Vec2.create(markers.width, markers.height));
-        ValueCell.updateIfChanged(markerData.dMarkerType, status === -1 ? 'groupInstance' : 'uniform');
         ValueCell.updateIfChanged(markerData.markerAverage, average);
         ValueCell.updateIfChanged(markerData.markerStatus, status);
         return markerData;
@@ -77,7 +82,6 @@ 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('uniform'),
         };
     }
 }
@@ -88,7 +92,6 @@ export function createEmptyMarkers(markerData?: MarkerData): MarkerData {
         ValueCell.updateIfChanged(markerData.uMarker, 0);
         ValueCell.update(markerData.tMarker, emptyMarkerTexture);
         ValueCell.update(markerData.uMarkerTexDim, Vec2.create(1, 1));
-        ValueCell.updateIfChanged(markerData.dMarkerType, 'uniform');
         ValueCell.updateIfChanged(markerData.markerAverage, 0);
         ValueCell.updateIfChanged(markerData.markerStatus, 0);
         return markerData;
@@ -99,7 +102,6 @@ export function createEmptyMarkers(markerData?: MarkerData): MarkerData {
             uMarkerTexDim: ValueCell.create(Vec2.create(1, 1)),
             markerAverage: ValueCell.create(0),
             markerStatus: ValueCell.create(0),
-            dMarkerType: ValueCell.create('uniform'),
         };
     }
 }

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

@@ -376,7 +376,7 @@ export function applyMeshSubstanceSmoothing(values: MeshValues, resolution: numb
         colorType: values.dSubstanceType.ref.value,
         boundingSphere: values.boundingSphere.ref.value,
         invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
-        itemSize: 3
+        itemSize: 4
     }, resolution, stride, webgl, colorTexture);
     if (smoothingData.kind === 'volume') {
         ValueCell.updateIfChanged(values.dSubstanceType, smoothingData.type);

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

@@ -625,6 +625,8 @@ export namespace Mesh {
         flatShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, 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),
     };
     export type Params = typeof Params
 
@@ -675,6 +677,8 @@ export namespace Mesh {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('mesh'),
+
             aPosition: mesh.vertexBuffer,
             aNormal: mesh.normalBuffer,
             aGroup: mesh.groupBuffer,
@@ -691,11 +695,13 @@ export namespace Mesh {
             ...transform,
 
             ...BaseGeometry.createValues(props, counts),
-            dDoubleSided: ValueCell.create(props.doubleSided),
+            uDoubleSided: ValueCell.create(props.doubleSided),
             dFlatShaded: ValueCell.create(props.flatShaded),
             dFlipSided: ValueCell.create(props.flipSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
+            uBumpFrequency: ValueCell.create(props.bumpFrequency),
+            uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
 
             meta: ValueCell.create(mesh.meta),
         };
@@ -709,11 +715,13 @@ export namespace Mesh {
 
     function updateValues(values: MeshValues, props: PD.Values<Params>) {
         BaseGeometry.updateValues(values, props);
-        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
+        ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded);
         ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
 
     function updateBoundingSphere(values: MeshValues, mesh: Mesh) {

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

@@ -182,6 +182,8 @@ export namespace Points {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('points'),
+
             aPosition: points.centerBuffer,
             aGroup: points.groupBuffer,
             boundingSphere: ValueCell.create(boundingSphere),

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

@@ -11,7 +11,7 @@ import { LocationIterator } from '../util/location-iterator';
 import { Location, NullLocation } from '../../mol-model/location';
 import { SizeTheme } from '../../mol-theme/size';
 import { Geometry } from './geometry';
-import { decodeFloatRGB, encodeFloatRGBtoArray } from '../../mol-util/float-packing';
+import { unpackRGBToInt, packIntToRGBArray } from '../../mol-util/number-packing';
 
 export type SizeType = 'uniform' | 'instance' | 'group' | 'groupInstance'
 
@@ -44,7 +44,7 @@ export function getMaxSize(sizeData: SizeData): number {
             let maxSize = 0;
             const array = sizeData.tSize.ref.value.array;
             for (let i = 0, il = array.length; i < il; i += 3) {
-                const value = decodeFloatRGB(array[i], array[i + 1], array[i + 2]);
+                const value = unpackRGBToInt(array[i], array[i + 1], array[i + 2]);
                 if (maxSize < value) maxSize = value;
             }
             return maxSize / sizeDataFactor;
@@ -103,7 +103,7 @@ export function createInstanceSize(locationIt: LocationIterator, sizeFn: Locatio
     locationIt.reset();
     while (locationIt.hasNext && !locationIt.isNextNewInstance) {
         const v = locationIt.move();
-        encodeFloatRGBtoArray(sizeFn(v.location) * sizeDataFactor, sizes.array, v.instanceIndex * 3);
+        packIntToRGBArray(sizeFn(v.location) * sizeDataFactor, sizes.array, v.instanceIndex * 3);
         locationIt.skipInstance();
     }
     return createTextureSize(sizes, 'instance', sizeData);
@@ -116,7 +116,7 @@ export function createGroupSize(locationIt: LocationIterator, sizeFn: LocationSi
     locationIt.reset();
     while (locationIt.hasNext && !locationIt.isNextNewInstance) {
         const v = locationIt.move();
-        encodeFloatRGBtoArray(sizeFn(v.location) * sizeDataFactor, sizes.array, v.groupIndex * 3);
+        packIntToRGBArray(sizeFn(v.location) * sizeDataFactor, sizes.array, v.groupIndex * 3);
     }
     return createTextureSize(sizes, 'group', sizeData);
 }
@@ -129,7 +129,7 @@ export function createGroupInstanceSize(locationIt: LocationIterator, sizeFn: Lo
     locationIt.reset();
     while (locationIt.hasNext) {
         const v = locationIt.move();
-        encodeFloatRGBtoArray(sizeFn(v.location) * sizeDataFactor, sizes.array, v.index * 3);
+        packIntToRGBArray(sizeFn(v.location) * sizeDataFactor, sizes.array, v.index * 3);
     }
     return createTextureSize(sizes, 'groupInstance', sizeData);
 }

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

@@ -129,6 +129,8 @@ export namespace Spheres {
         doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, 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),
     };
     export type Params = typeof Params
 
@@ -181,6 +183,8 @@ export namespace Spheres {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('spheres'),
+
             aPosition: spheres.centerBuffer,
             aMapping: spheres.mappingBuffer,
             aGroup: spheres.groupBuffer,
@@ -201,9 +205,11 @@ export namespace Spheres {
 
             ...BaseGeometry.createValues(props, counts),
             uSizeFactor: ValueCell.create(props.sizeFactor),
-            dDoubleSided: ValueCell.create(props.doubleSided),
+            uDoubleSided: ValueCell.create(props.doubleSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
+            uBumpFrequency: ValueCell.create(props.bumpFrequency),
+            uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
         };
     }
 
@@ -216,9 +222,11 @@ export namespace Spheres {
     function updateValues(values: SpheresValues, props: PD.Values<Params>) {
         BaseGeometry.updateValues(values, props);
         ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor);
-        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
+        ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
 
     function updateBoundingSphere(values: SpheresValues, spheres: Spheres) {

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

@@ -23,14 +23,14 @@ export type SubstanceData = {
 
 export function applySubstanceMaterial(array: Uint8Array, start: number, end: number, material: Material) {
     for (let i = start; i < end; ++i) {
-        Material.toArray(material, array, i * 3);
-        array[i * 3 + 2] = 255;
+        Material.toArray(material, array, i * 4);
+        array[i * 4 + 3] = 255;
     }
     return true;
 }
 
 export function clearSubstance(array: Uint8Array, start: number, end: number) {
-    array.fill(0, start * 3, end * 3);
+    array.fill(0, start * 4, end * 4);
     return true;
 }
 

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

@@ -39,35 +39,35 @@ export type FontAtlasMap = {
 }
 
 export class FontAtlas {
-    readonly props: Readonly<FontAtlasProps>
-    readonly mapped: { [k: string]: FontAtlasMap } = {}
-    readonly placeholder: FontAtlasMap
-    readonly texture: TextureImage<Uint8Array>
+    readonly props: Readonly<FontAtlasProps>;
+    readonly mapped: { [k: string]: FontAtlasMap } = {};
+    readonly placeholder: FontAtlasMap;
+    readonly texture: TextureImage<Uint8Array>;
 
-    private scratchW = 0
-    private scratchH = 0
-    private currentX = 0
-    private currentY = 0
-    private readonly scratchData: Uint8Array
+    private scratchW = 0;
+    private scratchH = 0;
+    private currentX = 0;
+    private currentY = 0;
+    private readonly scratchData: Uint8Array;
 
-    private readonly cutoff = 0.5
-    readonly buffer: number
-    private readonly radius: number
+    private readonly cutoff = 0.5;
+    readonly buffer: number;
+    private readonly radius: number;
 
-    private gridOuter: Float64Array
-    private gridInner: Float64Array
-    private f: Float64Array
-    private d: Float64Array
-    private z: Float64Array
-    private v: Int16Array
+    private gridOuter: Float64Array;
+    private gridInner: Float64Array;
+    private f: Float64Array;
+    private d: Float64Array;
+    private z: Float64Array;
+    private v: Int16Array;
 
-    private scratchCanvas: HTMLCanvasElement
-    private scratchContext: CanvasRenderingContext2D
+    private scratchCanvas: HTMLCanvasElement;
+    private scratchContext: CanvasRenderingContext2D;
 
-    readonly lineHeight: number
+    readonly lineHeight: number;
 
-    private readonly maxWidth: number
-    private readonly middle: number
+    private readonly maxWidth: number;
+    private readonly middle: number;
 
     constructor(props: Partial<FontAtlasProps> = {}) {
         const p = { ...PD.getDefaultValues(FontAtlasParams), ...props };

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

@@ -224,6 +224,8 @@ export namespace Text {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('text'),
+
             aPosition: text.centerBuffer,
             aMapping: text.mappingBuffer,
             aDepth: text.depthBuffer,

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

@@ -510,10 +510,10 @@ export function applyTextureMeshSubstanceSmoothing(values: TextureMeshValues, re
 
     stride *= 3; // triple because TextureMesh is never indexed (no elements buffer)
 
-    if (!webgl.namedTextures[ColorSmoothingRgbName]) {
-        webgl.namedTextures[ColorSmoothingRgbName] = webgl.resources.texture('image-uint8', 'rgb', 'ubyte', 'nearest');
+    if (!webgl.namedTextures[ColorSmoothingRgbaName]) {
+        webgl.namedTextures[ColorSmoothingRgbaName] = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
     }
-    const colorData = webgl.namedTextures[ColorSmoothingRgbName];
+    const colorData = webgl.namedTextures[ColorSmoothingRgbaName];
     colorData.load(values.tSubstance.ref.value);
 
     const smoothingData = calcTextureMeshColorSmoothing({

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

@@ -47,7 +47,7 @@ export interface TextureMesh {
 export namespace TextureMesh {
     export class DoubleBuffer {
         private index = 0;
-        private textures: ({ vertex: Texture, group: Texture, normal: Texture } | undefined)[] = []
+        private textures: ({ vertex: Texture, group: Texture, normal: Texture } | undefined)[] = [];
 
         get() {
             return this.textures[this.index];
@@ -113,6 +113,8 @@ export namespace TextureMesh {
         flatShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Boolean(false, 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),
     };
     export type Params = typeof Params
 
@@ -145,6 +147,8 @@ export namespace TextureMesh {
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
         return {
+            dGeometryType: ValueCell.create('textureMesh'),
+
             uGeoTexDim: textureMesh.geoTextureDim,
             tPosition: textureMesh.vertexTexture,
             tGroup: textureMesh.groupTexture,
@@ -163,12 +167,13 @@ export namespace TextureMesh {
             ...transform,
 
             ...BaseGeometry.createValues(props, counts),
-            dDoubleSided: ValueCell.create(props.doubleSided),
+            uDoubleSided: ValueCell.create(props.doubleSided),
             dFlatShaded: ValueCell.create(props.flatShaded),
             dFlipSided: ValueCell.create(props.flipSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
             dXrayShaded: ValueCell.create(props.xrayShaded),
-            dGeoTexture: ValueCell.create(true),
+            uBumpFrequency: ValueCell.create(props.bumpFrequency),
+            uBumpAmplitude: ValueCell.create(props.bumpAmplitude),
 
             meta: ValueCell.create(textureMesh.meta),
         };
@@ -182,11 +187,13 @@ export namespace TextureMesh {
 
     function updateValues(values: TextureMeshValues, props: PD.Values<Params>) {
         BaseGeometry.updateValues(values, props);
-        ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
+        ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded);
         ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
 
     function updateBoundingSphere(values: TextureMeshValues, textureMesh: TextureMesh) {