3.0.0-dev.6

- include analytics in deployed demos

.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

.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

@@ -6,6 +6,38 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [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)
@@ -30,7 +62,7 @@ Note that since we don't clearly distinguish between a public and private interf
 
 - 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
+    - ``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

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

@@ -246,6 +246,14 @@ 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 +810,58 @@ 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-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "molstar",
-  "version": "3.0.0-dev.4",
+  "version": "3.0.0-dev.6",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "3.0.0-dev.4",
+      "version": "3.0.0-dev.6",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.10",
@@ -12527,9 +12527,9 @@
       }
     },
     "node_modules/swagger-ui-dist": {
-      "version": "4.1.1",
-      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.1.1.tgz",
-      "integrity": "sha512-xvPMEpOCbd5S9Z1pJT/L/K/C2yAX89ZWJDxEECkVW1dENsKFLbu7sRY7b6UBqLXuTUfdM5owlgPrpwr24CRonA=="
+      "version": "4.1.3",
+      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.1.3.tgz",
+      "integrity": "sha512-WvfPSfAAMlE/sKS6YkW47nX/hA7StmhYnAHc6wWCXNL0oclwLj6UXv0hQCkLnDgvebi0MEV40SJJpVjKUgH1IQ=="
     },
     "node_modules/swap-case": {
       "version": "2.0.2",
@@ -23561,9 +23561,9 @@
       }
     },
     "swagger-ui-dist": {
-      "version": "4.1.1",
-      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.1.1.tgz",
-      "integrity": "sha512-xvPMEpOCbd5S9Z1pJT/L/K/C2yAX89ZWJDxEECkVW1dENsKFLbu7sRY7b6UBqLXuTUfdM5owlgPrpwr24CRonA=="
+      "version": "4.1.3",
+      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.1.3.tgz",
+      "integrity": "sha512-WvfPSfAAMlE/sKS6YkW47nX/hA7StmhYnAHc6wWCXNL0oclwLj6UXv0hQCkLnDgvebi0MEV40SJJpVjKUgH1IQ=="
     },
     "swap-case": {
       "version": "2.0.2",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.0-dev.4",
+  "version": "3.0.0-dev.6",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

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>
  */
@@ -39,6 +39,24 @@ function copyViewer() {
     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)) {
     console.log('\n###', 'create localPath');
     fs.mkdirSync(localPath, { recursive: true });
@@ -52,9 +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');
@@ -62,8 +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

@@ -230,7 +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/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 +56,8 @@
             var pixelScale = getParam('pixel-scale', '[^&]+').trim();
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
-            var viewer = new molstar.Viewer('app', {
+
+            molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
                 collapseLeftPanel: collapseLeftPanel,
@@ -68,28 +69,34 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
+            }).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>

src/apps/viewer/index.ts

@@ -10,13 +10,16 @@ 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 { 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 { 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';
@@ -25,7 +28,7 @@ import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers
 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 { 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';
@@ -33,7 +36,7 @@ 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 { StateObjectRef, StateObjectSelector } from '../../mol-state';
 import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
@@ -60,7 +63,8 @@ const Extensions = {
     'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
     'g3d': PluginSpec.Behavior(G3DFormat),
     'mp4-export': PluginSpec.Behavior(Mp4Export),
-    'geo-export': PluginSpec.Behavior(GeometryExport)
+    'geo-export': PluginSpec.Behavior(GeometryExport),
+    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
 };
 
 const DefaultViewerOptions = {
@@ -95,9 +99,10 @@ const DefaultViewerOptions = {
 type ViewerOptions = typeof DefaultViewerOptions;
 
 export class Viewer {
-    plugin: PluginUIContext
+    constructor(public plugin: PluginUIContext) {
+    }
 
-    constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
+    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
         const o = { ...DefaultViewerOptions, ...options };
         const defaultSpec = DefaultPluginUISpec();
 
@@ -149,7 +154,8 @@ export class Viewer {
                 [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
                 [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
                 [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
             ]
         };
 
@@ -157,7 +163,14 @@ export 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, {
+            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) {
@@ -251,6 +264,35 @@ export class Viewer {
         }));
     }
 
+    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({
@@ -409,4 +451,32 @@ export interface LoadTrajectoryParams {
     | { 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/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: [
@@ -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'
@@ -95,7 +95,7 @@ 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 +119,7 @@ class BasicWrapper {
                 }
             });
         }
-    }
+    };
 
     interactivity = {
         highlightOn: () => {
@@ -137,7 +137,7 @@ class BasicWrapper {
         clearHighlight: () => {
             this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
         }
-    }
+    };
 
     tests = {
         staticSuperposition: async () => {
@@ -168,7 +168,7 @@ 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

@@ -1,12 +1,12 @@
 /**
- * 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';
@@ -17,44 +17,46 @@ 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, color: Color(0x000000) } }
-        },
-        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 }]
+            }
         }
     }
 };
@@ -69,8 +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: {
@@ -88,25 +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) {
@@ -115,7 +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 }));
@@ -269,8 +269,8 @@ 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 +285,7 @@ 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 +306,7 @@ class MolStarProteopediaWrapper {
 
             await PluginCommands.State.Update(this.plugin, { state, tree });
         }
-    }
+    };
 
     private experimentalDataElement?: Element = void 0;
     experimentalData = {
@@ -330,17 +330,17 @@ 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 +397,7 @@ 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 +420,7 @@ 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/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/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/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/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/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/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

@@ -395,7 +395,11 @@ namespace Canvas3D {
                 }
 
                 if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                    if (!cameraChanged) {
+                        while (!multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p));
+                    } else {
+                        multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                    }
                 } else {
                     passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing, p.marking);
                 }
@@ -514,7 +518,7 @@ 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 +529,13 @@ 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;

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

@@ -31,14 +31,14 @@ 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);

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

@@ -49,13 +49,13 @@ 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);
@@ -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;

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

@@ -47,12 +47,12 @@ 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) {
@@ -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;

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/passes/draw.ts

@@ -54,27 +54,27 @@ function getDepthMergeRenderable(ctx: WebGLContext, depthTexturePrimitives: Text
 }
 
 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;

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; }

src/mol-canvas3d/passes/marking.ts

@@ -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>
 
@@ -66,11 +66,11 @@ 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;
@@ -317,15 +317,17 @@ 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;
     }
 
+    /** Return `true` while more samples are needed */
     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 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

@@ -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;
@@ -97,23 +97,23 @@ export class PickPass {
 }
 
 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;

src/mol-canvas3d/passes/postprocessing.ts

@@ -271,29 +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);
@@ -543,9 +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() {

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/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/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];

src/mol-geo/util/marching-cubes/algorithm.ts

@@ -72,7 +72,7 @@ export function computeMarchingCubesLines(params: MarchingCubesParams, lines?: L
 class MarchingCubesComputation {
     private size: number;
     private sliceSize: number;
-    private edgeFilter: number
+    private edgeFilter: number;
 
     private minX = 0; private minY = 0; private minZ = 0;
     private maxX = 0; private maxY = 0; private maxZ = 0;

src/mol-gl/shader/direct-volume.frag.ts

@@ -74,6 +74,7 @@ uniform vec3 uFogColor;
 uniform float uAlpha;
 uniform float uPickingAlphaThreshold;
 uniform bool uTransparentBackground;
+uniform float uXrayEdgeFalloff;
 
 uniform float uInteriorDarkening;
 uniform bool uInteriorColorFlag;

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.353, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */
@@ -942,6 +942,48 @@ export const mmCIF_Schema = {
          */
         method: Aliased<'X-RAY DIFFRACTION' | 'NEUTRON DIFFRACTION' | 'FIBER DIFFRACTION' | 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'SOLUTION NMR' | 'SOLID-STATE NMR' | 'SOLUTION SCATTERING' | 'POWDER DIFFRACTION' | 'INFRARED SPECTROSCOPY' | 'EPR' | 'FLUORESCENCE TRANSFER' | 'THEORETICAL MODEL'>(str),
     },
+    /**
+     * Data items in the SOFTWARE category record details about
+     * the software used in the structure analysis, which implies
+     * any software used in the generation of any data items
+     * associated with the structure determination and
+     * structure representation.
+     *
+     * These data items allow computer programs to be referenced
+     * in more detail than data items in the COMPUTING category do.
+     */
+    software: {
+        /**
+         * The classification of the program according to its
+         * major function.
+         */
+        classification: str,
+        /**
+         * The date the software was released.
+         */
+        date: str,
+        /**
+         * Description of the software.
+         */
+        description: str,
+        /**
+         * The name of the software.
+         */
+        name: str,
+        /**
+         * The classification of the software according to the most
+         * common types.
+         */
+        type: Aliased<'program' | 'library' | 'package' | 'filter' | 'jiffy' | 'other'>(str),
+        /**
+         * The version of the software.
+         */
+        version: str,
+        /**
+         * An ordinal index for this category
+         */
+        pdbx_ordinal: int,
+    },
     /**
      * Data items in the STRUCT category record details about the
      * description of the crystallographic structure.
@@ -4717,6 +4759,289 @@ export const mmCIF_Schema = {
          */
         dataset_list_id: int,
     },
+    /**
+     * Data items in the MA_MODEL_LIST category record the
+     * details of the models being deposited.
+     */
+    ma_model_list: {
+        /**
+         * A unique identifier for the model / model group combination.
+         */
+        ordinal_id: int,
+        /**
+         * A unique identifier for the structural model being deposited.
+         */
+        model_id: int,
+        /**
+         * An identifier to group structural models into collections or sets.
+         * A cluster of models and its representative can either be grouped together
+         * or can be separate groups in the ma_model_list table. The choice between
+         * the two options should be decided based on how the modeling was carried out
+         * and how the representative was chosen. If the representative is a member of
+         * the ensemble (i.e., best scoring model), then it is recommended that the
+         * representative and the ensemble belong to the same model group. If the
+         * representative is calculated from the ensemble (i.e., centroid), then it is
+         * recommended that the representative be separated into a different group.
+         * If the models do not need to be grouped into collections, then the
+         * _ma_model_list.model_group_id is the same as _ma_model_list.model_id.
+         */
+        model_group_id: int,
+        /**
+         * A decsriptive name for the model.
+         */
+        model_name: str,
+        /**
+         * A decsriptive name for the model group.
+         */
+        model_group_name: str,
+        /**
+         * The type of model.
+         */
+        model_type: Aliased<'Homology model' | 'Ab initio model' | 'Other'>(str),
+        /**
+         * The data_id identifier. This data item is a pointer to
+         * _ma_data.id in the MA_DATA category.
+         */
+        data_id: int,
+    },
+    /**
+     * Data items in the MA_TARGET_ENTITY category record details about
+     * the target entities. The details are provided for each entity
+     * being modeled.
+     */
+    ma_target_entity: {
+        /**
+         * A unique identifier for the distinct molecular entity of the target.
+         * This data item is a pointer to _entity.id in the ENTITY category.
+         */
+        entity_id: str,
+        /**
+         * The data_id identifier. This data item is a pointer to
+         * _ma_data.id in the MA_DATA category.
+         */
+        data_id: int,
+        /**
+         * The origin of the target entity.
+         */
+        origin: Aliased<'reference database' | 'designed'>(str),
+    },
+    /**
+     * Data items in the MA_TARGET_ENTITY_INSTANCE category record details about
+     * the instances of target entities modeled.
+     */
+    ma_target_entity_instance: {
+        /**
+         * A unique identifier for the instance of the entity.
+         */
+        asym_id: str,
+        /**
+         * A unique identifier for the distinct molecular entity of the target.
+         * This data item is a pointer to _ma_target_entity.entity_id in the
+         * MA_TARGET_ENTITY category.
+         */
+        entity_id: str,
+        /**
+         * Additional details about the entity instance.
+         */
+        details: str,
+    },
+    /**
+     * Data items in the MA_TARGET_REF_DB_DETAILS category record details about
+     * the reference databases for the target sequences.
+     */
+    ma_target_ref_db_details: {
+        /**
+         * An identifier for the target entity.
+         */
+        target_entity_id: str,
+        /**
+         * The name of the database containing reference information about
+         * this entity or biological unit.
+         */
+        db_name: Aliased<'UNP' | 'GB' | 'OrthoDB' | 'NCBI' | 'JGI' | 'Other'>(str),
+        /**
+         * The code for this entity or biological unit or for a closely
+         * related entity or biological unit in the named database.
+         * This can include the version number.
+         */
+        db_code: str,
+        /**
+         * Accession code assigned by the reference database.
+         */
+        db_accession: str,
+        /**
+         * Database code assigned by the reference database for a sequence isoform.   An isoform sequence is an
+         * alternative protein sequence that can be generated from the same gene by a single or by a combination of
+         * biological events such as: alternative promoter usage, alternative splicing, alternative initiation
+         * and ribosomal frameshifting.
+         */
+        seq_db_isoform: str,
+        /**
+         * Beginning index in the chemical sequence from the
+         * reference database.
+         */
+        seq_db_align_begin: str,
+        /**
+         * Ending index in the chemical sequence from the
+         * reference database.
+         */
+        seq_db_align_end: str,
+        /**
+         * Taxonomy identifier provided by NCBI.
+         */
+        ncbi_taxonomy_id: str,
+        /**
+         * Scientific name of the organism.
+         */
+        organism_scientific: str,
+    },
+    /**
+     * Data items in the MA_DATA category capture the different kinds of
+     * data used in the modeling. These can be multiple sequence
+     * alignments, spatial restraints, template structures etc.
+     */
+    ma_data: {
+        /**
+         * A unique identifier for the data.
+         */
+        id: int,
+        /**
+         * The type of data held in the dataset.
+         */
+        content_type: Aliased<'target' | 'template structure' | 'polymeric template library' | 'spatial restraints' | 'target-template alignment' | 'coevolution MSA' | 'model coordinates' | 'other'>(str),
+        /**
+         * Details for other content types.
+         */
+        content_type_other_details: str,
+        /**
+         * An author-given name for the content held in the dataset.
+         */
+        name: str,
+    },
+    /**
+     * Data items in the MA_SOFTWARE_GROUP category describes the
+     * collection of software into groups so that they can be used
+     * efficiently in the MA_PROTOCOL_STEP category.
+     */
+    ma_software_group: {
+        /**
+         * A unique identifier for the category.
+         */
+        ordinal_id: int,
+        /**
+         * An identifier for the group entry.
+         * If data does not need to be grouped, then _ma_software_group.group_id
+         * is the same as _ma_software_group.software_id.
+         */
+        group_id: int,
+        /**
+         * The identifier for the software.
+         * This data item is a pointer to _software.pdbx_ordinal
+         * in the SOFTWARE category.
+         */
+        software_id: int,
+    },
+    /**
+     * Data items in the MA_QA_METRIC category record the
+     * details of the metrics use to assess model quality.
+     */
+    ma_qa_metric: {
+        /**
+         * An identifier for the QA metric.
+         */
+        id: int,
+        /**
+         * Name of the QA metric.
+         */
+        name: str,
+        /**
+         * The type of QA metric.
+         */
+        type: Aliased<'zscore' | 'energy' | 'distance' | 'normalized score' | 'pLDDT' | 'PAE' | 'contact probability' | 'other'>(str),
+        /**
+         * The mode of calculation of the QA metric.
+         */
+        mode: Aliased<'local' | 'global' | 'local-pairwise'>(str),
+        /**
+         * Identifier to the set of software used to calculate the QA metric.
+         * This data item is a pointer to the _ma_software_group.group_id in the
+         * MA_SOFTWARE_GROUP category.
+         */
+        software_group_id: int,
+    },
+    /**
+     * Data items in the MA_QA_METRIC_GLOBAL category captures the
+     * details of the global QA metrics, calculated at the model-level.
+     */
+    ma_qa_metric_global: {
+        /**
+         * A unique identifier for the category.
+         */
+        ordinal_id: int,
+        /**
+         * The identifier for the structural model, for which global QA metric is provided.
+         * This data item is a pointer to _ma_model_list.model_id
+         * in the MA_MODEL_LIST category.
+         */
+        model_id: int,
+        /**
+         * The identifier for the QA metric.
+         * This data item is a pointer to _ma_qa_metric.id in the
+         * MA_QA_METRIC category.
+         */
+        metric_id: int,
+        /**
+         * The value of the global QA metric.
+         */
+        metric_value: float,
+    },
+    /**
+     * Data items in the MA_QA_METRIC_LOCAL category captures the
+     * details of the local QA metrics, calculated at the residue-level.
+     */
+    ma_qa_metric_local: {
+        /**
+         * A unique identifier for the category.
+         */
+        ordinal_id: int,
+        /**
+         * The identifier for the structural model, for which local QA metric is provided.
+         * This data item is a pointer to _ma_model_list.model_id
+         * in the MA_MODEL_LIST category.
+         */
+        model_id: int,
+        /**
+         * The identifier for the asym id of the residue in the
+         * structural model, for which local QA metric is provided.
+         * This data item is a pointer to _atom_site.label_asym_id
+         * in the ATOM_SITE category.
+         */
+        label_asym_id: str,
+        /**
+         * The identifier for the sequence index of the residue
+         * in the structural model, for which local QA metric is provided.
+         * This data item is a pointer to _atom_site.label_seq_id
+         * in the ATOM_SITE category.
+         */
+        label_seq_id: int,
+        /**
+         * The component identifier for the residue in the
+         * structural model, for which local QA metric is provided.
+         * This data item is a pointer to _atom_site.label_comp_id
+         * in the ATOM_SITE category.
+         */
+        label_comp_id: str,
+        /**
+         * The identifier for the QA metric.
+         * This data item is a pointer to _ma_qa_metric.id in the
+         * MA_QA_METRIC category.
+         */
+        metric_id: int,
+        /**
+         * The value of the local QA metric.
+         */
+        metric_value: float,
+    },
 };
 
 export type mmCIF_Schema = typeof mmCIF_Schema;

src/mol-math/geometry/boundary-helper.ts

@@ -12,12 +12,12 @@ import { Box3D } from './primitives/box3d';
 // implementing http://www.ep.liu.se/ecp/034/009/ecp083409.pdf
 
 export class BoundaryHelper {
-    private dir: Vec3[]
+    private dir: Vec3[];
 
-    private minDist: number[] = []
-    private maxDist: number[] = []
-    private extrema: Vec3[] = []
-    centroidHelper = new CentroidHelper()
+    private minDist: number[] = [];
+    private maxDist: number[] = [];
+    private extrema: Vec3[] = [];
+    centroidHelper = new CentroidHelper();
 
     private computeExtrema(i: number, p: Vec3) {
         const d = Vec3.dot(this.dir[i], p);

src/mol-math/geometry/lookup3d/grid.ts

@@ -27,7 +27,7 @@ class GridLookup3DImpl<T extends number = number> implements GridLookup3D<T> {
     private ctx: QueryContext;
     boundary: Lookup3D['boundary'];
     buckets: GridLookup3D['buckets'];
-    result: Result<T>
+    result: Result<T>;
 
     find(x: number, y: number, z: number, radius: number, result?: Result<T>): Result<T> {
         this.ctx.x = x;

src/mol-math/geometry/symmetry-operator.ts

@@ -59,7 +59,9 @@ namespace SymmetryOperator {
         ncsId = ncsId || -1;
         const suffix = getSuffix(info);
         if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
-        if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
+        if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) {
+            console.warn(`Symmetry operator (${name}) should be a composition of rotation and translation.`);
+        }
         return { name, assembly, matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId, suffix };
     }
 

src/mol-math/graph/inter-unit-graph.ts

@@ -11,11 +11,11 @@ export { InterUnitGraph };
 
 class InterUnitGraph<UnitId extends number, VertexIndex extends number, EdgeProps extends InterUnitGraph.EdgePropsBase = {}> {
     /** Number of inter-unit edges */
-    readonly edgeCount: number
+    readonly edgeCount: number;
     /** Array of inter-unit edges */
-    readonly edges: ReadonlyArray<InterUnitGraph.Edge<UnitId, VertexIndex, EdgeProps>>
-    private readonly edgeKeyIndex: Map<string, number>
-    private readonly vertexKeyIndex: Map<string, number[]>
+    readonly edges: ReadonlyArray<InterUnitGraph.Edge<UnitId, VertexIndex, EdgeProps>>;
+    private readonly edgeKeyIndex: Map<string, number>;
+    private readonly vertexKeyIndex: Map<string, number[]>;
 
     /** Get an array of unit-pair-edges that are connected to the given unit */
     getConnectedUnits(unit: UnitId): ReadonlyArray<InterUnitGraph.UnitPairEdges<UnitId, VertexIndex, EdgeProps>> {
@@ -134,13 +134,13 @@ namespace InterUnitGraph {
 
 
     export class Builder<UnitId extends number, VertexIndex extends number, EdgeProps extends InterUnitGraph.EdgePropsBase = {}> {
-        private uA: UnitId
-        private uB: UnitId
-        private mapAB: Map<number, EdgeInfo<VertexIndex, EdgeProps>[]>
-        private mapBA: Map<number, EdgeInfo<VertexIndex, EdgeProps>[]>
-        private linkedA: UniqueArray<VertexIndex, VertexIndex>
-        private linkedB: UniqueArray<VertexIndex, VertexIndex>
-        private linkCount: number
+        private uA: UnitId;
+        private uB: UnitId;
+        private mapAB: Map<number, EdgeInfo<VertexIndex, EdgeProps>[]>;
+        private mapBA: Map<number, EdgeInfo<VertexIndex, EdgeProps>[]>;
+        private linkedA: UniqueArray<VertexIndex, VertexIndex>;
+        private linkedB: UniqueArray<VertexIndex, VertexIndex>;
+        private linkCount: number;
 
         private map = new Map<number, UnitPairEdges<UnitId, VertexIndex, EdgeProps>[]>();
 

src/mol-model-formats/structure/common/component.ts

@@ -98,12 +98,12 @@ const CharmmIonComponents = (function () {
 })();
 
 export class ComponentBuilder {
-    private namesMap = new Map<string, string>()
-    private comps = new Map<string, Component>()
-    private ids: string[] = []
-    private names: string[] = []
-    private types: mmCIF_chemComp_schema['type']['T'][] = []
-    private mon_nstd_flags: mmCIF_chemComp_schema['mon_nstd_flag']['T'][] = []
+    private namesMap = new Map<string, string>();
+    private comps = new Map<string, Component>();
+    private ids: string[] = [];
+    private names: string[] = [];
+    private types: mmCIF_chemComp_schema['type']['T'][] = [];
+    private mon_nstd_flags: mmCIF_chemComp_schema['mon_nstd_flag']['T'][] = [];
 
     private set(c: Component) {
         this.comps.set(c.id, c);

src/mol-model-formats/structure/common/entity.ts

@@ -14,16 +14,16 @@ export type EntityCompound = { chains: string[], description: string }
 type EntityType = 'water' | 'polymer' | 'non-polymer'
 
 export class EntityBuilder {
-    private count = 0
-    private ids: string[] = []
-    private types: EntityType[] = []
-    private descriptions: string[][] = []
+    private count = 0;
+    private ids: string[] = [];
+    private types: EntityType[] = [];
+    private descriptions: string[][] = [];
 
-    private compoundsMap = new Map<string, string>()
-    private namesMap = new Map<string, string>()
-    private heteroMap = new Map<string, string>()
-    private chainMap = new Map<string, string>()
-    private waterId?: string
+    private compoundsMap = new Map<string, string>();
+    private namesMap = new Map<string, string>();
+    private heteroMap = new Map<string, string>();
+    private chainMap = new Map<string, string>();
+    private waterId?: string;
 
     private set(type: EntityType, description: string) {
         this.count += 1;

src/mol-model-formats/structure/common/property.ts

@@ -9,8 +9,8 @@ import { ModelFormat } from '../../format';
 import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 class FormatRegistry<T> {
-    private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()
-    private applicable = new Map<ModelFormat['kind'], (model: Model) => boolean>()
+    private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>();
+    private applicable = new Map<ModelFormat['kind'], (model: Model) => boolean>();
 
     add(kind: ModelFormat['kind'], obtain: (model: Model) => T | undefined, applicable?: (model: Model) => boolean) {
         this.map.set(kind, obtain);

src/mol-model-props/common/custom-property.ts

@@ -42,8 +42,8 @@ namespace CustomProperty {
     }
 
     export class Registry<Data> {
-        private providers = OrderedMap<string, Provider<Data, any, any>>().asMutable()
-        private defaultAutoAttachValues = new Map<string, boolean>()
+        private providers = OrderedMap<string, Provider<Data, any, any>>().asMutable();
+        private defaultAutoAttachValues = new Map<string, boolean>();
 
         /** Get params for all applicable property providers */
         getParams(data?: Data) {

src/mol-model-props/computed/interactions/common.ts

@@ -85,7 +85,7 @@ namespace InteractionsIntraContacts {
 
 export { InteractionsInterContacts };
 class InteractionsInterContacts extends InterUnitGraph<number, Features.FeatureIndex, InteractionsInterContacts.Props> {
-    private readonly elementKeyIndex: Map<string, number[]>
+    private readonly elementKeyIndex: Map<string, number[]>;
 
     getContactIndicesForElement(index: StructureElement.UnitIndex, unit: Unit): ReadonlyArray<number> {
         return this.elementKeyIndex.get(this.getElementKey(index, unit.id)) || [];

src/mol-model-props/integrative/pair-restraints.ts

@@ -20,8 +20,8 @@ function getPairKey(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: Str
 }
 
 export class PairRestraints<T extends PairRestraint> {
-    readonly count: number
-    private readonly pairKeyIndices: Map<string, number[]>
+    readonly count: number;
+    private readonly pairKeyIndices: Map<string, number[]>;
 
     /** Indices into this.pairs */
     getPairIndices(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): ReadonlyArray<number> {

src/mol-model/sequence/alignment/alignment.ts

@@ -21,11 +21,11 @@ export function align(seqA: ArrayLike<string>, seqB: ArrayLike<string>, options:
 }
 
 class Alignment {
-    readonly gapPenalty: number; readonly gapExtensionPenalty: number
-    readonly substMatrix: SubstitutionMatrixData | undefined
+    readonly gapPenalty: number; readonly gapExtensionPenalty: number;
+    readonly substMatrix: SubstitutionMatrixData | undefined;
 
-    readonly n: number; readonly m: number
-    readonly S: number[][] = []; readonly V: number[][] = []; readonly H: number[][] = []
+    readonly n: number; readonly m: number;
+    readonly S: number[][] = []; readonly V: number[][] = []; readonly H: number[][] = [];
 
     constructor(readonly seqA: ArrayLike<string>, readonly seqB: ArrayLike<string>, options: AlignmentOptions) {
         this.gapPenalty = options.gapPenalty;

src/mol-model/sequence/sequence.ts

@@ -86,14 +86,14 @@ namespace Sequence {
     }
 
     class ResidueNamesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
-        public length: number
-        public code: Column<Alphabet>
-        public label: Column<string>
-        public seqId: Column<number>
-        public compId: Column<string>
-        public microHet: ReadonlyMap<number, string[]> = new Map()
+        public length: number;
+        public code: Column<Alphabet>;
+        public label: Column<string>;
+        public seqId: Column<number>;
+        public compId: Column<string>;
+        public microHet: ReadonlyMap<number, string[]> = new Map();
 
-        private indexMap: Map<number, number>
+        private indexMap: Map<number, number>;
         index(seqId: number) {
             return this.indexMap.get(seqId)!;
         }
@@ -158,14 +158,14 @@ namespace Sequence {
     }
 
     class SequenceRangesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
-        public length: number
-        public code: Column<Alphabet>
-        public label: Column<string>
-        public seqId: Column<number>
-        public compId: Column<string>
-        public microHet: ReadonlyMap<number, string[]> = new Map()
+        public length: number;
+        public code: Column<Alphabet>;
+        public label: Column<string>;
+        public seqId: Column<number>;
+        public compId: Column<string>;
+        public microHet: ReadonlyMap<number, string[]> = new Map();
 
-        private minSeqId: number
+        private minSeqId: number;
         index(seqId: number) {
             return seqId - this.minSeqId;
         }

src/mol-model/structure/model/model.ts

@@ -286,6 +286,11 @@ export namespace Model {
         for (let i = 0, il = db.database_2.database_id.rowCount; i < il; ++i) {
             if (db.database_2.database_id.value(i) === 'PDB') return true;
         }
+        return false;
+    }
+
+    export function hasPdbId(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
         return (
             // 4 character PDB id
             model.entryId.match(/^[1-9][a-z0-9]{3,3}$/i) !== null ||
@@ -381,7 +386,7 @@ export namespace Model {
         const { db } = model.sourceData.data;
         return hasDensityMap(model) || (
             // check if from pdb archive but missing relevant meta data
-            isFromPdbArchive(model) && (
+            hasPdbId(model) && (
                 !db.exptl.method.isDefined ||
                 (isFromXray(model) && (
                     !db.pdbx_database_status.status_code_sf.isDefined ||

src/mol-model/structure/model/properties/atomic/hierarchy.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -206,6 +206,12 @@ export interface AtomicIndex {
      */
     findAtomsOnResidue(residueIndex: ResidueIndex, label_atom_ids: Set<string>): ElementIndex
 
+    /**
+     * Find element index of an atom on a given residue.
+     * @returns index or -1 if the atom is not present.
+     */
+    findElementOnResidue(residueIndex: ResidueIndex, type_symbol: ElementSymbol): ElementIndex
+
     // TODO: add indices that support comp_id?
 }
 

src/mol-model/structure/model/properties/utils/atomic-derived.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>
  */
@@ -7,7 +7,7 @@
 import { AtomicData, AtomNumber } from '../atomic';
 import { AtomicIndex, AtomicDerivedData, AtomicSegments } from '../atomic/hierarchy';
 import { ElementIndex, ResidueIndex } from '../../indexing';
-import { MoleculeType, getMoleculeType, getComponentType, PolymerType, getPolymerType } from '../../types';
+import { MoleculeType, getMoleculeType, getComponentType, PolymerType, getPolymerType, isPolymer, ElementSymbol } from '../../types';
 import { getAtomIdForAtomRole } from '../../../../../mol-model/structure/util';
 import { ChemicalComponentMap } from '../common';
 import { isProductionMode } from '../../../../../mol-util/debug';
@@ -63,6 +63,9 @@ export function getAtomicDerivedData(data: AtomicData, segments: AtomicSegments,
         if (traceIndex === -1) {
             const coarseAtomId = getAtomIdForAtomRole(polyType, 'coarseBackbone');
             traceIndex = index.findAtomsOnResidue(i, coarseAtomId);
+            if (traceIndex === -1 && isPolymer(molType)) {
+                traceIndex = index.findElementOnResidue(i, ElementSymbol('C'));
+            }
         }
         traceElementIndex[i] = traceIndex;
 

src/mol-model/structure/model/properties/utils/atomic-index.ts

@@ -1,5 +1,5 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -12,6 +12,7 @@ import { ChainIndex, ResidueIndex, EntityIndex, ElementIndex } from '../../index
 import { AtomicIndex, AtomicHierarchy } from '../atomic/hierarchy';
 import { cantorPairing } from '../../../../../mol-data/util';
 import { Column } from '../../../../../mol-data/db';
+import { ElementSymbol } from '../../types';
 
 function getResidueId(seq_id: number, ins_code: string) {
     if (!ins_code) return seq_id;
@@ -43,6 +44,7 @@ interface Mapping {
     label_atom_id: Column<string>,
     auth_atom_id: Column<string>,
     label_alt_id: Column<string>,
+    type_symbol: Column<ElementSymbol>,
     segments: AtomicSegments,
 
     chain_index_entity_index: EntityIndex[],
@@ -64,6 +66,7 @@ function createMapping(entities: Entities, data: AtomicData, segments: AtomicSeg
         label_atom_id: data.atoms.label_atom_id,
         auth_atom_id: data.atoms.auth_atom_id,
         label_alt_id: data.atoms.label_alt_id,
+        type_symbol: data.atoms.type_symbol,
         chain_index_entity_index: new Int32Array(data.chains._rowCount) as any,
         entity_index_label_asym_id: new Map(),
         chain_index_label_seq_id: new Map(),
@@ -173,6 +176,10 @@ class Index implements AtomicIndex {
         return findAtomByNames(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, label_atom_ids);
     }
 
+    findElementOnResidue(rI: ResidueIndex, type_symbol: ElementSymbol) {
+        return findAtomByElement(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.type_symbol, type_symbol);
+    }
+
     constructor(private map: Mapping) {
         this.entityIndex = map.entities.getEntityIndex;
         this.residueOffsets = this.map.segments.residueAtomSegments.offsets;
@@ -201,6 +208,13 @@ function findAtomByNameAndAltLoc(start: ElementIndex, end: ElementIndex, nameDat
     return -1 as ElementIndex;
 }
 
+function findAtomByElement(start: ElementIndex, end: ElementIndex, data: Column<ElementSymbol>, typeSymbol: ElementSymbol): ElementIndex {
+    for (let i = start; i < end; i++) {
+        if (data.value(i) === typeSymbol) return i;
+    }
+    return -1 as ElementIndex;
+}
+
 export function getAtomicIndex(data: AtomicData, entities: Entities, segments: AtomicSegments): AtomicIndex {
     const map = createMapping(entities, data, segments);
 

src/mol-model/structure/model/types.ts

@@ -321,6 +321,12 @@ export function getMoleculeType(compType: string, compId: string): MoleculeType
         if (SaccharideCompIdMap.has(compId)) {
             // trust our saccharide table more than given 'non-polymer' or 'other' component type
             return MoleculeType.Saccharide;
+        } else if (AminoAcidNames.has(compId)) {
+            return MoleculeType.Protein;
+        } else if (RnaBaseNames.has(compId)) {
+            return MoleculeType.RNA;
+        } else if (DnaBaseNames.has(compId)) {
+            return MoleculeType.DNA;
         } else {
             return MoleculeType.Other;
         }

src/mol-model/structure/structure/structure.ts

@@ -938,7 +938,7 @@ namespace Structure {
 
     export class StructureBuilder {
         private units: Unit[] = [];
-        private invariantId = idFactory()
+        private invariantId = idFactory();
 
         private chainGroupId = -1;
         private inChainGroup = false;

src/mol-model/structure/structure/unit/bonds.ts

@@ -180,18 +180,18 @@ namespace Bond {
     }
 
     export class ElementBondIterator implements Iterator<ElementBondData> {
-        private current: ElementBondData = {} as any
+        private current: ElementBondData = {} as any;
 
-        private structure: Structure
-        private unit: Unit.Atomic
-        private index: StructureElement.UnitIndex
+        private structure: Structure;
+        private unit: Unit.Atomic;
+        private index: StructureElement.UnitIndex;
 
-        private interBondIndices: ReadonlyArray<number>
-        private interBondCount: number
-        private interBondIndex: number
+        private interBondIndices: ReadonlyArray<number>;
+        private interBondCount: number;
+        private interBondIndex: number;
 
-        private intraBondEnd: number
-        private intraBondIndex: number
+        private intraBondEnd: number;
+        private intraBondIndex: number;
 
         hasNext: boolean;
         move(): ElementBondData {

src/mol-model/structure/structure/unit/rings.ts

@@ -29,7 +29,7 @@ class UnitRings {
         readonly ringComponentIndex: ReadonlyArray<UnitRings.ComponentIndex>,
         readonly ringComponents: ReadonlyArray<ReadonlyArray<UnitRings.Index>>
     };
-    private _aromaticRings?: ReadonlyArray<UnitRings.Index>
+    private _aromaticRings?: ReadonlyArray<UnitRings.Index>;
 
     private get index() {
         if (this._index) return this._index;
@@ -122,6 +122,7 @@ namespace UnitRing {
         }
         if (aromaticBondCount === 2 * ring.length) return true;
         if (!hasAromaticRingElement) return false;
+        if (ring.length < 5) return false;
 
         const ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring));
         return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold;

src/mol-model/structure/structure/util/unit-transforms.ts

@@ -12,8 +12,8 @@ import { fillIdentityTransform } from '../../../../mol-geo/geometry/transform-da
 const tmpMat = Mat4();
 
 export class StructureUnitTransforms {
-    private unitTransforms: Float32Array
-    private groupUnitTransforms: Float32Array[] = []
+    private unitTransforms: Float32Array;
+    private groupUnitTransforms: Float32Array[] = [];
     /** maps unit.id to offset of transform in unitTransforms */
     private unitOffsetMap = IntMap.Mutable<number>();
     private groupIndexMap = IntMap.Mutable<number>();

src/mol-plugin-state/actions/structure.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -18,19 +18,23 @@ import { Download } from '../transforms/data';
 import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
 import { Asset } from '../../mol-util/assets';
 import { PluginConfig } from '../../mol-plugin/config';
+import { getFileInfo } from '../../mol-util/file-info';
 
-const DownloadModelRepresentationOptions = (plugin: PluginContext) => PD.Group({
-    type: RootStructureDefinition.getParams(void 0, 'auto').type,
-    representation: PD.Select(PresetStructureRepresentations.auto.id,
-        plugin.builders.structure.representation.getPresets().map(p => [p.id, p.display.name, p.display.group] as any),
-        { description: 'Which representation preset to use.' }),
-    representationParams: PD.Group(StructureRepresentationPresetProvider.CommonParams, { isHidden: true }),
-    asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
-}, { isExpanded: false });
+const DownloadModelRepresentationOptions = (plugin: PluginContext) => {
+    const representationDefault = plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+    return PD.Group({
+        type: RootStructureDefinition.getParams(void 0, 'auto').type,
+        representation: PD.Select(representationDefault,
+            plugin.builders.structure.representation.getPresets().map(p => [p.id, p.display.name, p.display.group] as any),
+            { description: 'Which representation preset to use.' }),
+        representationParams: PD.Group(StructureRepresentationPresetProvider.CommonParams, { isHidden: true }),
+        asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
+    }, { isExpanded: false });
+};
 
 export const PdbDownloadProvider = {
     'rcsb': PD.Group({
-        encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
+        encoding: PD.Select('bcif', PD.arrayToOptions(['cif', 'bcif'] as const)),
     }, { label: 'RCSB PDB', isFlat: true }),
     'pdbe': PD.Group({
         variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'updtaed-bcif' | 'archival', string][]),
@@ -58,7 +62,7 @@ const DownloadStructure = StateAction.build({
                 'pdb-dev': PD.Group({
                     provider: PD.Group({
                         id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
-                        encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
+                        encoding: PD.Select('bcif', PD.arrayToOptions(['cif', 'bcif'] as const)),
                     }, { pivot: 'id' }),
                     options
                 }, { isFlat: true, label: 'PDBDEV' }),
@@ -66,6 +70,14 @@ const DownloadStructure = StateAction.build({
                     id: PD.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
                     options
                 }, { isFlat: true, label: 'SWISS-MODEL', description: 'Loads the best homology model or experimental structure' }),
+                'alphafolddb': PD.Group({
+                    id: PD.Text('Q8W3K0', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
+                    options
+                }, { isFlat: true, label: 'AlphaFold DB', description: 'Loads the predicted model if available' }),
+                'modelarchive': PD.Group({
+                    id: PD.Text('ma-bak-cepc-0003', { label: 'Accession Code(s)', description: 'One or more comma/space separated ACs.' }),
+                    options
+                }, { isFlat: true, label: 'Model Archive' }),
                 'pubchem': PD.Group({
                     id: PD.Text('2244,2245', { label: 'PubChem ID', description: 'One or more comma/space separated IDs.' }),
                     options
@@ -84,7 +96,7 @@ const DownloadStructure = StateAction.build({
 
     const src = params.source;
     let downloadParams: StateTransformer.Params<Download>[];
-    let asTrajectory = false, format: BuiltInTrajectoryFormat = 'mmcif';
+    let asTrajectory = false, format: BuiltInTrajectoryFormat | 'auto' = 'mmcif';
 
     switch (src.name) {
         case 'url':
@@ -92,7 +104,7 @@ const DownloadStructure = StateAction.build({
             format = src.params.format;
             break;
         case 'pdb':
-            downloadParams = src.params.provider.server.name === 'pdbe'
+            downloadParams = await (src.params.provider.server.name === 'pdbe'
                 ? src.params.provider.server.params.variant === 'updated'
                     ? getDownloadParams(src.params.provider.id, id => `https://www.ebi.ac.uk/pdbe/static/entry/${id.toLowerCase()}_updated.cif`, id => `PDBe: ${id} (updated cif)`, false)
                     : src.params.provider.server.params.variant === 'updated-bcif'
@@ -100,11 +112,12 @@ const DownloadStructure = StateAction.build({
                         : getDownloadParams(src.params.provider.id, id => `https://www.ebi.ac.uk/pdbe/static/entry/${id.toLowerCase()}.cif`, id => `PDBe: ${id} (cif)`, false)
                 : src.params.provider.server.params.encoding === 'cif'
                     ? getDownloadParams(src.params.provider.id, id => `https://files.rcsb.org/download/${id.toUpperCase()}.cif`, id => `RCSB: ${id} (cif)`, false)
-                    : getDownloadParams(src.params.provider.id, id => `https://models.rcsb.org/${id.toUpperCase()}.bcif`, id => `RCSB: ${id} (bcif)`, true);
+                    : getDownloadParams(src.params.provider.id, id => `https://models.rcsb.org/${id.toUpperCase()}.bcif`, id => `RCSB: ${id} (bcif)`, true)
+            );
             asTrajectory = !!src.params.options.asTrajectory;
             break;
         case 'pdb-dev':
-            downloadParams = getDownloadParams(src.params.provider.id,
+            downloadParams = await getDownloadParams(src.params.provider.id,
                 id => {
                     const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
                     return src.params.provider.encoding === 'bcif'
@@ -117,19 +130,34 @@ const DownloadStructure = StateAction.build({
             asTrajectory = !!src.params.options.asTrajectory;
             break;
         case 'swissmodel':
-            downloadParams = getDownloadParams(src.params.id, id => `https://swissmodel.expasy.org/repository/uniprot/${id.toUpperCase()}.pdb`, id => `SWISS-MODEL: ${id}`, false);
+            downloadParams = await getDownloadParams(src.params.id, id => `https://swissmodel.expasy.org/repository/uniprot/${id.toUpperCase()}.pdb`, id => `SWISS-MODEL: ${id}`, false);
             asTrajectory = !!src.params.options.asTrajectory;
             format = 'pdb';
             break;
+        case 'alphafolddb':
+            downloadParams = await getDownloadParams(src.params.id, async id => {
+                const url = `https://www.alphafold.ebi.ac.uk/api/prediction/${id.toUpperCase()}`;
+                const info = await plugin.runTask(plugin.fetch({ url, type: 'json' }));
+                if (Array.isArray(info) && info.length > 0) return info[0].cifUrl;
+                throw new Error(`No AlphaFold DB entry for '${id}'`);
+            }, id => `AlphaFold DB: ${id}`, false);
+            asTrajectory = !!src.params.options.asTrajectory;
+            format = 'mmcif';
+            break;
+        case 'modelarchive':
+            downloadParams = await getDownloadParams(src.params.id, id => `https://www.modelarchive.org/doi/10.5452/${id.toLowerCase()}.cif`, id => `Model Archive: ${id}`, false);
+            asTrajectory = !!src.params.options.asTrajectory;
+            format = 'mmcif';
+            break;
         case 'pubchem':
-            downloadParams = getDownloadParams(src.params.id, id => `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${id.trim()}/record/SDF/?record_type=3d`, id => `PubChem: ${id}`, false);
+            downloadParams = await getDownloadParams(src.params.id, id => `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${id.trim()}/record/SDF/?record_type=3d`, id => `PubChem: ${id}`, false);
             asTrajectory = !!src.params.options.asTrajectory;
             format = 'mol';
             break;
         default: throw new Error(`${(src as any).name} not supported.`);
     }
 
-    const representationPreset: any = params.source.params.options.representation || PresetStructureRepresentations.auto.id;
+    const representationPreset: any = params.source.params.options.representation || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
     const showUnitcell = representationPreset !== PresetStructureRepresentations.empty.id;
 
     const structure = src.params.options.type.name === 'auto' ? void 0 : src.params.options.type;
@@ -151,7 +179,11 @@ const DownloadStructure = StateAction.build({
         } else {
             for (const download of downloadParams) {
                 const data = await plugin.builders.data.download(download, { state: { isGhost: true } });
-                const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+                const provider = format === 'auto'
+                    ? plugin.dataFormats.auto(getFileInfo(Asset.getUrl(download.url)), data.cell?.obj!)
+                    : plugin.dataFormats.get(format);
+                if (!provider) throw new Error('unknown file format');
+                const trajectory = await plugin.builders.structure.parseTrajectory(data, provider);
 
                 await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
                     structure,
@@ -164,11 +196,11 @@ const DownloadStructure = StateAction.build({
     }).runInContext(ctx);
 }));
 
-function getDownloadParams(src: string, url: (id: string) => string, label: (id: string) => string, isBinary: boolean): StateTransformer.Params<Download>[] {
+async function getDownloadParams(src: string, url: (id: string) => string | Promise<string>, label: (id: string) => string, isBinary: boolean): Promise<StateTransformer.Params<Download>[]> {
     const ids = src.split(/[,\s]/).map(id => id.trim()).filter(id => !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)));
     const ret: StateTransformer.Params<Download>[] = [];
     for (const id of ids) {
-        ret.push({ url: Asset.Url(url(id)), isBinary, label: label(id) });
+        ret.push({ url: Asset.Url(await url(id)), isBinary, label: label(id) });
     }
     return ret;
 }
@@ -176,7 +208,7 @@ function getDownloadParams(src: string, url: (id: string) => string, label: (id:
 export const UpdateTrajectory = StateAction.build({
     display: { name: 'Update Trajectory' },
     params: {
-        action: PD.Select<'advance' | 'reset'>('advance', [['advance', 'Advance'], ['reset', 'Reset']]),
+        action: PD.Select('advance', PD.arrayToOptions(['advance', 'reset'] as const)),
         by: PD.Optional(PD.Numeric(1, { min: -1, max: 1, step: 1 }))
     }
 })(({ params, state }) => {

src/mol-plugin-state/builder/structure/hierarchy-preset.ts

@@ -17,6 +17,7 @@ import { Vec3 } from '../../../mol-math/linear-algebra';
 import { Model } from '../../../mol-model/structure';
 import { getStructureQuality } from '../../../mol-repr/util';
 import { OperatorNameColorThemeProvider } from '../../../mol-theme/color/operator-name';
+import { PluginConfig } from '../../../mol-plugin/config';
 
 export interface TrajectoryHierarchyPresetProvider<P = any, S = {}> extends PresetProvider<PluginStateObject.Molecule.Trajectory, P, S> { }
 export function TrajectoryHierarchyPresetProvider<P, S>(preset: TrajectoryHierarchyPresetProvider<P, S>) { return preset; }
@@ -61,7 +62,8 @@ const defaultPreset = TrajectoryHierarchyPresetProvider({
         const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
 
         const unitcell = params.showUnitcell === void 0 || !!params.showUnitcell ? await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true }) : void 0;
-        const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', params.representationPresetParams);
+        const representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+        const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, params.representationPresetParams);
 
         return {
             model,
@@ -112,7 +114,8 @@ const allModels = TrajectoryHierarchyPresetProvider({
             structures.push(structure);
 
             const quality = structure.obj ? getStructureQuality(structure.obj.data, { elementCountFactor: tr.frameCount }) : 'medium';
-            await builder.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'model-index' }, quality });
+            const representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+            await builder.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'model-index' }, quality });
         }
 
         return { models, structures };
@@ -137,7 +140,8 @@ async function applyCrystalSymmetry(props: { ijkMin: Vec3, ijkMax: Vec3, theme?:
     const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
 
     const unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: false });
-    const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: props.theme } });
+    const representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+    const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: props.theme } });
 
     return {
         model,
@@ -207,7 +211,8 @@ const crystalContacts = TrajectoryHierarchyPresetProvider({
         const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
 
         const unitcell = await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true });
-        const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } });
+        const representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+        const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } });
 
         return {
             model,

src/mol-plugin-state/formats/registry.ts

@@ -14,11 +14,11 @@ import { BuiltInShapeFormats } from './shape';
 import { BuiltInStructureFormats } from './structure';
 
 export class DataFormatRegistry {
-    private _list: { name: string, provider: DataFormatProvider }[] = []
-    private _map = new Map<string, DataFormatProvider>()
-    private _extensions: Set<string> | undefined = undefined
-    private _binaryExtensions: Set<string> | undefined = undefined
-    private _options: [string, string, string][] | undefined = undefined
+    private _list: { name: string, provider: DataFormatProvider }[] = [];
+    private _map = new Map<string, DataFormatProvider>();
+    private _extensions: Set<string> | undefined = undefined;
+    private _binaryExtensions: Set<string> | undefined = undefined;
+    private _options: [string, string, string][] | undefined = undefined;
 
     get types(): [string, string][] {
         return this._list.map(e => [e.name, e.provider.label] as [string, string]);

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -7,7 +7,7 @@
 
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { QueryContext, Structure, StructureQuery, StructureSelection, StructureProperties, StructureElement } from '../../mol-model/structure';
-import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol } from '../../mol-model/structure/model/types';
+import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol, PolymerNames } from '../../mol-model/structure/model/types';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { Expression } from '../../mol-script/language/expression';
@@ -320,33 +320,46 @@ const branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate
 ]), { category: StructureSelectionCategory.Internal, isHidden: true });
 
 const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
-    MS.struct.combinator.merge([
-        MS.struct.modifier.union([
-            MS.struct.generator.atomGroups({
-                'entity-test': MS.core.logic.and([
-                    MS.core.logic.or([
-                        MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
-                        MS.core.rel.neq([MS.ammp('entityPrdId'), ''])
-                    ]),
-                    MS.core.logic.not([MS.core.str.match([
-                        MS.re('(oligosaccharide|lipid|ion)', 'i'),
-                        MS.ammp('entitySubtype')
-                    ])])
+    MS.struct.modifier.exceptBy({
+        0: MS.struct.modifier.union([
+            MS.struct.combinator.merge([
+                MS.struct.modifier.union([
+                    MS.struct.generator.atomGroups({
+                        'entity-test': MS.core.logic.and([
+                            MS.core.logic.or([
+                                MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
+                                MS.core.rel.neq([MS.ammp('entityPrdId'), ''])
+                            ]),
+                            MS.core.logic.not([MS.core.str.match([
+                                MS.re('(oligosaccharide|lipid|ion)', 'i'),
+                                MS.ammp('entitySubtype')
+                            ])])
+                        ]),
+                        'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                        'residue-test': MS.core.logic.not([
+                            MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
+                        ])
+                    })
                 ]),
-                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                'residue-test': MS.core.logic.not([
-                    MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
+                MS.struct.modifier.union([
+                    MS.struct.generator.atomGroups({
+                        'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+                        'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                        'residue-test': _nonPolymerResidueTest
+                    })
                 ])
-            })
+            ]),
         ]),
-        MS.struct.modifier.union([
+        by: MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
                 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                'residue-test': _nonPolymerResidueTest
+                'residue-test': MS.core.set.has([
+                    MS.set(...SetUtils.toArray(PolymerNames)), MS.ammp('label_comp_id')
+                ])
             })
         ])
-    ]),
+    })
 ]), { category: StructureSelectionCategory.Type });
 
 // don't include branched entities as they have their own link representation
@@ -729,9 +742,9 @@ export const StructureSelectionQueries = {
 };
 
 export class StructureSelectionQueryRegistry {
-    list: StructureSelectionQuery[] = []
-    options: [StructureSelectionQuery, string, string][] = []
-    version = 1
+    list: StructureSelectionQuery[] = [];
+    options: [StructureSelectionQuery, string, string][] = [];
+    version = 1;
 
     add(q: StructureSelectionQuery) {
         this.list.push(q);

src/mol-plugin-state/manager/interactivity.ts

@@ -36,7 +36,7 @@ class InteractivityManager extends StatefulPluginComponent<InteractivityManagerS
     readonly lociSelects: InteractivityManager.LociSelectManager;
     readonly lociHighlights: InteractivityManager.LociHighlightManager;
 
-    private _props = PD.getDefaultValues(InteractivityManager.Params)
+    private _props = PD.getDefaultValues(InteractivityManager.Params);
 
     readonly events = {
         propsUpdated: this.ev()
@@ -84,9 +84,9 @@ namespace InteractivityManager {
 
     export abstract class LociMarkManager {
         protected providers: LociMarkProvider[] = [];
-        protected sel: StructureSelectionManager
+        protected sel: StructureSelectionManager;
 
-        readonly props: Readonly<Props> = PD.getDefaultValues(Params)
+        readonly props: Readonly<Props> = PD.getDefaultValues(Params);
 
         setProps(props: Partial<Props>) {
             Object.assign(this.props, props);
@@ -141,7 +141,7 @@ namespace InteractivityManager {
                 this.mark(p, MarkerAction.RemoveHighlight, noRender);
             }
             this.prev.length = 0;
-        }
+        };
 
         highlight(current: Representation.Loci, applyGranularity = true) {
             const normalized = this.normalizedLoci(current, applyGranularity);

src/mol-plugin-state/manager/loci-label.ts

@@ -41,7 +41,7 @@ export class LociLabelManager {
         this.showLabels();
     }
 
-    private locis: Representation.Loci[] = []
+    private locis: Representation.Loci[] = [];
 
     private mark(loci: Representation.Loci, action: MarkerAction) {
         const idx = this.locis.findIndex(l => Representation.Loci.areEqual(loci, l));
@@ -54,9 +54,9 @@ export class LociLabelManager {
         }
     }
 
-    private isDirty = false
-    private labels: LociLabel[] = []
-    private groupedLabels = new Map<string, LociLabel[]>()
+    private isDirty = false;
+    private labels: LociLabel[] = [];
+    private groupedLabels = new Map<string, LociLabel[]>();
 
     private showLabels() {
         this.ctx.behaviors.labels.highlight.next({ labels: this.getLabels() });

src/mol-plugin-state/manager/structure/component.ts

@@ -14,7 +14,7 @@ import { StateBuilder, StateObjectRef, StateTransformer } from '../../../mol-sta
 import { Task } from '../../../mol-task';
 import { ColorTheme } from '../../../mol-theme/color';
 import { SizeTheme } from '../../../mol-theme/size';
-import { UUID } from '../../../mol-util';
+import { shallowEqual, UUID } from '../../../mol-util';
 import { ColorNames } from '../../../mol-util/color/names';
 import { objectForEach } from '../../../mol-util/object';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -42,7 +42,7 @@ interface StructureComponentManagerState {
 class StructureComponentManager extends StatefulPluginComponent<StructureComponentManagerState> {
     readonly events = {
         optionsUpdated: this.ev<undefined>()
-    }
+    };
 
     get currentStructures() {
         return this.plugin.managers.structure.hierarchy.selection.structures;
@@ -82,7 +82,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
             if (r.cell.transform.transformer !== StructureRepresentation3D) continue;
 
             const params = r.cell.transform.params as StateTransformer.Params<StructureRepresentation3D>;
-            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || params.type.params.material !== material) {
+            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || !shallowEqual(params.type.params.material, material)) {
                 update.to(r.cell).update(old => {
                     old.type.params.ignoreHydrogens = ignoreHydrogens;
                     old.type.params.quality = quality;

src/mol-plugin-state/manager/structure/focus.ts

@@ -41,7 +41,7 @@ const HISTORY_CAPACITY = 8;
 export class StructureFocusManager extends StatefulPluginComponent<StructureFocusManagerState> {
     readonly events = {
         historyUpdated: this.ev<undefined>()
-    }
+    };
 
     readonly behaviors = {
         current: this.ev.behavior<FocusEntry | undefined>(void 0)

src/mol-plugin-state/manager/structure/hierarchy.ts

@@ -25,7 +25,7 @@ export class StructureHierarchyManager extends PluginComponent {
             models: [] as ReadonlyArray<ModelRef>,
             structures: [] as ReadonlyArray<StructureRef>
         }
-    }
+    };
 
     readonly behaviors = {
         selection: this.ev.behavior({
@@ -34,7 +34,7 @@ export class StructureHierarchyManager extends PluginComponent {
             models: this.selection.models,
             structures: this.selection.structures
         })
-    }
+    };
 
     private get dataState() {
         return this.plugin.state.data;

src/mol-plugin-state/manager/structure/selection.ts

@@ -45,9 +45,9 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
             remove: this.ev<StructureElement.Loci>(),
             clear: this.ev<undefined>()
         }
-    }
+    };
 
-    private referenceLoci: StructureElement.Loci | undefined
+    private referenceLoci: StructureElement.Loci | undefined;
 
     get entries() { return this.state.entries; }
     get additionsHistory() { return this.state.additionsHistory; }