3.0.1

emit drag event whenever started within viewport

CHANGELOG.md

@@ -6,6 +6,59 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.0.1] - 2022-01-27
+
+- Fix marking pass not working with ``transparentBackground``
+- Fix pdbe xray maps url not https
+- Fix entity-id color theme broken for non-IHM models
+- Improve/fix marking of ``InteractionsInterUnitVisual`` (mark when all contact-feature members are given)
+- Add missing "entity-id" and "enity-source" options for carbon coloring to "element-symbol" color theme
+- Fix VolumeServer/query CLI
+- Support automatic iso-value adjustment for VolumeServer data in ``Viewer.loadVolumeFromUrl``
+- Emit drag event whenever started within viewport (not only for non-empty loci)
+
+## [v3.0.0] - 2022-01-23
+
+- Assembly handling tweaks:
+    - Do not include suffix for "identity assembly operators"
+    - Do not include assembly-related categories to export if the structure was composed from an assembly
+    - Special case for ``structAsymMap`` if Mol* asym id operator mapping is present
+- Support for opening ZIP files with multiple entries
+- Add Model Export extension
+- Bugfix: Automatically treat empty string as "non-present" value in BinaryCIF writer.
+- Fix coarse model support in entity-id color theme
+- Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
+- Add custom colors to "element-symbol", "molecule-type", "residue-name", and "secondary-structure" themes
+- Support/bugfixes for ``atom_site.pdbx_sifts_xref`` categories
+- Improve/fix marking of ``InteractionsIntraUnitVisual`` (mark when all contact-feature members are given)
+
+## [v3.0.0-dev.10] - 2022-01-17
+
+- Fix ``getOperatorsForIndex``
+- Pass animation info (current frame & count) to state animations
+    - Fix camera stutter for "camera spin" animation
+- Add formal charge parsing support for MOL/SDF files (thanks @ptourlas)
+- [Breaking] Cleaner looking ``MembraneOrientationVisuals`` defaults
+- [Breaking] Add rock animation to trackball controls
+    - Add ``animate`` to ``TrackballControlsParams``, remove ``spin`` and ``spinSpeed``
+    - Add ``animate`` to ``SimpleSettingsParams``, remove ``spin``
+- Add "camera rock" state animation
+- Add support for custom colors to "molecule-type" theme
+- [Breaking] Add style parameter to "illustrative" color theme
+    - Defaults to "entity-id" style instead of "chain-id"
+- Add "illustrative" representation preset
+
+## [v3.0.0-dev.9] - 2022-01-09
+
+- Add PDBj as a ``pdb-provider`` option
+- Move Viewer APP to a separate file to allow use without importing light theme & index.html
+- Add symmetry support for mol2 files (only spacegroup setting 1)
+- Fix mol2 files element symbol assignment
+- Improve bond assignment from ``IndexPairBonds``
+    - Add ``key`` field for mapping to source data
+    - Fix assignment of bonds with unphysical length
+- Fix label/stats of single atom selection in multi-chain units
+
 ## [v3.0.0-dev.8] - 2021-12-31
 
 - Add ``PluginFeatureDetection`` and disable WBOIT in Safari 15.

README.md

@@ -11,6 +11,13 @@ When using Mol*, please cite:
 
 David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
 
+### Protein Data Bank Integrations
+
+- The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
+
+- [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
+
+
 ## Project Structure Overview
 
 The core of Mol* consists of these modules (see under `src/`):

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.0-dev.8",
+  "version": "3.0.1",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -13,7 +13,7 @@
   "scripts": {
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
-    "test": "npm run lint && jest",
+    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
     "jest": "jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "clean": "node ./scripts/clean.js",
@@ -86,45 +86,46 @@
     "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
     "Ludovic Autin <autin@scripps.edu>",
     "Michal Malý <michal.maly@ibt.cas.cz>",
-    "Jiří Černý <jiri.cerny@ibt.cas.cz>"
+    "Jiří Černý <jiri.cerny@ibt.cas.cz>",
+    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.1.0",
-    "@graphql-codegen/cli": "^2.3.0",
-    "@graphql-codegen/time": "^3.1.0",
-    "@graphql-codegen/typescript": "^2.4.1",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.1",
-    "@graphql-codegen/typescript-operations": "^2.2.1",
+    "@graphql-codegen/add": "^3.1.1",
+    "@graphql-codegen/cli": "^2.4.0",
+    "@graphql-codegen/time": "^3.1.1",
+    "@graphql-codegen/typescript": "^2.4.2",
+    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
+    "@graphql-codegen/typescript-graphql-request": "^4.3.3",
+    "@graphql-codegen/typescript-operations": "^2.2.2",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
-    "@types/jest": "^27.0.3",
-    "@typescript-eslint/eslint-plugin": "^5.5.0",
-    "@typescript-eslint/parser": "^5.5.0",
+    "@types/jest": "^27.4.0",
+    "@typescript-eslint/eslint-plugin": "^5.10.0",
+    "@typescript-eslint/parser": "^5.10.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^6.4.0",
-    "cpx2": "^4.0.0",
+    "concurrently": "^7.0.0",
+    "cpx2": "^4.1.2",
     "crypto-browserify": "^3.12.0",
     "css-loader": "^6.5.1",
-    "eslint": "^8.3.0",
+    "eslint": "^8.7.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.0.0",
-    "graphql": "^15.7.2",
-    "http-server": "^14.0.0",
-    "jest": "^27.3.1",
-    "mini-css-extract-plugin": "^2.4.5",
+    "graphql": "^16.2.0",
+    "http-server": "^14.1.0",
+    "jest": "^27.4.7",
+    "mini-css-extract-plugin": "^2.5.2",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass": "^1.43.5",
-    "sass-loader": "^12.3.0",
-    "simple-git": "^2.47.0",
+    "sass": "^1.49.0",
+    "sass-loader": "^12.4.0",
+    "simple-git": "^2.48.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^27.0.7",
-    "typescript": "^4.5.2",
-    "webpack": "^5.64.4",
+    "ts-jest": "^27.1.3",
+    "typescript": "^4.5.5",
+    "webpack": "^5.67.0",
     "webpack-cli": "^4.9.1"
   },
   "dependencies": {
@@ -132,22 +133,22 @@
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.10",
+    "@types/node": "^16.11.21",
     "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.37",
+    "@types/react": "^17.0.38",
     "@types/react-dom": "^17.0.11",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
-    "body-parser": "^1.19.0",
+    "body-parser": "^1.19.1",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.17.1",
+    "express": "^4.17.2",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.7",
-    "immutable": "^3.8.2",
-    "node-fetch": "^2.6.2",
-    "rxjs": "^7.4.0",
-    "swagger-ui-dist": "^4.1.1",
+    "immer": "^9.0.12",
+    "immutable": "^4.0.0",
+    "node-fetch": "^2.6.7",
+    "rxjs": "^7.5.2",
+    "swagger-ui-dist": "^4.2.1",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"
@@ -155,8 +156,5 @@
   "peerDependencies": {
     "react": "^17.0.2",
     "react-dom": "^17.0.2"
-  },
-  "optionalDependencies": {
-    "gl": "^4.9.2"
   }
 }

src/apps/viewer/app.ts

@@ -0,0 +1,491 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { CellPack } from '../../extensions/cellpack';
+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { GeometryExport } from '../../extensions/geo-export';
+import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
+import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
+import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { ModelExport } from '../../extensions/model-export';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { Volume } from '../../mol-model/volume';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
+import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
+import { createPluginUI } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectRef, StateObjectSelector } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+
+const CustomFormats = [
+    ['g3d', G3dProvider] as const
+];
+
+const Extensions = {
+    'cellpack': PluginSpec.Behavior(CellPack),
+    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
+    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
+    'g3d': PluginSpec.Behavior(G3DFormat),
+    'model-export': PluginSpec.Behavior(ModelExport),
+    'mp4-export': PluginSpec.Behavior(Mp4Export),
+    'geo-export': PluginSpec.Behavior(GeometryExport),
+    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+};
+
+const DefaultViewerOptions = {
+    customFormats: CustomFormats as [string, DataFormatProvider][],
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
+    collapseRightPanel: false,
+    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: PluginConfig.General.PixelScale.defaultValue,
+    pickScale: PluginConfig.General.PickScale.defaultValue,
+    pickPadding: PluginConfig.General.PickPadding.defaultValue,
+    enableWboit: PluginConfig.General.EnableWboit.defaultValue,
+    preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+};
+type ViewerOptions = typeof DefaultViewerOptions;
+
+export class Viewer {
+    constructor(public plugin: PluginUIContext) {
+    }
+
+    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
+        const definedOptions = {} as any;
+        // filter for defined properies only so the default values
+        // are property applied
+        for (const p of Object.keys(options) as (keyof ViewerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
+        const defaultSpec = DefaultPluginUISpec();
+
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
+            behaviors: [
+                ...defaultSpec.behaviors,
+                ...o.extensions.map(e => Extensions[e]),
+            ],
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
+            customFormats: o?.customFormats,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: o.collapseRightPanel ? 'hidden' : 'full',
+                        top: 'full',
+                    }
+                },
+            },
+            components: {
+                ...defaultSpec.components,
+                controls: {
+                    ...defaultSpec.components?.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                },
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+            },
+            config: [
+                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.PickScale, o.pickScale],
+                [PluginConfig.General.PickPadding, o.pickPadding],
+                [PluginConfig.General.EnableWboit, o.enableWboit],
+                [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
+            ]
+        };
+
+        const element = typeof elementOrId === 'string'
+            ? document.getElementById(elementOrId)
+            : elementOrId;
+        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
+        const plugin = await createPluginUI(element, spec, {
+            onBeforeUIRender: plugin => {
+                // the preset needs to be added before the UI renders otherwise
+                // "Download Structure" wont be able to pick it up
+                plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
+            }
+        });
+        return new Viewer(plugin);
+    }
+
+    setRemoteSnapshot(id: string) {
+        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
+        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
+    }
+
+    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
+        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
+    }
+
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'url',
+                params: {
+                    url: Asset.Url(url),
+                    format: format as any,
+                    isBinary,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const plugin = this.plugin;
+
+        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
+    }
+
+    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
+        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    }
+
+    loadPdb(pdb: string, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb' as const,
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue as any
+                        }
+                    },
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    loadPdbDev(pdbDev: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev' as const,
+                params: {
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    loadEmdb(emdb: string, options?: { detail?: number }) {
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds' as const,
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: options?.detail ?? 3,
+                }
+            }
+        }));
+    }
+
+    loadAlphaFoldDb(afdb: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'alphafolddb' as const,
+                params: {
+                    id: afdb,
+                    options: {
+                        ...params.source.params.options,
+                        representation: 'preset-structure-representation-ma-quality-assessment-plddt'
+                    },
+                }
+            }
+        }));
+    }
+
+    loadModelArchive(id: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'modelarchive' as const,
+                params: {
+                    id,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
+        const plugin = this.plugin;
+
+        if (!plugin.dataFormats.get(format)) {
+            throw new Error(`Unknown density format: ${format}`);
+        }
+
+        if (options?.isLazy) {
+            const update = this.plugin.build();
+            update.toRoot().apply(StateTransforms.Data.LazyVolume, {
+                url,
+                format,
+                entryId: options?.entryId,
+                isBinary,
+                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
+            });
+            return update.commit();
+        }
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+
+            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
+
+            const repr = plugin.build();
+            for (const iso of isovalues) {
+                const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume;
+                const volumeData = volume.cell!.obj!.data;
+                repr
+                    .to(volume)
+                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                        type: 'isosurface',
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
+                        color: 'uniform',
+                        colorParams: { value: iso.color }
+                    }));
+            }
+
+            await repr.commit();
+        });
+    }
+
+    /**
+     * @example
+     *  viewer.loadTrajectory({
+     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+     *      preset: 'all-models' // or 'default'
+     *  });
+     */
+    async loadTrajectory(params: LoadTrajectoryParams) {
+        const plugin = this.plugin;
+
+        let model: StateObjectSelector, coords: StateObjectSelector;
+
+        if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
+            const data = params.model.kind === 'model-data'
+                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+            const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
+            model = await plugin.builders.structure.createModel(trajectory);
+        } else {
+            const data = params.model.kind === 'topology-data'
+                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+            const provider = plugin.dataFormats.get(params.model.format);
+            model = await provider!.parse(plugin, data);
+        }
+
+        {
+            const data = params.coordinates.kind === 'coordinates-data'
+                ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
+                : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
+
+            const provider = plugin.dataFormats.get(params.coordinates.format);
+            coords = await provider!.parse(plugin, data);
+        }
+
+        const trajectory = await plugin.build().toRoot()
+            .apply(TrajectoryFromModelAndCoordinates, {
+                modelRef: model.ref,
+                coordinatesRef: coords.ref
+            }, { dependsOn: [model.ref, coords.ref] })
+            .commit();
+
+        const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
+
+        return { model, coords, preset };
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next(void 0);
+    }
+}
+
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams
+}
+
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative',
+    value: number,
+    color: Color,
+    alpha?: number,
+    volumeIndex?: number
+}
+
+export interface LoadTrajectoryParams {
+    model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
+    | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
+    | { kind: 'topology-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
+    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    modelLabel?: string,
+    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
+    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    coordinatesLabel?: string,
+    preset?: keyof PresetTrajectoryHierarchy
+}
+
+export const ViewerAutoPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-viewer-auto',
+    display: {
+        name: 'Automatic (w/ Annotation)', group: 'Annotation',
+        description: 'Show standard automatic representation but colored by quality assessment (if available in the model).'
+    },
+    isApplicable(a) {
+        return (
+            !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')) ||
+            !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))
+        );
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT'))) {
+            return await QualityAssessmentPLDDTPreset.apply(ref, params, plugin);
+        } else if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))) {
+            return await QualityAssessmentQmeanPreset.apply(ref, params, plugin);
+        } else {
+            return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
+        }
+    }
+});

src/apps/viewer/index.html

@@ -57,7 +57,7 @@
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
 
             molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
@@ -71,7 +71,7 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: !disableWboit,
+                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
                 preferWebgl1: preferWebgl1,
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();

src/apps/viewer/index.ts

@@ -1,484 +1,12 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
-import { CellPack } from '../../extensions/cellpack';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
-import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { GeometryExport } from '../../extensions/geo-export';
-import { 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 { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
-import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
-import { createPluginUI } from '../../mol-plugin-ui';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginConfig } from '../../mol-plugin/config';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { PluginState } from '../../mol-plugin/state';
-import { StateObjectRef, StateObjectSelector } from '../../mol-state';
-import { Asset } from '../../mol-util/assets';
-import { Color } from '../../mol-util/color';
-import '../../mol-util/polyfill';
-import { ObjectKeys } from '../../mol-util/type-helpers';
 import './embedded.html';
 import './favicon.ico';
 import './index.html';
-
 require('mol-plugin-ui/skin/light.scss');
-
-export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setDebugMode, setProductionMode } from '../../mol-util/debug';
-
-const CustomFormats = [
-    ['g3d', G3dProvider] as const
-];
-
-const Extensions = {
-    'cellpack': PluginSpec.Behavior(CellPack),
-    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
-    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
-    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
-    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
-    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
-    'g3d': PluginSpec.Behavior(G3DFormat),
-    'mp4-export': PluginSpec.Behavior(Mp4Export),
-    'geo-export': PluginSpec.Behavior(GeometryExport),
-    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
-};
-
-const DefaultViewerOptions = {
-    customFormats: CustomFormats as [string, DataFormatProvider][],
-    extensions: ObjectKeys(Extensions),
-    layoutIsExpanded: true,
-    layoutShowControls: true,
-    layoutShowRemoteState: true,
-    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
-    layoutShowSequence: true,
-    layoutShowLog: true,
-    layoutShowLeftPanel: true,
-    collapseLeftPanel: false,
-    collapseRightPanel: false,
-    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
-    pixelScale: PluginConfig.General.PixelScale.defaultValue,
-    pickScale: PluginConfig.General.PickScale.defaultValue,
-    pickPadding: PluginConfig.General.PickPadding.defaultValue,
-    enableWboit: PluginConfig.General.EnableWboit.defaultValue,
-    preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
-
-    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
-    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
-    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
-    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
-    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
-    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
-    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
-    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
-    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
-    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
-};
-type ViewerOptions = typeof DefaultViewerOptions;
-
-export class Viewer {
-    constructor(public plugin: PluginUIContext) {
-    }
-
-    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
-        const defaultSpec = DefaultPluginUISpec();
-
-        const spec: PluginUISpec = {
-            actions: defaultSpec.actions,
-            behaviors: [
-                ...defaultSpec.behaviors,
-                ...o.extensions.map(e => Extensions[e]),
-            ],
-            animations: [...defaultSpec.animations || []],
-            customParamEditors: defaultSpec.customParamEditors,
-            customFormats: o?.customFormats,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    controlsDisplay: o.layoutControlsDisplay,
-                    regionState: {
-                        bottom: 'full',
-                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
-                        right: o.collapseRightPanel ? 'hidden' : 'full',
-                        top: 'full',
-                    }
-                },
-            },
-            components: {
-                ...defaultSpec.components,
-                controls: {
-                    ...defaultSpec.components?.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                },
-                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
-            },
-            config: [
-                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
-                [PluginConfig.General.PixelScale, o.pixelScale],
-                [PluginConfig.General.PickScale, o.pickScale],
-                [PluginConfig.General.PickPadding, o.pickPadding],
-                [PluginConfig.General.EnableWboit, o.enableWboit],
-                [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
-                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
-                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
-                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
-                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
-                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
-                [PluginConfig.State.DefaultServer, o.pluginStateServer],
-                [PluginConfig.State.CurrentServer, o.pluginStateServer],
-                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
-                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
-                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
-                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
-                [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
-            ]
-        };
-
-        const element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        const plugin = await createPluginUI(element, spec, {
-            onBeforeUIRender: plugin => {
-                // the preset needs to be added before the UI renders otherwise
-                // "Download Structure" wont be able to pick it up
-                plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
-            }
-        });
-        return new Viewer(plugin);
-    }
-
-    setRemoteSnapshot(id: string) {
-        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
-        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
-    }
-
-    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
-        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
-    }
-
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'url',
-                params: {
-                    url: Asset.Url(url),
-                    format: format as any,
-                    isBinary,
-                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const plugin = this.plugin;
-
-        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
-        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
-
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
-    }
-
-    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
-        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
-        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
-    }
-
-    loadPdb(pdb: string, options?: LoadStructureOptions) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'pdb' as const,
-                params: {
-                    provider: {
-                        id: pdb,
-                        server: {
-                            name: provider,
-                            params: PdbDownloadProvider[provider].defaultValue as any
-                        }
-                    },
-                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    loadPdbDev(pdbDev: string) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'pdb-dev' as const,
-                params: {
-                    provider: {
-                        id: pdbDev,
-                        encoding: 'bcif',
-                    },
-                    options: params.source.params.options,
-                }
-            }
-        }));
-    }
-
-    loadEmdb(emdb: string, options?: { detail?: number }) {
-        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
-            source: {
-                name: 'pdb-emd-ds' as const,
-                params: {
-                    provider: {
-                        id: emdb,
-                        server: provider,
-                    },
-                    detail: options?.detail ?? 3,
-                }
-            }
-        }));
-    }
-
-    loadAlphaFoldDb(afdb: string) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'alphafolddb' as const,
-                params: {
-                    id: afdb,
-                    options: {
-                        ...params.source.params.options,
-                        representation: 'preset-structure-representation-ma-quality-assessment-plddt'
-                    },
-                }
-            }
-        }));
-    }
-
-    loadModelArchive(id: string) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'modelarchive' as const,
-                params: {
-                    id,
-                    options: params.source.params.options,
-                }
-            }
-        }));
-    }
-
-    /**
-     * @example Load X-ray density from volume server
-        viewer.loadVolumeFromUrl({
-            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
-            format: 'dscif',
-            isBinary: true
-        }, [{
-            type: 'relative',
-            value: 1.5,
-            color: 0x3362B2
-        }, {
-            type: 'relative',
-            value: 3,
-            color: 0x33BB33,
-            volumeIndex: 1
-        }, {
-            type: 'relative',
-            value: -3,
-            color: 0xBB3333,
-            volumeIndex: 1
-        }], {
-            entryId: ['2FO-FC', 'FO-FC'],
-            isLazy: true
-        });
-     * *********************
-     * @example Load EM density from volume server
-        viewer.loadVolumeFromUrl({
-            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
-            format: 'dscif',
-            isBinary: true
-        }, [{
-            type: 'relative',
-            value: 1,
-            color: 0x3377aa
-        }], {
-            entryId: 'EMD-30210',
-            isLazy: true
-        });
-     */
-    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
-        const plugin = this.plugin;
-
-        if (!plugin.dataFormats.get(format)) {
-            throw new Error(`Unknown density format: ${format}`);
-        }
-
-        if (options?.isLazy) {
-            const update = this.plugin.build();
-            update.toRoot().apply(StateTransforms.Data.LazyVolume, {
-                url,
-                format,
-                entryId: options?.entryId,
-                isBinary,
-                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
-            });
-            return update.commit();
-        }
-
-        return plugin.dataTransaction(async () => {
-            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
-
-            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
-            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
-
-            const repr = plugin.build();
-            for (const iso of isovalues) {
-                repr
-                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
-                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
-                        type: 'isosurface',
-                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                        color: 'uniform',
-                        colorParams: { value: iso.color }
-                    }));
-            }
-
-            await repr.commit();
-        });
-    }
-
-    /**
-     * @example
-     *  viewer.loadTrajectory({
-     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
-     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
-     *      preset: 'all-models' // or 'default'
-     *  });
-     */
-    async loadTrajectory(params: LoadTrajectoryParams) {
-        const plugin = this.plugin;
-
-        let model: StateObjectSelector, coords: StateObjectSelector;
-
-        if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
-            const data = params.model.kind === 'model-data'
-                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
-                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
-
-            const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
-            model = await plugin.builders.structure.createModel(trajectory);
-        } else {
-            const data = params.model.kind === 'topology-data'
-                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
-                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
-
-            const provider = plugin.dataFormats.get(params.model.format);
-            model = await provider!.parse(plugin, data);
-        }
-
-        {
-            const data = params.coordinates.kind === 'coordinates-data'
-                ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
-                : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
-
-            const provider = plugin.dataFormats.get(params.coordinates.format);
-            coords = await provider!.parse(plugin, data);
-        }
-
-        const trajectory = await plugin.build().toRoot()
-            .apply(TrajectoryFromModelAndCoordinates, {
-                modelRef: model.ref,
-                coordinatesRef: coords.ref
-            }, { dependsOn: [model.ref, coords.ref] })
-            .commit();
-
-        const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
-
-        return { model, coords, preset };
-    }
-
-    handleResize() {
-        this.plugin.layout.events.updated.next(void 0);
-    }
-}
-
-export interface LoadStructureOptions {
-    representationParams?: StructureRepresentationPresetProvider.CommonParams
-}
-
-export interface VolumeIsovalueInfo {
-    type: 'absolute' | 'relative',
-    value: number,
-    color: Color,
-    alpha?: number,
-    volumeIndex?: number
-}
-
-export interface LoadTrajectoryParams {
-    model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
-    | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
-    | { kind: 'topology-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
-    modelLabel?: string,
-    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
-    coordinatesLabel?: string,
-    preset?: keyof PresetTrajectoryHierarchy
-}
-
-export 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);
-        }
-    }
-});
+export * from './app';

src/examples/basic-wrapper/index.ts

@@ -74,12 +74,20 @@ class BasicWrapper {
     toggleSpin() {
         if (!this.plugin.canvas3d) return;
 
+        const trackball = this.plugin.canvas3d.props.trackball;
         PluginCommands.Canvas3D.SetSettings(this.plugin, {
-            settings: props => {
-                props.trackball.spin = !props.trackball.spin;
+            settings: {
+                trackball: {
+                    ...trackball,
+                    animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } }
+                }
             }
         });
-        if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
+        if (this.plugin.canvas3d.props.trackball.animate.name !== 'spin') {
+            PluginCommands.Camera.Reset(this.plugin, {});
+        }
     }
 
     private animateModelIndexTargetFps() {

src/examples/proteopedia-wrapper/index.ts

@@ -256,7 +256,16 @@ class MolStarProteopediaWrapper {
     toggleSpin() {
         if (!this.plugin.canvas3d) return;
         const trackball = this.plugin.canvas3d.props.trackball;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: {
+                trackball: {
+                    ...trackball,
+                    animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } }
+                }
+            }
+        });
     }
 
     viewport = {

src/extensions/anvil/representation.ts

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

src/extensions/model-export/export.ts

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

src/extensions/model-export/index.ts

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

src/extensions/model-export/ui.tsx

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

src/extensions/mp4-export/encoder.ts

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

src/extensions/rcsb/graphql/types.ts

@@ -4,7 +4,7 @@ export type InputMaybe<T> = Maybe<T>;
 export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
 export type MakeOptional<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]?: Maybe<T[SubKey]> };
 export type MakeMaybe<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]: Maybe<T[SubKey]> };
-// Generated on 2021-11-25T14:34:23-08:00
+// Generated on 2022-01-15T19:52:34-08:00
 
 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -11113,11 +11113,11 @@ export type RcsbUniprotAlignments = {
 
 export type RcsbUniprotAlignmentsCoreEntityAlignments = {
   /** Aligned region */
-  readonly aligned_regions?: Maybe<ReadonlyArray<Maybe<CoreEntityAlignmentsAlignedRegions>>>;
+  readonly aligned_regions: ReadonlyArray<Maybe<CoreEntityAlignmentsAlignedRegions>>;
   /** core_entity identifiers */
   readonly core_entity_identifiers?: Maybe<CoreEntityAlignmentsCoreEntityIdentifiers>;
   /** Alignment scores */
-  readonly scores?: Maybe<CoreEntityAlignmentsScores>;
+  readonly scores: CoreEntityAlignmentsScores;
 };
 
 export type RcsbUniprotAnnotation = {

src/mol-canvas3d/canvas3d.ts

@@ -404,7 +404,7 @@ namespace Canvas3D {
 
                 const ctx = { renderer, camera: cam, scene, helper };
                 if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    const forceOn = !cameraChanged && allowMulti && !controls.props.spin;
+                    const forceOn = !cameraChanged && allowMulti && !controls.isAnimating;
                     multiSampleHelper.render(ctx, p, true, forceOn);
                 } else {
                     passes.draw.render(ctx, p, true);
@@ -444,7 +444,7 @@ namespace Canvas3D {
             }
 
             draw();
-            if (!camera.transition.inTransition && !controls.props.spin && !webgl.isContextLost) {
+            if (!camera.transition.inTransition && !webgl.isContextLost) {
                 interactionHelper.tick(currentTime);
             }
         }

src/mol-canvas3d/controls/trackball.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -13,7 +13,7 @@ import { Viewport } from '../camera/util';
 import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys, GestureInput } from '../../mol-util/input/input-observer';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera } from '../camera';
-import { absMax } from '../../mol-math/misc';
+import { absMax, degToRad } from '../../mol-math/misc';
 import { Binding } from '../../mol-util/binding';
 
 const B = ButtonsType;
@@ -40,8 +40,16 @@ export const TrackballControlsParams = {
     zoomSpeed: PD.Numeric(7.0, { min: 1, max: 15, step: 1 }),
     panSpeed: PD.Numeric(1.0, { min: 0.1, max: 5, step: 0.1 }),
 
-    spin: PD.Boolean(false, { description: 'Spin the 3D scene around the x-axis in view space' }),
-    spinSpeed: PD.Numeric(1, { min: -20, max: 20, step: 1 }),
+    animate: PD.MappedStatic('off', {
+        off: PD.EmptyGroup(),
+        spin: PD.Group({
+            speed: PD.Numeric(1, { min: -20, max: 20, step: 1 }),
+        }, { description: 'Spin the 3D scene around the x-axis in view space' }),
+        rock: PD.Group({
+            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }),
+            angle: PD.Numeric(10, { min: 0, max: 90, step: 1 }, { description: 'How many degrees to rotate in each direction.' }),
+        }, { description: 'Rock the 3D scene around the x-axis in view space' })
+    }),
 
     staticMoving: PD.Boolean(true, { isHidden: true }),
     dynamicDampingFactor: PD.Numeric(0.2, {}, { isHidden: true }),
@@ -72,7 +80,8 @@ export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 
 export { TrackballControls };
 interface TrackballControls {
-    viewport: Viewport
+    readonly viewport: Viewport
+    readonly isAnimating: boolean
 
     readonly props: Readonly<TrackballControlsProps>
     setProps: (props: Partial<TrackballControlsProps>) => void
@@ -144,6 +153,11 @@ namespace TrackballControls {
             );
         }
 
+        function getRotateFactor() {
+            const aspectRatio = input.width / input.height;
+            return p.rotateSpeed * input.pixelRatio * aspectRatio;
+        }
+
         const rotAxis = Vec3();
         const rotQuat = Quat();
         const rotEyeDir = Vec3();
@@ -156,8 +170,7 @@ namespace TrackballControls {
             const dy = _rotCurr[1] - _rotPrev[1];
             Vec3.set(rotMoveDir, dx, dy, 0);
 
-            const aspectRatio = input.width / input.height;
-            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed * input.pixelRatio * aspectRatio;
+            const angle = Vec3.magnitude(rotMoveDir) * getRotateFactor();
 
             if (angle) {
                 Vec3.sub(_eye, camera.position, camera.target);
@@ -306,7 +319,10 @@ namespace TrackballControls {
         /** Update the object's position, direction and up vectors */
         function update(t: number) {
             if (lastUpdated === t) return;
-            if (p.spin && lastUpdated > 0) spin(t - lastUpdated);
+            if (lastUpdated > 0) {
+                if (p.animate.name === 'spin') spin(t - lastUpdated);
+                else if (p.animate.name === 'rock') rock(t - lastUpdated);
+            }
 
             Vec3.sub(_eye, camera.position, camera.target);
 
@@ -345,6 +361,7 @@ namespace TrackballControls {
             if (!isStart && !_isInteracting) return;
 
             _isInteracting = true;
+            resetRock(); // start rocking from the center after interactions
 
             const dragRotate = Binding.match(p.bindings.dragRotate, buttons, modifiers);
             const dragRotateZ = Binding.match(p.bindings.dragRotateZ, buttons, modifiers);
@@ -434,11 +451,34 @@ namespace TrackballControls {
 
         const _spinSpeed = Vec2.create(0.005, 0);
         function spin(deltaT: number) {
-            if (p.spinSpeed === 0) return;
+            if (p.animate.name !== 'spin' || p.animate.params.speed === 0 || _isInteracting) return;
 
-            const frameSpeed = (p.spinSpeed || 0) / 1000;
+            const frameSpeed = p.animate.params.speed / 1000;
             _spinSpeed[0] = 60 * Math.min(Math.abs(deltaT), 1000 / 8) / 1000 * frameSpeed;
-            if (!_isInteracting) Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
+            Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
+        }
+
+        let _rockPhase = 0;
+        const _rockSpeed = Vec2.create(0.005, 0);
+        function rock(deltaT: number) {
+            if (p.animate.name !== 'rock' || p.animate.params.speed === 0 || _isInteracting) return;
+
+            const dt = deltaT / 1000 * p.animate.params.speed;
+            const maxAngle = degToRad(p.animate.params.angle) / getRotateFactor();
+            const angleA = Math.sin(_rockPhase * Math.PI * 2) * maxAngle;
+            const angleB = Math.sin((_rockPhase + dt) * Math.PI * 2) * maxAngle;
+
+            _rockSpeed[0] = angleB - angleA;
+            Vec2.add(_rotCurr, _rotPrev, _rockSpeed);
+
+            _rockPhase += dt;
+            if (_rockPhase >= 1) {
+                _rockPhase = 0;
+            }
+        }
+
+        function resetRock() {
+            _rockPhase = 0;
         }
 
         function start(t: number) {
@@ -448,9 +488,13 @@ namespace TrackballControls {
 
         return {
             viewport,
+            get isAnimating() { return p.animate.name !== 'off'; },
 
             get props() { return p as Readonly<TrackballControlsProps>; },
             setProps: (props: Partial<TrackballControlsProps>) => {
+                if (props.animate?.name === 'rock' && p.animate.name !== 'rock') {
+                    resetRock(); // start rocking from the center
+                }
                 Object.assign(p, props);
             },
 

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

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

src/mol-canvas3d/passes/draw.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -310,12 +310,12 @@ export class DrawPass {
             const markingDepthTest = props.marking.ghostEdgeStrength < 1;
             if (markingDepthTest) {
                 this.marking.depthTarget.bind();
-                renderer.clear(false);
+                renderer.clear(false, true);
                 renderer.renderMarkingDepth(scene.primitives, camera, null);
             }
 
             this.marking.maskTarget.bind();
-            renderer.clear(false);
+            renderer.clear(false, true);
             renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
 
             this.marking.update(props.marking);

src/mol-gl/renderer.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -53,7 +53,7 @@ interface Renderer {
     readonly stats: RendererStats
     readonly props: Readonly<RendererProps>
 
-    clear: (toBackgroundColor: boolean) => void
+    clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void
     clearDepth: () => void
     update: (camera: ICamera) => void
 
@@ -523,13 +523,13 @@ namespace Renderer {
         };
 
         return {
-            clear: (toBackgroundColor: boolean) => {
+            clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => {
                 state.enable(gl.SCISSOR_TEST);
                 state.enable(gl.DEPTH_TEST);
                 state.colorMask(true, true, true, true);
                 state.depthMask(true);
 
-                if (transparentBackground) {
+                if (transparentBackground && !ignoreTransparentBackground) {
                     state.clearColor(0, 0, 0, 0);
                 } else if (toBackgroundColor) {
                     state.clearColor(bgColor[0], bgColor[1], bgColor[2], 1);

src/mol-io/reader/_spec/mol.spec.ts

@@ -1,5 +1,12 @@
+/**
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 
-import { parseMol } from '../mol/parser';
+import { parseMol, formalChargeMapper } from '../mol/parser';
 
 const MolString = `2244
   -OEChem-04072009073D
@@ -49,6 +56,48 @@ const MolString = `2244
  13 20  1  0  0  0  0
 M  END`;
 
+const MolStringWithAtomBlockCharge = `
+  Ketcher  1 72215442D 1   1.00000     0.00000     0
+
+  4  3  0  0  0  0            999 V2000
+    0.0000    0.0000    0.0000 C   0  1  0  0  0  0  0  0  0  0  0  0
+    0.8660    0.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8660    0.5000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+  1  4  2  0  0  0  0
+  3  1  1  0  0  0  0
+  2  1  1  0  0  0  0
+M  END`;
+
+const MolStringWithPropertyBlockCharge = `
+  Ketcher  1 72215442D 1   1.00000     0.00000     0
+
+  4  3  0  0  0  0            999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.8660    0.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8660    0.5000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+  1  4  2  0  0  0  0
+  3  1  1  0  0  0  0
+  2  1  1  0  0  0  0
+M  CHG  3   2  -1   3   1   4   1
+M  END`;
+
+const MolStringWithMultipleChargeLines = `
+  Ketcher  1 72215442D 1   1.00000     0.00000     0
+
+  4  3  0  0  0  0            999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.8660    0.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8660    0.5000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+  1  4  2  0  0  0  0
+  3  1  1  0  0  0  0
+  2  1  1  0  0  0  0
+M  CHG  1   2  -1
+M  CHG  2   3   1   4   1
+M  END`;
+
 describe('mol reader', () => {
     it('basic', async () => {
         const parsed = await parseMol(MolString).run();
@@ -70,4 +119,63 @@ describe('mol reader', () => {
         expect(bonds.atomIdxB.value(20)).toBe(20);
         expect(bonds.order.value(20)).toBe(1);
     });
+    it('property block charges', async () => {
+        const parsed = await parseMol(MolStringWithPropertyBlockCharge).run();
+        if (parsed.isError) {
+            throw new Error(parsed.message);
+        }
+        const { formalCharges } = parsed.result;
+
+        expect(formalCharges.atomIdx.rowCount).toBe(3);
+        expect(formalCharges.charge.rowCount).toBe(3);
+
+        expect(formalCharges.atomIdx.value(0)).toBe(2);
+        expect(formalCharges.atomIdx.value(1)).toBe(3);
+
+        expect(formalCharges.charge.value(0)).toBe(-1);
+        expect(formalCharges.charge.value(1)).toBe(1);
+    });
+    it('multiple charge lines', async () => {
+        const parsed = await parseMol(MolStringWithMultipleChargeLines).run();
+        if (parsed.isError) {
+            throw new Error(parsed.message);
+        }
+        const { formalCharges } = parsed.result;
+
+        expect(formalCharges.atomIdx.rowCount).toBe(3);
+        expect(formalCharges.charge.rowCount).toBe(3);
+
+        expect(formalCharges.atomIdx.value(0)).toBe(2);
+        expect(formalCharges.atomIdx.value(1)).toBe(3);
+
+        expect(formalCharges.charge.value(0)).toBe(-1);
+        expect(formalCharges.charge.value(1)).toBe(1);
+    });
+
+    it('atom block charge mapping', async () => {
+        expect(formalChargeMapper(7)).toBe(-3);
+        expect(formalChargeMapper(6)).toBe(-2);
+        expect(formalChargeMapper(5)).toBe(-1);
+        expect(formalChargeMapper(0)).toBe(0);
+        expect(formalChargeMapper(3)).toBe(1);
+        expect(formalChargeMapper(2)).toBe(2);
+        expect(formalChargeMapper(1)).toBe(3);
+        expect(formalChargeMapper(4)).toBe(0);
+    });
+    it('atom block charges', async () => {
+        const parsed = await parseMol(MolStringWithAtomBlockCharge).run();
+        if (parsed.isError) {
+            throw new Error(parsed.message);
+        }
+        const { atoms, formalCharges } = parsed.result;
+
+        /* No property block charges */
+        expect(formalCharges.atomIdx.rowCount).toBe(0);
+        expect(formalCharges.charge.rowCount).toBe(0);
+
+        expect(atoms.formal_charge.value(0)).toBe(1);
+        expect(atoms.formal_charge.value(1)).toBe(0);
+        expect(atoms.formal_charge.value(2)).toBe(0);
+        expect(atoms.formal_charge.value(3)).toBe(0);
+    });
 });

src/mol-io/reader/_spec/mol2.spec.ts

@@ -244,6 +244,84 @@ GASTEIGER
     25    13    23    1
     26    13    24    1`;
 
+const Mol2StringCrysin = `@<TRIPOS>MOLECULE
+1144204
+    12    11     2     0     0
+SMALL
+USER_CHARGES
+****
+Generated from the CSD
+
+@<TRIPOS>ATOM
+     1 Cl1      0.0925   3.6184   1.9845   Cl        1 RES1  -1.0000
+     2 C1      -4.7391   0.3350   0.4215   C.ar      2 RES2   0.0000
+     3 C2      -3.4121   0.2604   0.9351   C.ar      2 RES2   0.0000
+     4 C3      -2.9169   1.2555   1.7726   C.ar      2 RES2   0.0000
+     5 C4      -3.7118   2.3440   2.1099   C.ar      2 RES2   0.0000
+     6 C5      -5.0314   2.4052   1.6209   C.ar      2 RES2   0.0000
+     7 C6      -5.5372   1.4057   0.7962   C.ar      2 RES2   0.0000
+     8 C7      -6.9925   1.4547   0.3334   C.3       2 RES2   0.0000
+     9 C8      -7.8537   0.5554   1.1859   C.3       2 RES2   0.0000
+    10 N1      -9.3089   0.7134   0.8192   N.3       2 RES2   1.0000
+    11 O1      -2.6613  -0.8147   0.5707   O.3       2 RES2   0.0000
+    12 O2      -1.6204   1.0919   2.2584   O.3       2 RES2   0.0000
+@<TRIPOS>BOND
+     1     2     3   ar
+     2     3     4   ar
+     3     4     5   ar
+     4     5     6   ar
+     5     6     7   ar
+     6     7     2   ar
+     7     8     7    1
+     8     9     8    1
+     9    10     9    1
+    10    11     3    1
+    11    12     4    1
+@<TRIPOS>SUBSTRUCTURE
+     1 RES1        1 GROUP             0 ****  ****    0
+     2 RES2        2 GROUP             0 ****  ****    0
+@<TRIPOS>CRYSIN
+   10.5150   11.1300    7.9380   90.0000   90.0000   90.0000    29     5
+@<TRIPOS>MOLECULE
+   1144204
+    12    11     2     0     0
+SMALL
+USER_CHARGES
+****
+Generated from the CSD
+
+@<TRIPOS>ATOM
+     1 Cl1      0.0925   3.6184   1.9845   Cl        1 RES1  -1.0000
+     2 C1      -4.7391   0.3350   0.4215   C.ar      2 RES2   0.0000
+     3 C2      -3.4121   0.2604   0.9351   C.ar      2 RES2   0.0000
+     4 C3      -2.9169   1.2555   1.7726   C.ar      2 RES2   0.0000
+     5 C4      -3.7118   2.3440   2.1099   C.ar      2 RES2   0.0000
+     6 C5      -5.0314   2.4052   1.6209   C.ar      2 RES2   0.0000
+     7 C6      -5.5372   1.4057   0.7962   C.ar      2 RES2   0.0000
+     8 C7      -6.9925   1.4547   0.3334   C.3       2 RES2   0.0000
+     9 C8      -7.8537   0.5554   1.1859   C.3       2 RES2   0.0000
+    10 N1      -9.3089   0.7134   0.8192   N.3       2 RES2   1.0000
+    11 O1      -2.6613  -0.8147   0.5707   O.3       2 RES2   0.0000
+    12 O2      -1.6204   1.0919   2.2584   O.3       2 RES2   0.0000
+@<TRIPOS>BOND
+     1     2     3   ar
+     2     3     4   ar
+     3     4     5   ar
+     4     5     6   ar
+     5     6     7   ar
+     6     7     2   ar
+     7     8     7    1
+     8     9     8    1
+     9    10     9    1
+    10    11     3    1
+    11    12     4    1
+@<TRIPOS>SUBSTRUCTURE
+     1 RES1        1 GROUP             0 ****  ****    0
+     2 RES2        2 GROUP             0 ****  ****    0
+@<TRIPOS>CRYSIN
+   10.5150   11.1300    7.9380   90.0000   90.0000   90.0000    29     5
+`;
+
 describe('mol2 reader', () => {
     it('basic', async () => {
         const parsed = await parseMol2(Mol2String, '').run();
@@ -397,4 +475,29 @@ describe('mol2 reader', () => {
         // optional bond fields
         expect(bonds.status_bits.value(0)).toBe('');
     });
+
+    it('crysin', async () => {
+        const parsed = await parseMol2(Mol2StringCrysin, '').run();
+        if (parsed.isError) {
+            throw new Error(parsed.message);
+        }
+        const mol2File = parsed.result;
+
+        // number of structures
+        expect(mol2File.structures.length).toBe(2);
+
+        // crysin fields
+        for (const data of mol2File.structures) {
+            expect(data.crysin).toEqual({
+                a: 10.5150,
+                b: 11.1300,
+                c: 7.9380,
+                alpha: 90.0,
+                beta: 90.0,
+                gamma: 90.0,
+                spaceGroup: 29,
+                setting: 5
+            });
+        }
+    });
 });

src/mol-io/reader/_spec/sdf.spec.ts

@@ -1,3 +1,10 @@
+/**
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 
 import { parseSdf } from '../sdf/parser';
 
@@ -458,6 +465,38 @@ describe('sdf reader', () => {
         expect(compound3.dataItems.data.value(21)).toBe('2\n5\n10');
     });
 
+    it('charge parsing in V2000', async () => {
+        const parsed = await parseSdf(SdfString).run();
+        if (parsed.isError) {
+            throw new Error(parsed.message);
+        }
+        const compound1 = parsed.result.compounds[0];
+        const compound2 = parsed.result.compounds[1];
+        const compound3 = parsed.result.compounds[2];
+
+        const formalCharges1 = {
+            atomIdx: compound1.molFile.formalCharges.atomIdx,
+            charge: compound1.molFile.formalCharges.charge
+        };
+        const formalCharges2 = {
+            atomIdx: compound2.molFile.formalCharges.atomIdx,
+            charge: compound2.molFile.formalCharges.charge
+        };
+        const formalCharges3 = {
+            atomIdx: compound3.molFile.formalCharges.atomIdx,
+            charge: compound3.molFile.formalCharges.charge
+        };
+
+        expect(formalCharges1.atomIdx.rowCount).toBe(3);
+        expect(formalCharges2.atomIdx.rowCount).toBe(3);
+        expect(formalCharges3.atomIdx.rowCount).toBe(0);
+
+        expect(formalCharges1.charge.rowCount === formalCharges1.atomIdx.rowCount).toBe(true);
+        expect(formalCharges2.charge.rowCount === formalCharges2.atomIdx.rowCount).toBe(true);
+        expect(formalCharges3.charge.rowCount === formalCharges3.atomIdx.rowCount).toBe(true);
+    });
+
+
     it('v3000', async () => {
         const parsed = await parseSdf(V3000SdfString).run();
         if (parsed.isError) {
@@ -486,6 +525,11 @@ describe('sdf reader', () => {
         expect(compound1.molFile.bonds.atomIdxB.value(10)).toBe(9);
         expect(compound1.molFile.bonds.order.value(10)).toBe(2);
 
+        expect(compound1.molFile.formalCharges.atomIdx.rowCount).toBe(13);
+        for (let i = 0; i < compound1.molFile.atoms.count; i++) {
+            expect(compound1.molFile.formalCharges.charge.value(i)).toBe(0);
+        }
+
         expect(compound1.dataItems.dataHeader.rowCount).toBe(2);
         expect(compound1.dataItems.data.rowCount).toBe(2);
 

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

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 5.353, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */
@@ -682,7 +682,7 @@ export const mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased<'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'MDF' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
+        database_id: Aliased<'AFDB' | 'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'MA' | 'MDF' | 'MODBASE' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'SMR' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.

src/mol-io/reader/mol/parser.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 
 import { Column } from '../../../mol-data/db';
@@ -10,6 +11,7 @@ import { TokenColumnProvider as TokenColumn } from '../common/text/column/token'
 import { TokenBuilder, Tokenizer } from '../common/text/tokenizer';
 import { ReaderResult as Result } from '../result';
 
+
 /** Subset of the MolFile V2000 format */
 export interface MolFile {
     readonly title: string,
@@ -20,7 +22,8 @@ export interface MolFile {
         readonly x: Column<number>,
         readonly y: Column<number>,
         readonly z: Column<number>,
-        readonly type_symbol: Column<string>
+        readonly type_symbol: Column<string>,
+        readonly formal_charge: Column<number>
     },
     readonly bonds: {
         readonly count: number
@@ -28,6 +31,57 @@ export interface MolFile {
         readonly atomIdxB: Column<number>,
         readonly order: Column<number>
     }
+    readonly formalCharges: {
+        readonly atomIdx: Column<number>;
+        readonly charge: Column<number>;
+    }
+}
+
+/*
+    The atom lines in a .mol file have the following structure:
+
+    xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
+    ---------------------------------------------------------------------
+
+    Below is a breakdown of each component and its start/end indices:
+
+    xxxxx.xxxx  (X COORDINATE, 1-10)
+    yyyyy.yyyy  (Y COORDINATE, 10-20)
+    zzzzz.zzzz  (Z COORDINATE, 20-30)
+    _           (30 IS EMPTY)
+    aaa         (ATOM SYMBOL, 31-34)
+    dd          (MASS DIFF, 34-36)
+    ccc         (FORMAL CHARGE, 36-39)
+    sss         (ATOM STEREO PARITY, 39-42)
+    hhh         (HYDROGEN COUNT+1, 42-45)
+    bbb         (STEREO CARE BOX, 45-48)
+    vvv         (VALENCE, 48-51)
+    HHH         (H0 DESIGNATOR, 51-54)
+    rrr         (UNUSED, 54-57)
+    iii         (UNUSED, 57-60)
+    mmm         (ATOM-ATOM MAPPING NUMBER, 60-63)
+    nnn         (INVERSION/RETENTION FLAG, 63-66)
+    eee         (EXACT CHANGE FLAG, 66-69)
+*/
+
+/**
+ * @param key - The value found at the atom block.
+ * @returns The actual formal charge based on the mapping.
+ */
+export function formalChargeMapper(key: number) {
+    switch (key) {
+        case 7: return -3;
+        case 6: return -2;
+        case 5: return -1;
+        case 0: return 0;
+        case 3: return 1;
+        case 2: return 2;
+        case 1: return 3;
+        case 4: return 0;
+        default:
+            console.error(`Value ${key} is outside the 0-7 range, defaulting to 0.`);
+            return 0;
+    }
 }
 
 export function handleAtoms(tokenizer: Tokenizer, count: number): MolFile['atoms'] {
@@ -35,6 +89,7 @@ export function handleAtoms(tokenizer: Tokenizer, count: number): MolFile['atoms
     const y = TokenBuilder.create(tokenizer.data, count * 2);
     const z = TokenBuilder.create(tokenizer.data, count * 2);
     const type_symbol = TokenBuilder.create(tokenizer.data, count * 2);
+    const formal_charge = TokenBuilder.create(tokenizer.data, count * 2);
 
     for (let i = 0; i < count; ++i) {
         Tokenizer.markLine(tokenizer);
@@ -47,6 +102,8 @@ export function handleAtoms(tokenizer: Tokenizer, count: number): MolFile['atoms
         TokenBuilder.addUnchecked(z, tokenizer.tokenStart, tokenizer.tokenEnd);
         Tokenizer.trim(tokenizer, s + 31, s + 34);
         TokenBuilder.addUnchecked(type_symbol, tokenizer.tokenStart, tokenizer.tokenEnd);
+        Tokenizer.trim(tokenizer, s + 36, s + 39);
+        TokenBuilder.addUnchecked(formal_charge, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer.position = position;
     }
 
@@ -55,7 +112,8 @@ export function handleAtoms(tokenizer: Tokenizer, count: number): MolFile['atoms
         x: TokenColumn(x)(Column.Schema.float),
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
-        type_symbol: TokenColumn(type_symbol)(Column.Schema.str)
+        type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        formal_charge: TokenColumn(formal_charge)(Column.Schema.int)
     };
 }
 
@@ -84,6 +142,76 @@ export function handleBonds(tokenizer: Tokenizer, count: number): MolFile['bonds
     };
 }
 
+interface FormalChargesRawData {
+    atomIdx: Array<number>;
+    charge: Array<number>;
+}
+export function handleFormalCharges(tokenizer: Tokenizer, lineStart: number, formalCharges: FormalChargesRawData) {
+
+    Tokenizer.trim(tokenizer, lineStart + 6, lineStart + 9);
+    const numOfCharges = parseInt(Tokenizer.getTokenString(tokenizer));
+    for (let i = 0; i < numOfCharges; ++i) {
+        /*
+        M  CHG  3   1  -1   2   0   2  -1
+                |   |   |   |   |
+                |   |   |   |   |__charge2 (etc.)
+                |   |   |   |
+                |   |   |   |__atomIdx2
+                |   |   |
+                |   |   |__charge1
+                |   |
+                |   |__atomIdx1 (cursor at position 12)
+                |
+                |___numOfCharges
+        */
+        const offset = 9 + (i * 8);
+
+        Tokenizer.trim(tokenizer, lineStart + offset, lineStart + offset + 4);
+        const _atomIdx = Tokenizer.getTokenString(tokenizer);
+        formalCharges.atomIdx.push(+_atomIdx);
+        Tokenizer.trim(tokenizer, lineStart + offset + 4, lineStart + offset + 8);
+        const _charge = Tokenizer.getTokenString(tokenizer);
+        formalCharges.charge.push(+_charge);
+    }
+    /* Once the line is read, move to the next one. */
+    Tokenizer.eatLine(tokenizer);
+}
+
+/** Call an appropriate handler based on the property type.
+ * (For now it only calls the formal charge handler, additional handlers can
+ * be added for other properties.)
+ */
+export function handlePropertiesBlock(tokenizer: Tokenizer): MolFile['formalCharges'] {
+
+    const _atomIdx: Array<number> = [];
+    const _charge: Array<number> = [];
+    const _formalCharges: FormalChargesRawData = { atomIdx: _atomIdx, charge: _charge };
+
+    while (tokenizer.position < tokenizer.length) {
+        const { position: s } = tokenizer;
+
+        Tokenizer.trim(tokenizer, s + 3, s + 6);
+        const propertyType = Tokenizer.getTokenString(tokenizer);
+
+        if (propertyType === 'END') break;
+        Tokenizer.eatLine(tokenizer);
+
+        switch (propertyType) {
+            case 'CHG':
+                handleFormalCharges(tokenizer, s, _formalCharges);
+                break;
+            default:
+                break;
+        }
+    }
+
+    const formalCharges: MolFile['formalCharges'] = {
+        atomIdx: Column.ofIntArray(_formalCharges.atomIdx),
+        charge: Column.ofIntArray(_formalCharges.charge)
+    };
+    return formalCharges;
+}
+
 function parseInternal(data: string): Result<MolFile> {
     const tokenizer = Tokenizer(data);
 
@@ -98,12 +226,15 @@ function parseInternal(data: string): Result<MolFile> {
     const atoms = handleAtoms(tokenizer, atomCount);
     const bonds = handleBonds(tokenizer, bondCount);
 
+    const formalCharges = handlePropertiesBlock(tokenizer);
+
     const result: MolFile = {
         title,
         program,
         comment,
         atoms,
-        bonds
+        bonds,
+        formalCharges,
     };
     return Result.success(result);
 }

src/mol-io/reader/mol2/parser.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -259,6 +259,36 @@ async function handleBonds(state: State): Promise<Schema.Mol2Bonds> {
     return ret;
 }
 
+function handleCrysin(state: State) {
+    const { tokenizer } = state;
+
+    while (tokenizer.position < tokenizer.data.length) {
+        const l = getTokenString(tokenizer);
+        if (l === '@<TRIPOS>MOLECULE') {
+            return;
+        } else if (l === '@<TRIPOS>CRYSIN') {
+            break;
+        } else {
+            markLine(tokenizer);
+        }
+    }
+
+    if (tokenizer.position >= tokenizer.data.length) return;
+
+    markLine(tokenizer);
+    const values = getTokenString(tokenizer).trim().split(reWhitespace);
+    return {
+        a: parseFloat(values[0]),
+        b: parseFloat(values[1]),
+        c: parseFloat(values[2]),
+        alpha: parseFloat(values[3]),
+        beta: parseFloat(values[4]),
+        gamma: parseFloat(values[5]),
+        spaceGroup: parseInt(values[6], 10),
+        setting: parseInt(values[7], 10),
+    };
+}
+
 async function parseInternal(ctx: RuntimeContext, data: string, name: string): Promise<Result<Schema.Mol2File>> {
     const tokenizer = Tokenizer(data);
 
@@ -269,7 +299,8 @@ async function parseInternal(ctx: RuntimeContext, data: string, name: string): P
         handleMolecule(state);
         const atoms = await handleAtoms(state);
         const bonds = await handleBonds(state);
-        structures.push({ molecule: state.molecule, atoms, bonds });
+        const crysin = handleCrysin(state);
+        structures.push({ molecule: state.molecule, atoms, bonds, crysin });
         skipWhitespace(tokenizer);
         while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
             markLine(tokenizer);

src/mol-io/reader/mol2/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,6 +11,7 @@ import { Column } from '../../../mol-data/db';
 // @<TRIPOS>MOLECULE
 // @<TRIPOS>ATOM
 // @<TRIPOS>BOND
+// @<TRIPOS>CRYSIN
 //
 // note that the format is not a fixed column format but white space separated
 
@@ -56,10 +57,22 @@ export interface Mol2Bonds {
     status_bits: Column<string>
 }
 
+export interface Mol2Crysin {
+    a: number
+    b: number
+    c: number
+    alpha: number
+    beta: number
+    gamma: number
+    spaceGroup: number
+    setting: number
+}
+
 export interface Mol2Structure {
     molecule: Readonly<Mol2Molecule>,
     atoms: Readonly<Mol2Atoms>,
     bonds: Readonly<Mol2Bonds>
+    crysin?: Readonly<Mol2Crysin>
 }
 
 export interface Mol2File {

src/mol-io/reader/sdf/parser-v3-util.ts

@@ -1,3 +1,10 @@
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
+
 import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';
 import { Tokenizer, TokenBuilder, Tokens } from '../common/text/tokenizer';
@@ -61,6 +68,9 @@ export function handleAtomsV3(
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
         type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        /* No support for formal charge parsing in V3000 molfiles at the moment,
+        so all charges default to 0.*/
+        formal_charge: Column.ofConst(0, atomCount, Column.Schema.int)
     };
 }
 

src/mol-io/reader/sdf/parser.ts

@@ -1,12 +1,14 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 
 import { Column } from '../../../mol-data/db';
-import { MolFile, handleAtoms, handleBonds } from '../mol/parser';
+import { MolFile, handleAtoms, handleBonds, handlePropertiesBlock } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
@@ -29,6 +31,7 @@ export interface SdfFile {
 
 
 const delimiter = '$$$$';
+
 function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, data: Column<string> } {
     const dataHeader = TokenBuilder.create(tokenizer.data, 32);
     const data = TokenBuilder.create(tokenizer.data, 32);
@@ -93,12 +96,20 @@ function handleMolFile(tokenizer: Tokenizer) {
         return;
     }
 
+    /* No support for formal charge parsing in V3000 molfiles at the moment,
+    so all charges default to 0.*/
+    const nullFormalCharges: MolFile['formalCharges'] = {
+        atomIdx: Column.ofConst(0, atomCount, Column.Schema.int),
+        charge: Column.ofConst(0, atomCount, Column.Schema.int)
+    };
+
     const atoms = molIsV3 ? handleAtomsV3(tokenizer, atomCount) : handleAtoms(tokenizer, atomCount);
     const bonds = molIsV3 ? handleBondsV3(tokenizer, bondCount) : handleBonds(tokenizer, bondCount);
+    const formalCharges = molIsV3 ? nullFormalCharges : handlePropertiesBlock(tokenizer);
     const dataItems = handleDataItems(tokenizer);
 
     return {
-        molFile: { title, program, comment, atoms, bonds },
+        molFile: { title, program, comment, atoms, bonds, formalCharges },
         dataItems
     };
 }

src/mol-io/writer/cif/encoder/binary.ts

@@ -191,8 +191,14 @@ function getFieldData(field: Field<any, any>, arrayCtor: ArrayCtor<string | numb
                     array[offset] = '';
                 allPresent = false;
             } else {
-                mask[offset] = Column.ValueKind.Present;
-                array[offset] = getter(key, d, offset);
+                const value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = Column.ValueKind.NotPresent;
+                    allPresent = false;
+                } else {
+                    mask[offset] = Column.ValueKind.Present;
+                }
+                array[offset] = value;
             }
             offset++;
         }

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

@@ -52,24 +52,30 @@ namespace SymmetryOperator {
     export const RotationTranslationEpsilon = 0.005;
 
     export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number }
-    export function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator {
+    export function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator {
         let { assembly, ncsId, hkl, spgrOp } = info || { };
         const _hkl = hkl ? Vec3.clone(hkl) : Vec3();
         spgrOp = defaults(spgrOp, -1);
         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 };
+        const isIdentity = Mat4.isIdentity(matrix);
+        const suffix = getSuffix(info, isIdentity);
+        if (isIdentity) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
         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 };
     }
 
-    function getSuffix(info?: CreateInfo) {
+    function isSymmetryOperator(x: any): x is SymmetryOperator {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+
+    function getSuffix(info?: CreateInfo | SymmetryOperator, isIdentity?: boolean) {
         if (!info) return '';
 
         if (info.assembly) {
-            return `_${info.assembly.operId}`;
+            if (isSymmetryOperator(info)) return info.suffix;
+            return isIdentity ? '' : `_${info.assembly.operId}`;
         }
 
         if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {

src/mol-model-formats/structure/basic/atomic.ts

@@ -7,21 +7,21 @@
 
 import { Column, Table } from '../../../mol-data/db';
 import { Interval, Segmentation } from '../../../mol-data/int';
-import { UUID } from '../../../mol-util/uuid';
-import { ElementIndex, ChainIndex } from '../../../mol-model/structure';
+import { toDatabase } from '../../../mol-io/reader/cif/schema';
+import { SymmetryOperator } from '../../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { ChainIndex, ElementIndex } from '../../../mol-model/structure';
+import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
 import { Model } from '../../../mol-model/structure/model/model';
 import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../../mol-model/structure/model/properties/atomic';
-import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
-import { ElementSymbol } from '../../../mol-model/structure/model/types';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
 import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
-import { AtomSite } from './schema';
+import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
+import { ElementSymbol } from '../../../mol-model/structure/model/types';
+import { UUID } from '../../../mol-util/uuid';
 import { ModelFormat } from '../../format';
-import { SymmetryOperator } from '../../../mol-math/geometry';
 import { MmcifFormat } from '../mmcif';
-import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
-import { toDatabase } from '../../../mol-io/reader/cif/schema';
-import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { AtomSite } from './schema';
 
 function findHierarchyOffsets(atom_site: AtomSite) {
     if (atom_site._rowCount === 0) return { residues: [], chains: [] };

src/mol-model-formats/structure/basic/coarse.ts

@@ -30,7 +30,7 @@ export interface CoarseData {
 
 export const EmptyCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any };
 
-export function getCoarse(data: CoarseData, properties: Model['properties']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
+export function getCoarse(data: CoarseData, chemicalComponentMap: Model['properties']['chemicalComponentMap']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
     const { ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;
 
     if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0) return EmptyCoarse;
@@ -38,12 +38,12 @@ export function getCoarse(data: CoarseData, properties: Model['properties']): {
     const sphereData = getData(ihm_sphere_obj_site);
     const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
     const sphereKeys = getCoarseKeys(sphereData, data.entities);
-    const sphereRanges = getCoarseRanges(sphereData, properties.chemicalComponentMap);
+    const sphereRanges = getCoarseRanges(sphereData, chemicalComponentMap);
 
     const gaussianData = getData(ihm_gaussian_obj_site);
     const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
     const gaussianKeys = getCoarseKeys(gaussianData, data.entities);
-    const gaussianRanges = getCoarseRanges(gaussianData, properties.chemicalComponentMap);
+    const gaussianRanges = getCoarseRanges(gaussianData, chemicalComponentMap);
 
     return {
         hierarchy: {

src/mol-model-formats/structure/basic/entities.ts

@@ -11,7 +11,7 @@ import { getEntityType, getEntitySubtype } from '../../../mol-model/structure/mo
 import { ElementIndex, EntityIndex, Model } from '../../../mol-model/structure/model';
 import { BasicData, BasicSchema, Entity } from './schema';
 
-export function getEntities(data: BasicData, properties: Model['properties']): Entities {
+export function getEntityData(data: BasicData): Entities {
     let entityData: Entity;
 
     if (!data.entity.id.isDefined) {
@@ -121,28 +121,32 @@ export function getEntities(data: BasicData, properties: Model['properties']): E
 
     const subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype });
 
-    //
-
-    const prdIds: string[] = new Array(entityData._rowCount);
-    prdIds.fill('');
-
-    if (data.pdbx_molecule && data.pdbx_molecule.prd_id.isDefined) {
-        const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
-        for (let i = 0; i < _rowCount; ++i) {
-            const asymId = asym_id.value(i);
-            const entityId = properties.structAsymMap.get(asymId)?.entity_id;
-            if (entityId !== undefined) {
-                prdIds[getEntityIndex(entityId)] = prd_id.value(i);
-            }
-        }
-    }
-
-    const prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
-
     return {
         data: entityData,
         subtype: subtypeColumn,
-        prd_id: prdIdColumn,
         getEntityIndex
     };
+}
+
+export function getEntitiesWithPRD(data: BasicData, entities: Entities, structAsymMap: Model['properties']['structAsymMap']): Entities {
+    if (!data.pdbx_molecule || !data.pdbx_molecule.prd_id.isDefined) {
+        return entities;
+    }
+
+    const prdIds: string[] = new Array(entities.data._rowCount);
+    prdIds.fill('');
+    const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
+    for (let i = 0; i < _rowCount; ++i) {
+        const asymId = asym_id.value(i);
+        const entityId = structAsymMap.get(asymId)?.entity_id;
+        if (entityId !== undefined) {
+            prdIds[entities.getEntityIndex(entityId)] = prd_id.value(i);
+        }
+    }
+    const prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
+
+    return {
+        ...entities,
+        prd_id: prdIdColumn
+    };
 }

src/mol-model-formats/structure/basic/parser.ts

@@ -18,13 +18,13 @@ import { sortAtomSite } from './sort';
 import { ModelFormat } from '../../format';
 import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
 import { AtomSite, BasicData } from './schema';
-import { getProperties } from './properties';
-import { getEntities } from './entities';
+import { getChemicalComponentMap, getMissingResidues, getSaccharideComponentMap, getStructAsymMap } from './properties';
+import { getEntitiesWithPRD, getEntityData } from './entities';
 import { getModelGroupName } from './util';
 import { ArrayTrajectory } from '../../../mol-model/structure/trajectory';
 
 export async function createModels(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
-    const properties = getProperties(data);
+    const properties = getCommonProperties(data, format);
     const models = data.ihm_model_list._rowCount > 0
         ? await readIntegrative(ctx, data, properties, format)
         : await readStandard(ctx, data, properties, format);
@@ -36,9 +36,18 @@ export async function createModels(data: BasicData, format: ModelFormat, ctx: Ru
     return new ArrayTrajectory(models);
 }
 
-/** Standard atomic model */
-function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: Model['properties'], format: ModelFormat, previous?: Model): Model {
+type CommonProperties = Omit<Model['properties'], 'structAsymMap'>
 
+function getCommonProperties(data: BasicData, format: ModelFormat): CommonProperties {
+    return {
+        missingResidues: getMissingResidues(data),
+        chemicalComponentMap: getChemicalComponentMap(data),
+        saccharideComponentMap: getSaccharideComponentMap(data)
+    };
+}
+
+/** Standard atomic model */
+function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: CommonProperties, format: ModelFormat, previous?: Model): Model {
     const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
     const modelNum = atom_site.pdbx_PDB_model_num.value(0);
     if (previous && atomic.sameAsPrevious) {
@@ -54,6 +63,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
     const coarse = EmptyCoarse;
     const sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy);
     const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence);
+    const structAsymMap = getStructAsymMap(atomic.hierarchy);
 
     const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
         ? data.entry.id.value(0) : format.name;
@@ -70,7 +80,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
         sourceData: format,
         modelNum,
         parent: undefined,
-        entities,
+        entities: getEntitiesWithPRD(data, entities, structAsymMap),
         sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -78,7 +88,10 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties,
+        properties: {
+            ...properties,
+            structAsymMap
+        },
         customProperties: new CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -86,9 +99,9 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
 }
 
 /** Integrative model with atomic/coarse parts */
-function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Model['properties'], format: ModelFormat): Model {
+function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: CommonProperties, format: ModelFormat): Model {
     const atomic = getAtomicHierarchyAndConformation(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap, format);
-    const coarse = getCoarse(ihm, properties);
+    const coarse = getCoarse(ihm, properties.chemicalComponentMap);
     const sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
     const atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);
 
@@ -101,6 +114,8 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
     if (ihm.model_name) label.push(ihm.model_name);
     if (ihm.model_group_name) label.push(ihm.model_group_name);
 
+    const structAsymMap = getStructAsymMap(atomic.hierarchy, data);
+
     return {
         id: UUID.create22(),
         entryId: entry,
@@ -109,7 +124,7 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
         sourceData: format,
         modelNum: ihm.model_id,
         parent: undefined,
-        entities: ihm.entities,
+        entities: getEntitiesWithPRD(data, ihm.entities, structAsymMap),
         sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
@@ -117,7 +132,10 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties,
+        properties: {
+            ...properties,
+            structAsymMap
+        },
         customProperties: new CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -132,12 +150,12 @@ function findModelEnd(num: Column<number>, startIndex: number) {
     return endIndex;
 }
 
-async function readStandard(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
+async function readStandard(ctx: RuntimeContext, data: BasicData, properties: CommonProperties, format: ModelFormat) {
     const models: Model[] = [];
 
     if (data.atom_site) {
         const atomCount = data.atom_site.id.rowCount;
-        const entities = getEntities(data, properties);
+        const entities = getEntityData(data);
 
         let modelStart = 0;
         while (modelStart < atomCount) {
@@ -170,8 +188,8 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
 
 
 
-async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
-    const entities = getEntities(data, properties);
+async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: CommonProperties, format: ModelFormat) {
+    const entities = getEntityData(data);
     // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
     const atom_sites_modelColumn = data.atom_site.ihm_model_id.isDefined
         ? data.atom_site.ihm_model_id : data.atom_site.pdbx_PDB_model_num;
@@ -206,7 +224,7 @@ async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties:
                 model_id: id,
                 model_name: model_name.value(i),
                 model_group_name: getModelGroupName(id, data),
-                entities: entities,
+                entities,
                 atom_site,
                 atom_site_sourceIndex,
                 ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)!.table : Table.window(data.ihm_sphere_obj_site, data.ihm_sphere_obj_site._schema, 0, 0),

src/mol-model-formats/structure/basic/properties.ts

@@ -5,15 +5,16 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import { Table } from '../../../mol-data/db';
 import { Model } from '../../../mol-model/structure/model/model';
+import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
 import { ChemicalComponent, MissingResidue, StructAsym } from '../../../mol-model/structure/model/properties/common';
-import { getMoleculeType, MoleculeType, getDefaultChemicalComponent } from '../../../mol-model/structure/model/types';
-import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
+import { getDefaultChemicalComponent, getMoleculeType, MoleculeType } from '../../../mol-model/structure/model/types';
+import { SaccharideCompIdMap, SaccharideComponent, SaccharideComponentMap, SaccharidesSnfgMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
 import { memoize1 } from '../../../mol-util/memoize';
 import { BasicData } from './schema';
-import { Table } from '../../../mol-data/db';
 
-function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
+export function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
     const map = new Map<string, MissingResidue>();
     const getKey = (model_num: number, asym_id: string, seq_id: number) => {
         return `${model_num}|${asym_id}|${seq_id}`;
@@ -36,7 +37,7 @@ function getMissingResidues(data: BasicData): Model['properties']['missingResidu
     };
 }
 
-function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
+export function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
     const map = new Map<string, ChemicalComponent>();
 
     if (data.chem_comp._rowCount > 0) {
@@ -53,7 +54,7 @@ function getChemicalComponentMap(data: BasicData): Model['properties']['chemical
     return map;
 }
 
-function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
+export function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
     const map = new Map<string, SaccharideComponent>();
 
     if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -108,22 +109,18 @@ const getUniqueComponentNames = memoize1((data: BasicData) => {
 });
 
 
-function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap'] {
+export function getStructAsymMap(atomic: AtomicHierarchy, data?: BasicData): Model['properties']['structAsymMap'] {
     const map = new Map<string, StructAsym>();
 
-    const { label_asym_id, auth_asym_id, label_entity_id } = data.atom_site;
-    for (let i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+    const { auth_asym_id, label_asym_id, label_entity_id } = atomic.chains;
+
+    for (let i = 0, _i = atomic.chains._rowCount; i < _i; i ++) {
         const id = label_asym_id.value(i);
-        if (!map.has(id)) {
-            map.set(id, {
-                id,
-                auth_id: auth_asym_id.value(i),
-                entity_id: label_entity_id.value(i)
-            });
-        }
+        map.set(id, { id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
     }
 
-    if (data.struct_asym._rowCount > 0) {
+    // to get asym mapping for coarse/ihm data
+    if (data?.struct_asym._rowCount) {
         const { id, entity_id } = data.struct_asym;
         for (let i = 0, il = id.rowCount; i < il; ++i) {
             const _id = id.value(i);
@@ -136,14 +133,6 @@ function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap']
             }
         }
     }
-    return map;
-}
 
-export function getProperties(data: BasicData): Model['properties'] {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
+    return map;
 }

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

@@ -1,12 +1,13 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 
 import { Column, Table } from '../../mol-data/db';
-import { MolFile } from '../../mol-io/reader/mol/parser';
+import { MolFile, formalChargeMapper } from '../../mol-io/reader/mol/parser';
 import { MoleculeType } from '../../mol-model/structure/model/types';
 import { RuntimeContext, Task } from '../../mol-task';
 import { createModels } from './basic/parser';
@@ -18,13 +19,24 @@ import { IndexPairBonds } from './property/bonds/index-pair';
 import { Trajectory } from '../../mol-model/structure';
 
 export async function getMolModels(mol: MolFile, format: ModelFormat<any> | undefined, ctx: RuntimeContext) {
-    const { atoms, bonds } = mol;
+    const { atoms, bonds, formalCharges } = mol;
 
     const MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
     const A = Column.ofConst('A', mol.atoms.count, Column.Schema.str);
     const type_symbol = Column.asArrayColumn(atoms.type_symbol);
     const seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
 
+    const computedFormalCharges = new Int32Array(mol.atoms.count);
+    if (formalCharges.atomIdx.rowCount > 0) {
+        for (let i = 0; i < formalCharges.atomIdx.rowCount; i++) {
+            computedFormalCharges[formalCharges.atomIdx.value(i) - 1] = formalCharges.charge.value(i);
+        }
+    } else {
+        for (let i = 0; i < mol.atoms.count; i++) {
+            computedFormalCharges[i] = formalChargeMapper(atoms.formal_charge.value(i));
+        }
+    }
+
     const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
         auth_asym_id: A,
         auth_atom_id: type_symbol,
@@ -45,6 +57,7 @@ export async function getMolModels(mol: MolFile, format: ModelFormat<any> | unde
         type_symbol,
 
         pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
+        pdbx_formal_charge: Column.ofIntArray(computedFormalCharges)
     }, atoms.count);
 
     const entityBuilder = new EntityBuilder();

src/mol-model-formats/structure/mol2.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column, Table } from '../../mol-data/db';
-import { Model } from '../../mol-model/structure/model';
+import { Model, Symmetry } from '../../mol-model/structure/model';
 import { BondType, MoleculeType } from '../../mol-model/structure/model/types';
 import { RuntimeContext, Task } from '../../mol-task';
 import { createModels } from './basic/parser';
@@ -14,22 +14,34 @@ import { ComponentBuilder } from './common/component';
 import { EntityBuilder } from './common/entity';
 import { ModelFormat } from '../format';
 import { IndexPairBonds } from './property/bonds/index-pair';
-import { Mol2File } from '../../mol-io/reader/mol2/schema';
+import { Mol2Crysin, Mol2File } from '../../mol-io/reader/mol2/schema';
 import { AtomPartialCharge } from './property/partial-charge';
 import { Trajectory, ArrayTrajectory } from '../../mol-model/structure';
 import { guessElementSymbolString } from './util';
+import { ModelSymmetry } from './property/symmetry';
+import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';
+import { Vec3 } from '../../mol-math/linear-algebra';
 
 async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
     const models: Model[] = [];
 
     for (let i = 0, il = mol2.structures.length; i < il; ++i) {
-        const { atoms, bonds, molecule } = mol2.structures[i];
+        const { molecule, atoms, bonds, crysin } = mol2.structures[i];
 
         const A = Column.ofConst('A', atoms.count, Column.Schema.str);
 
         const type_symbol = new Array<string>(atoms.count);
+        let hasAtomType = false;
         for (let i = 0; i < atoms.count; ++i) {
-            type_symbol[i] = guessElementSymbolString(atoms.atom_name.value(i));
+            if (atoms.atom_type.value(i).includes('.')) {
+                hasAtomType = true;
+                break;
+            }
+        }
+        for (let i = 0; i < atoms.count; ++i) {
+            type_symbol[i] = hasAtomType
+                ? atoms.atom_type.value(i).split('.')[0].toUpperCase()
+                : guessElementSymbolString(atoms.atom_name.value(i));
         }
 
         const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -74,6 +86,7 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
         if (_models.frameCount > 0) {
             const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array));
             const indexB = Column.ofIntArray(Column.mapToArray(bonds.target_atom_id, x => x - 1, Int32Array));
+            const key = bonds.bond_id;
             const order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => {
                 switch (x) {
                     case 'ar': // aromatic
@@ -100,7 +113,7 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
                         return BondType.Flag.Covalent;
                 }
             }, Int8Array));
-            const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order, flag }, count: atoms.count });
+            const pairBonds = IndexPairBonds.fromData({ pairs: { key, indexA, indexB, order, flag }, count: atoms.count });
 
             const first = _models.representative;
             IndexPairBonds.Provider.set(first, pairBonds);
@@ -110,6 +123,11 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
                 type: molecule.charge_type
             });
 
+            if (crysin) {
+                const symmetry = getSymmetry(crysin);
+                if (symmetry) ModelSymmetry.Provider.set(first, symmetry);
+            }
+
             models.push(first);
         }
     }
@@ -117,6 +135,24 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
     return new ArrayTrajectory(models);
 }
 
+function getSymmetry(crysin: Mol2Crysin): Symmetry | undefined {
+    // TODO handle `crysin.setting`
+    if (crysin.setting !== 1) return;
+
+    const spaceCell = SpacegroupCell.create(
+        crysin.spaceGroup,
+        Vec3.create(crysin.a, crysin.b, crysin.c),
+        Vec3.scale(Vec3(), Vec3.create(crysin.alpha, crysin.beta, crysin.gamma), Math.PI / 180)
+    );
+
+    return {
+        spacegroup: Spacegroup.create(spaceCell),
+        assemblies: [],
+        isNonStandardCrystalFrame: false,
+        ncsOperators: []
+    };
+}
+
 //
 
 export { Mol2Format };

src/mol-model-formats/structure/property/bonds/index-pair.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,9 +10,9 @@ import { Column } from '../../../../mol-data/db';
 import { FormatPropertyProvider } from '../../common/property';
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { ElementIndex } from '../../../../mol-model/structure';
-import { DefaultBondMaxRadius } from '../../../../mol-model/structure/structure/unit/bonds/common';
 
 export type IndexPairsProps = {
+    readonly key: ArrayLike<number>
     readonly order: ArrayLike<number>
     readonly distance: ArrayLike<number>
     readonly flag: ArrayLike<BondType.Flag>
@@ -22,17 +22,19 @@ export type IndexPairBonds = { bonds: IndexPairs, maxDistance: number }
 
 function getGraph(indexA: ArrayLike<ElementIndex>, indexB: ArrayLike<ElementIndex>, props: Partial<IndexPairsProps>, count: number): IndexPairs {
     const builder = new IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
+    const key = new Int32Array(builder.slotCount);
     const order = new Int8Array(builder.slotCount);
     const distance = new Array(builder.slotCount);
     const flag = new Array(builder.slotCount);
     for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
         builder.addNextEdge();
+        builder.assignProperty(key, props.key ? props.key[i] : -1);
         builder.assignProperty(order, props.order ? props.order[i] : 1);
         builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
         builder.assignProperty(flag, props.flag ? props.flag[i] : BondType.Flag.Covalent);
     }
 
-    return builder.createGraph({ order, distance, flag });
+    return builder.createGraph({ key, order, distance, flag });
 }
 
 export namespace IndexPairBonds {
@@ -45,15 +47,33 @@ export namespace IndexPairBonds {
     export type Data = {
         pairs: {
             indexA: Column<number>,
-            indexB: Column<number>
+            indexB: Column<number>,
+            key?: Column<number>,
             order?: Column<number>,
+            /**
+             * Useful for bonds in periodic cells. That is, only bonds within the given
+             * distance are added. This allows for bond between periodic image but
+             * avoids unwanted bonds with wrong distances. If negative, test using the
+             * `maxDistance` option from `Props`.
+             */
             distance?: Column<number>,
             flag?: Column<BondType.Flag>,
         },
         count: number
     }
 
-    export const DefaultProps = { maxDistance: DefaultBondMaxRadius };
+    export const DefaultProps = {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
+        maxDistance: -1
+    };
     export type Props = typeof DefaultProps
 
     export function fromData(data: Data, props: Partial<Props> = {}): IndexPairBonds {
@@ -61,11 +81,12 @@ export namespace IndexPairBonds {
         const { pairs, count } = data;
         const indexA = pairs.indexA.toArray() as ArrayLike<ElementIndex>;
         const indexB = pairs.indexB.toArray() as ArrayLike<ElementIndex>;
+        const key = pairs.key && pairs.key.toArray();
         const order = pairs.order && pairs.order.toArray();
         const distance = pairs.distance && pairs.distance.toArray();
         const flag = pairs.flag && pairs.flag.toArray();
         return {
-            bonds: getGraph(indexA, indexB, { order, distance, flag }, count),
+            bonds: getGraph(indexA, indexB, { key, order, distance, flag }, count),
             maxDistance: p.maxDistance
         };
     }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -98,29 +98,20 @@ class InteractionsInterContacts extends InterUnitGraph<number, Features.FeatureI
     constructor(map: Map<number, InterUnitGraph.UnitPairEdges<number, Features.FeatureIndex, InteractionsInterContacts.Props>[]>, unitsFeatures: IntMap<Features>) {
         super(map);
 
-        let count = 0;
-        const elementKeyIndex = new Map<string, number[]>();
-
-        const add = (index: StructureElement.UnitIndex, unitId: number) => {
-            const vertexKey = this.getElementKey(index, unitId);
-            const e = elementKeyIndex.get(vertexKey);
-            if (e === undefined) elementKeyIndex.set(vertexKey, [count]);
-            else e.push(count);
-        };
-
-        this.map.forEach(pairEdgesArray => {
-            pairEdgesArray.forEach(({ unitA, connectedIndices }) => {
-                connectedIndices.forEach(indexA => {
-                    const { offsets: offsetsA, members: membersA } = unitsFeatures.get(unitA);
-                    for (let j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
-                        add(membersA[j], unitA);
-                    }
-                    count += 1;
-                });
-            });
-        });
-
-        this.elementKeyIndex = elementKeyIndex;
+        this.elementKeyIndex = new Map<string, number[]>();
+        for (let i = 0, il = this.edges.length; i < il; ++i) {
+            const { unitA, indexA } = this.edges[i];
+            const { offsets, members } = unitsFeatures.get(unitA);
+            for (let j = offsets[indexA], jl = offsets[indexA + 1]; j < jl; ++j) {
+                const vertexKey = this.getElementKey(members[j], unitA);
+                const e = this.elementKeyIndex.get(vertexKey);
+                if (e === undefined) {
+                    this.elementKeyIndex.set(vertexKey, [i]);
+                } else {
+                    e.push(i);
+                }
+            }
+        }
     }
 }
 namespace InteractionsInterContacts {

src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -74,10 +74,11 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
                 if (!childUnitA) return true;
 
                 const unitA = structure.unitMap.get(b.unitA);
-                const fA = unitsFeatures.get(b.unitA);
-                // TODO: check all members
-                const eA = unitA.elements[fA.members[fA.offsets[b.indexA]]];
-                if (!SortedArray.has(childUnitA.elements, eA)) return true;
+                const { offsets, members } = unitsFeatures.get(b.unitA);
+                for (let i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
+                    const eA = unitA.elements[members[i]];
+                    if (!SortedArray.has(childUnitA.elements, eA)) return true;
+                }
             }
 
             return false;
@@ -144,6 +145,9 @@ function getInteractionLoci(pickingId: PickingId, structure: Structure, id: numb
     return EmptyLoci;
 }
 
+const __unitMap = new Map<number, OrderedSet<StructureElement.UnitIndex>>();
+const __contactIndicesSet = new Set<number>();
+
 function eachInteraction(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean) {
     let changed = false;
     if (Interactions.isLoci(loci)) {
@@ -162,21 +166,48 @@ function eachInteraction(loci: Loci, structure: Structure, apply: (interval: Int
         if (!Structure.areEquivalent(loci.structure, structure)) return false;
         if (isMarking && loci.elements.length === 1) return false; // only a single unit
 
-        const contacts = InteractionsProvider.get(structure).value?.contacts;
-        if (!contacts) return false;
+        const interactions = InteractionsProvider.get(structure).value;
+        if (!interactions) return false;
+
+        const { contacts, unitsFeatures } = interactions;
+
+        for (const e of loci.elements) __unitMap.set(e.unit.id, e.indices);
 
-        // TODO when isMarking, all elements of contact features need to be in the loci
         for (const e of loci.elements) {
             const { unit } = e;
             if (!Unit.isAtomic(unit)) continue;
-            if (isMarking && OrderedSet.size(e.indices) === 1) continue;
 
             OrderedSet.forEach(e.indices, v => {
                 for (const idx of contacts.getContactIndicesForElement(v, unit)) {
-                    if (apply(Interval.ofSingleton(idx))) changed = true;
+                    __contactIndicesSet.add(idx);
                 }
             });
         }
+
+        __contactIndicesSet.forEach(i => {
+            if (isMarking) {
+                const { indexA, unitA, indexB, unitB } = contacts.edges[i];
+
+                const indicesA = __unitMap.get(unitA);
+                const indicesB = __unitMap.get(unitB);
+                if (!indicesA || !indicesB) return;
+
+                const { offsets: offsetsA, members: membersA } = unitsFeatures.get(unitA);
+                for (let j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
+                    if (!OrderedSet.has(indicesA, membersA[j])) return;
+                }
+
+                const { offsets: offsetsB, members: membersB } = unitsFeatures.get(unitB);
+                for (let j = offsetsB[indexB], jl = offsetsB[indexB + 1]; j < jl; ++j) {
+                    if (!OrderedSet.has(indicesB, membersB[j])) return;
+                }
+            }
+
+            if (apply(Interval.ofSingleton(i))) changed = true;
+        });
+
+        __unitMap.clear();
+        __contactIndicesSet.clear();
     }
     return changed;
 }

src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -56,11 +56,19 @@ async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit:
             const sizeB = theme.size.size(location);
             return Math.min(sizeA, sizeB) * sizeFactor;
         },
-        ignore: (edgeIndex: number) => (
-            flag[edgeIndex] === InteractionFlag.Filtered ||
-            // TODO: check all members
-            (!!childUnit && !SortedArray.has(childUnit.elements, unit.elements[members[offsets[a[edgeIndex]]]]))
-        )
+        ignore: (edgeIndex: number) => {
+            if (flag[edgeIndex] === InteractionFlag.Filtered) return true;
+
+            if (childUnit) {
+                const f = a[edgeIndex];
+                for (let i = offsets[f], jl = offsets[f + 1]; i < jl; ++i) {
+                    const e = unit.elements[members[offsets[i]]];
+                    if (!SortedArray.has(childUnit.elements, e)) return true;
+                }
+            }
+
+            return false;
+        }
     };
 
     const m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
@@ -123,6 +131,8 @@ function getInteractionLoci(pickingId: PickingId, structureGroup: StructureGroup
     return EmptyLoci;
 }
 
+const __contactIndicesSet = new Set<number>();
+
 function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean) {
     let changed = false;
     if (Interactions.isLoci(loci)) {
@@ -156,21 +166,37 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int
 
         const { offset } = contacts;
         const { offsets: fOffsets, indices: fIndices } = features.elementsIndex;
+        const { members, offsets } = features;
 
-        // TODO: when isMarking, all elements of contact features need to be in the loci
         for (const e of loci.elements) {
             const unitIdx = group.unitIndexMap.get(e.unit.id);
-            if (unitIdx !== undefined) continue;
-            if (isMarking && OrderedSet.size(e.indices) === 1) continue;
+            if (unitIdx === undefined) continue;
 
             OrderedSet.forEach(e.indices, v => {
                 for (let i = fOffsets[v], il = fOffsets[v + 1]; i < il; ++i) {
                     const fI = fIndices[i];
                     for (let j = offset[fI], jl = offset[fI + 1]; j < jl; ++j) {
-                        if (apply(Interval.ofSingleton(unitIdx * groupCount + j))) changed = true;
+                        __contactIndicesSet.add(j);
                     }
                 }
             });
+
+            __contactIndicesSet.forEach(i => {
+                if (isMarking) {
+                    const fA = contacts.a[i];
+                    for (let j = offsets[fA], jl = offsets[fA + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members[j])) return;
+                    }
+                    const fB = contacts.b[i];
+                    for (let j = offsets[fB], jl = offsets[fB + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members[j])) return;
+                    }
+                }
+
+                if (apply(Interval.ofSingleton(unitIdx * groupCount + i))) changed = true;
+            });
+
+            __contactIndicesSet.clear();
         }
     }
     return changed;

src/mol-model-props/sequence/best-database-mapping.ts

@@ -29,7 +29,7 @@ namespace BestDatabaseSequenceMapping {
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('db_name') >= 0,
+        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('pdbx_sifts_xref_db_name') >= 0,
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
@@ -40,7 +40,7 @@ namespace BestDatabaseSequenceMapping {
         const data = Provider.get(model).value;
         if (!data) return '';
         const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         return data.accession[rI];
     }
 
@@ -49,7 +49,7 @@ namespace BestDatabaseSequenceMapping {
         const data = Provider.get(model).value;
         if (!data) return;
         const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         const dbName = data.dbName[rI];
         if (!dbName) return;
         return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
@@ -59,10 +59,10 @@ namespace BestDatabaseSequenceMapping {
         if (!MmcifFormat.is(model.sourceData)) return;
 
         const { atom_site } = model.sourceData.data.frame.categories;
-        const db_name = atom_site.getField('db_name');
-        const db_acc = atom_site.getField('db_acc');
-        const db_num = atom_site.getField('db_num');
-        const db_res = atom_site.getField('db_res');
+        const db_name = atom_site.getField('pdbx_sifts_xref_db_name');
+        const db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
+        const db_num = atom_site.getField('pdbx_sifts_xref_db_num');
+        const db_res = atom_site.getField('pdbx_sifts_xref_db_res');
 
         if (!db_name || !db_acc || !db_num || !db_res) return;
 
@@ -77,17 +77,17 @@ namespace BestDatabaseSequenceMapping {
             const row = atomSourceIndex.value(residueOffsets[i]);
 
             if (db_name.valueKind(row) !== Column.ValueKind.Present) {
-                dbName[row] = '';
-                accession[row] = '';
-                num[row] = 0;
-                residue[row] = '';
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = 0;
+                residue[i] = '';
                 continue;
             }
 
-            dbName[row] = db_name.str(row);
-            accession[row] = db_acc.str(row);
-            num[row] = db_num.int(row);
-            residue[row] = db_res.str(row);
+            dbName[i] = db_name.str(row);
+            accession[i] = db_acc.str(row);
+            num[i] = db_num.int(row);
+            residue[i] = db_res.str(row);
         }
 
         return { dbName, accession, num, residue };

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

@@ -52,6 +52,10 @@ function isWithoutSymmetry(structure: Structure) {
     return structure.units.every(u => u.conformation.operator.isIdentity);
 }
 
+function isWithoutOperator(structure: Structure) {
+    return isWithoutSymmetry(structure) && structure.units.every(u => !u.conformation.operator.assembly && !u.conformation.operator.suffix);
+}
+
 const Categories = [
     // Basics
     copy_mmCif_category('entry'),
@@ -63,9 +67,9 @@ const Categories = [
     copy_mmCif_category('symmetry', isWithoutSymmetry),
 
     // Assemblies
-    copy_mmCif_category('pdbx_struct_assembly', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_oper_list', isWithoutSymmetry),
+    copy_mmCif_category('pdbx_struct_assembly', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_oper_list', isWithoutOperator),
 
     // Secondary structure
     _struct_conf,
@@ -250,10 +254,10 @@ function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExp
 }
 
 
-function to_mmCIF(name: string, structure: Structure, asBinary = false) {
+function to_mmCIF(name: string, structure: Structure, asBinary = false, params?: encode_mmCIF_categories_Params) {
     const enc = CifWriter.createEncoder({ binary: asBinary });
     enc.startDataBlock(name);
-    encode_mmCIF_categories(enc, structure);
+    encode_mmCIF_categories(enc, structure, params);
     return enc.getData();
 }
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -63,6 +63,28 @@ export interface CoarseHierarchy {
     gaussians: CoarseElements
 }
 
+const EmptyCoarseElements: CoarseElements = {
+    chainKey: [],
+    entityKey: [],
+    findSequenceKey: () => -1 as ElementIndex,
+    findChainKey: () => -1 as ChainIndex,
+    getEntityFromChain: () => -1 as EntityIndex,
+
+    count: 0,
+    entity_id: Column.Undefined(0, Column.Schema.str),
+    asym_id: Column.Undefined(0, Column.Schema.str),
+    seq_id_begin: Column.Undefined(0, Column.Schema.int),
+    seq_id_end: Column.Undefined(0, Column.Schema.int),
+    chainElementSegments: Segmentation.create([]),
+
+    polymerRanges: SortedRanges.ofSortedRanges([]),
+    gapRanges: SortedRanges.ofSortedRanges([]),
+};
+
 export namespace CoarseHierarchy {
-    export const Empty: CoarseHierarchy = { isDefined: false } as any;
+    export const Empty: CoarseHierarchy = {
+        isDefined: false,
+        spheres: EmptyCoarseElements,
+        gaussians: EmptyCoarseElements
+    };
 }

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

@@ -22,7 +22,7 @@ export const EntitySubtype = Column.Schema.Aliased<EntitySubtype>(Column.Schema.
 export interface Entities {
     data: mmCIF_Database['entity'],
     subtype: Column<EntitySubtype>,
-    prd_id: Column<string>,
+    prd_id?: Column<string>,
     getEntityIndex(id: string): EntityIndex
 }
 

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

@@ -72,6 +72,7 @@ export namespace Stats {
             }
         } else if (size === 1) {
             if (Unit.Traits.is(unit.traits, Unit.Trait.MultiChain)) {
+                // handled in `handleUnitChainsSimple`
                 return;
             } else {
                 stats.elementCount += 1;
@@ -193,6 +194,12 @@ export namespace Stats {
                 if (stats.chainCount === 1) {
                     Location.set(stats.firstChainLoc, structure, unit, offsets[cI]);
                 }
+            } else if (size === 1) {
+                // need to handle here, skipped in `handleElement`
+                stats.elementCount += 1;
+                if (stats.elementCount === 1) {
+                    Location.set(stats.firstElementLoc, structure, unit, eI);
+                }
             }
         }
     }

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

@@ -126,6 +126,7 @@ const coarse = {
     z: atom.z,
 
     asym_id: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element)),
+    entity_id: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entity_id.value(l.element)),
     seq_id_begin: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element)),
     seq_id_end: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element)),
 
@@ -162,7 +163,7 @@ const entity = {
     pdbx_ec: p(l => l.unit.model.entities.data.pdbx_ec.value(eK(l))),
 
     subtype: p(l => l.unit.model.entities.subtype.value(eK(l))),
-    prd_id: p(l => l.unit.model.entities.prd_id.value(eK(l))),
+    prd_id: p(l => l.unit.model.entities.prd_id?.value(eK(l)) ?? ''),
 };
 
 const _emptyList: any[] = [];

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

@@ -184,16 +184,13 @@ function getOperatorsForRange(symmetry: Symmetry, ijkMin: Vec3, ijkMax: Vec3, mo
         operators[0] = Spacegroup.getSymmetryOperator(spacegroup, 0, 0, 0, 0);
     }
 
-    const { toFractional } = spacegroup.cell;
-    const ref = Vec3.transformMat4(Vec3(), modelCenter, toFractional);
-
     for (let op = 0; op < spacegroup.operators.length; op++) {
         for (let i = ijkMin[0]; i <= ijkMax[0]; i++) {
             for (let j = ijkMin[1]; j <= ijkMax[1]; j++) {
                 for (let k = ijkMin[2]; k <= ijkMax[2]; k++) {
                     // check if we have added identity as the 1st operator.
                     if (!ncsCount && op === 0 && i === 0 && j === 0 && k === 0) continue;
-                    operators.push(...getOperatorsForIndex(symmetry, op, i, j, k, ref));
+                    operators.push(...getOperatorsForIndex(symmetry, op, i, j, k, modelCenter));
                 }
             }
         }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -110,6 +110,15 @@ export function getElementThreshold(i: number) {
     return r;
 }
 
+export function getPairingThreshold(elementIndexA: number, elementIndexB: number, thresholdA: number, thresholdB: number) {
+    const thresholdAB = getElementPairThreshold(elementIndexA, elementIndexB);
+    return thresholdAB > 0
+        ? thresholdAB
+        : elementIndexB < 0
+            ? thresholdA
+            : (thresholdA + thresholdB) / 1.95; // not sure if avg or min but max is too big
+}
+
 const H_ID = __ElementIndex['H']!;
 export function isHydrogen(i: number) {
     return i === H_ID;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,7 +8,7 @@
 import { BondType, MoleculeType } from '../../../model/types';
 import { Structure } from '../../structure';
 import { Unit } from '../../unit';
-import { getElementIdx, getElementPairThreshold, getElementThreshold, isHydrogen, BondComputationProps, MetalsSet, DefaultBondComputationProps } from './common';
+import { getElementIdx, getElementThreshold, isHydrogen, BondComputationProps, MetalsSet, DefaultBondComputationProps, getPairingThreshold } from './common';
 import { InterUnitBonds, InterUnitEdgeProps } from './data';
 import { SortedArray } from '../../../../../mol-data/int';
 import { Vec3, Mat4 } from '../../../../../mol-math/linear-algebra';
@@ -82,11 +82,31 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
 
                 const _bI = SortedArray.indexOf(unitB.elements, bI) as StructureElement.UnitIndex;
                 if (_bI < 0) continue;
-                if (type_symbolA.value(aI) === 'H' && type_symbolB.value(bI) === 'H') continue;
+
+                const aeI = getElementIdx(type_symbolA.value(aI));
+                const beI = getElementIdx(type_symbolA.value(bI));
 
                 const d = distance[i];
                 const dist = getDistance(unitA, aI, unitB, bI);
-                if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
+
+                let add = false;
+                if (d >= 0) {
+                    add = equalEps(dist, d, 0.3);
+                } else if (maxDistance >= 0) {
+                    add = dist < maxDistance;
+                } else {
+                    const pairingThreshold = getPairingThreshold(
+                        aeI, beI, getElementThreshold(aeI), getElementThreshold(beI)
+                    );
+                    add = dist < pairingThreshold;
+
+                    if (isHydrogen(aeI) && isHydrogen(beI)) {
+                        // TODO handle molecular hydrogen
+                        add = false;
+                    }
+                }
+
+                if (add) {
                     builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
                 }
             }
@@ -155,13 +175,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
             const dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0) continue;
 
-            const thresholdAB = getElementPairThreshold(aeI, beI);
-            const pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + getElementThreshold(beI)) / 1.95; // not sure if avg or min but max is too big
-
+            const pairingThreshold = getPairingThreshold(aeI, beI, thresholdA, getElementThreshold(beI));
             if (dist <= pairingThreshold) {
                 const atomIdB = label_atom_idB.value(bI);
                 const compIdB = label_comp_idB.value(residueIndexB[bI]);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -9,7 +9,7 @@ import { BondType } from '../../../model/types';
 import { IntraUnitBonds } from './data';
 import { Unit } from '../../unit';
 import { IntAdjacencyGraph } from '../../../../../mol-math/graph';
-import { BondComputationProps, getElementIdx, MetalsSet, getElementThreshold, isHydrogen, getElementPairThreshold, DefaultBondComputationProps } from './common';
+import { BondComputationProps, getElementIdx, MetalsSet, getElementThreshold, isHydrogen, DefaultBondComputationProps, getPairingThreshold } from './common';
 import { SortedArray } from '../../../../../mol-data/int';
 import { getIntraBondOrderFromTable } from '../../../model/properties/atomic/bonds';
 import { StructureElement } from '../../element';
@@ -62,7 +62,8 @@ function findIndexPairBonds(unit: Unit.Atomic) {
 
     for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
         const aI = atoms[_aI];
-        const isHa = type_symbol.value(aI) === 'H';
+        const aeI = getElementIdx(type_symbol.value(aI));
+        const isHa = isHydrogen(aeI);
 
         const srcA = sourceIndex.value(aI);
 
@@ -72,11 +73,30 @@ function findIndexPairBonds(unit: Unit.Atomic) {
 
             const _bI = SortedArray.indexOf(unit.elements, bI) as StructureElement.UnitIndex;
             if (_bI < 0) continue;
-            if (isHa && type_symbol.value(bI) === 'H') continue;
+
+            const beI = getElementIdx(type_symbol.value(bI));
 
             const d = distance[i];
             const dist = getDistance(unit, aI, bI);
-            if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
+
+            let add = false;
+            if (d >= 0) {
+                add = equalEps(dist, d, 0.3);
+            } else if (maxDistance >= 0) {
+                add = dist < maxDistance;
+            } else {
+                const pairingThreshold = getPairingThreshold(
+                    aeI, beI, getElementThreshold(aeI), getElementThreshold(beI)
+                );
+                add = dist < pairingThreshold;
+
+                if (isHa && isHydrogen(beI)) {
+                    // TODO handle molecular hydrogen
+                    add = false;
+                }
+            }
+
+            if (add) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
                 orders[orders.length] = order[i];
@@ -214,13 +234,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
             const dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0) continue;
 
-            const thresholdAB = getElementPairThreshold(aeI, beI);
-            const pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + getElementThreshold(beI)) / 1.95; // not sure if avg or min but max is too big
-
+            const pairingThreshold = getPairingThreshold(aeI, beI, thresholdA, getElementThreshold(beI));
             if (dist <= pairingThreshold) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;

src/mol-model/structure/structure/util/superposition-db-mapping.ts

@@ -5,6 +5,7 @@
  */
 
 import { Segmentation } from '../../../../mol-data/int';
+import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
 import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
 import { ElementIndex } from '../../model/indexing';
@@ -33,6 +34,7 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]
     for (const p of pairs) {
         const [a, b] = getPositionTables(index, p.i, p.j, p.count);
         const transform = MinimizeRmsd.compute({ a, b });
+        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
         ret.push({ transform, pivot: p.i, other: p.j });
     }
 
@@ -51,6 +53,8 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:
 
         const l = Math.min(a[2] - a[1], b[2] - b[1]);
 
+        // TODO: allow to use just backbone atoms?
+        // TODO: check if residue types match?
         for (let i = 0; i < l; i++) {
             let eI = (a[1] + i) as ElementIndex;
             xs.x[o] = a[0].conformation.x(eI);
@@ -122,7 +126,6 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
         if (unit.kind !== Unit.Kind.Atomic) continue;
 
         const { elements, model } = unit;
-        const { offsets: residueOffset } = model.atomicHierarchy.residueAtomSegments;
 
         const map = BestDatabaseSequenceMapping.Provider.get(model).value;
         if (!map) return;
@@ -137,23 +140,27 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
             residuesIt.setSegment(chainSegment);
             while (residuesIt.hasNext) {
                 const residueSegment = residuesIt.move();
-                const eI = elements[residueSegment.start];
-                const rI = residueOffset[eI];
+                const rI = residueSegment.index;
 
                 if (!dbName[rI]) continue;
 
+                const start = elements[residueSegment.start];
+                const end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+
                 const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;
 
                 if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, eI, elements[residueSegment.end]] } });
+                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
                 } else {
                     const entry = index.get(key)!;
 
                     if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, eI, elements[residueSegment.end]];
+                        entry.pivots[sI] = [unit, start, end];
                     }
                 }
             }
         }
     }
+
+    console.log(index);
 }

src/mol-model/volume/volume.ts

@@ -15,6 +15,7 @@ import { ModelFormat } from '../../mol-model-formats/format';
 import { CustomProperties } from '../custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { toPrecision } from '../../mol-util/number';
+import { DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 export interface Volume {
     readonly label?: string
@@ -84,6 +85,23 @@ export namespace Volume {
         }
     }
 
+    // Converts iso value to relative if using downsample VolumeServer data
+    export function adjustedIsoValue(volume: Volume, value: number, kind: 'absolute' | 'relative') {
+        if (kind === 'relative') return IsoValue.relative(value);
+
+        const absolute = IsoValue.absolute(value);
+        if (DscifFormat.is(volume.sourceData)) {
+            const stats = {
+                min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
+                max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
+                mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
+                sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
+            };
+            return Volume.IsoValue.toRelative(absolute, stats);
+        }
+        return absolute;
+    }
+
     const defaultStats: Grid['stats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
     export function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']) {
         const sts = stats || defaultStats;

src/mol-plugin-state/actions/file.ts

@@ -7,8 +7,10 @@
 import { PluginContext } from '../../mol-plugin/context';
 import { StateAction } from '../../mol-state';
 import { Task } from '../../mol-task';
+import { Asset } from '../../mol-util/assets';
 import { getFileInfo } from '../../mol-util/file-info';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { unzip } from '../../mol-util/zip/zip';
 import { PluginStateObject } from '../objects';
 
 export const OpenFiles = StateAction.build({
@@ -33,24 +35,37 @@ export const OpenFiles = StateAction.build({
             plugin.log.error('No file(s) selected');
             return;
         }
+
+        const processFile = async (file: Asset.File) => {
+            const info = getFileInfo(file.file!);
+            const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
+            const { data } = await plugin.builders.data.readFile({ file, isBinary });
+            const provider = params.format.name === 'auto'
+                ? plugin.dataFormats.auto(info, data.cell?.obj!)
+                : plugin.dataFormats.get(params.format.params);
+
+            if (!provider) {
+                plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
+                return;
+            }
+
+            // need to await so that the enclosing Task finishes after the update is done.
+            const parsed = await provider.parse(plugin, data);
+            if (params.visuals) {
+                await provider.visuals?.(plugin, parsed);
+            }
+        };
+
         for (const file of params.files) {
             try {
-                const info = getFileInfo(file.file!);
-                const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
-                const { data } = await plugin.builders.data.readFile({ file, isBinary });
-                const provider = params.format.name === 'auto'
-                    ? plugin.dataFormats.auto(info, data.cell?.obj!)
-                    : plugin.dataFormats.get(params.format.params);
-
-                if (!provider) {
-                    plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
-                    continue;
-                }
-
-                // need to await so that the enclosing Task finishes after the update is done.
-                const parsed = await provider.parse(plugin, data);
-                if (params.visuals) {
-                    await provider.visuals?.(plugin, parsed);
+                if (file.file && file.name.toLowerCase().endsWith('.zip')) {
+                    const zippedFiles = await unzip(taskCtx, await file.file.arrayBuffer());
+                    for (const [fn, filedata] of Object.entries(zippedFiles)) {
+                        const asset = Asset.File(new File([filedata as Uint8Array], fn));
+                        await processFile(asset);
+                    }
+                } else {
+                    await processFile(file);
                 }
             } catch (e) {
                 console.error(e);

src/mol-plugin-state/actions/structure.ts

@@ -19,6 +19,7 @@ import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAn
 import { Asset } from '../../mol-util/assets';
 import { PluginConfig } from '../../mol-plugin/config';
 import { getFileInfo } from '../../mol-util/file-info';
+import { assertUnreachable } from '../../mol-util/type-helpers';
 
 const DownloadModelRepresentationOptions = (plugin: PluginContext) => {
     const representationDefault = plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
@@ -39,6 +40,7 @@ export const PdbDownloadProvider = {
     'pdbe': PD.Group({
         variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'updtaed-bcif' | 'archival', string][]),
     }, { label: 'PDBe', isFlat: true }),
+    'pdbj': PD.EmptyGroup({ label: 'PDBj' }),
 };
 export type PdbDownloadProvider = keyof typeof PdbDownloadProvider;
 
@@ -104,15 +106,14 @@ const DownloadStructure = StateAction.build({
             format = src.params.format;
             break;
         case 'pdb':
-            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: ${id} (updated cif)`, false)
-                    : src.params.provider.server.params.variant === 'updated-bcif'
-                        ? getDownloadParams(src.params.provider.id, id => `https://www.ebi.ac.uk/pdbe/entry-files/download/${id.toLowerCase()}.bcif`, id => `PDBe: ${id} (updated cif)`, true)
-                        : getDownloadParams(src.params.provider.id, id => `https://www.ebi.ac.uk/pdbe/static/entry/${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)
+            downloadParams = await (
+                src.params.provider.server.name === 'pdbe'
+                    ? getPdbeDownloadParams(src)
+                    : src.params.provider.server.name === 'pdbj'
+                        ? getPdbjDownloadParams(src)
+                        : src.params.provider.server.name === 'rcsb'
+                            ? getRcsbDownloadParams(src)
+                            : assertUnreachable(src as never)
             );
             asTrajectory = !!src.params.options.asTrajectory;
             break;
@@ -205,6 +206,27 @@ async function getDownloadParams(src: string, url: (id: string) => string | Prom
     return ret;
 }
 
+async function getPdbeDownloadParams(src: ReturnType<DownloadStructure['createDefaultParams']>['source']) {
+    if (src.name !== 'pdb' || src.params.provider.server.name !== 'pdbe') throw new Error('expected pdbe');
+    return 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: ${id} (updated cif)`, false)
+        : src.params.provider.server.params.variant === 'updated-bcif'
+            ? getDownloadParams(src.params.provider.id, id => `https://www.ebi.ac.uk/pdbe/entry-files/download/${id.toLowerCase()}.bcif`, id => `PDBe: ${id} (updated cif)`, true)
+            : getDownloadParams(src.params.provider.id, id => `https://www.ebi.ac.uk/pdbe/static/entry/${id.toLowerCase()}.cif`, id => `PDBe: ${id} (cif)`, false);
+}
+
+async function getPdbjDownloadParams(src: ReturnType<DownloadStructure['createDefaultParams']>['source']) {
+    if (src.name !== 'pdb' || src.params.provider.server.name !== 'pdbj') throw new Error('expected pdbj');
+    return getDownloadParams(src.params.provider.id, id => `https://data.pdbjbk1.pdbj.org/pub/pdb/data/structures/divided/mmCIF/${id.toLowerCase().substring(1, 3)}/${id.toLowerCase()}.cif`, id => `PDBj: ${id} (cif)`, false);
+}
+
+async function getRcsbDownloadParams(src: ReturnType<DownloadStructure['createDefaultParams']>['source']) {
+    if (src.name !== 'pdb' || src.params.provider.server.name !== 'rcsb') throw new Error('expected rcsb');
+    return src.params.provider.server.params.encoding === 'cif'
+        ? getDownloadParams(src.params.provider.id, id => `https://files.rcsb.org/download/${id.toUpperCase()}.cif`, id => `RCSB PDB: ${id} (cif)`, false)
+        : getDownloadParams(src.params.provider.id, id => `https://models.rcsb.org/${id.toUpperCase()}.bcif`, id => `RCSB PDB: ${id} (bcif)`, true);
+}
+
 export const UpdateTrajectory = StateAction.build({
     display: { name: 'Update Trajectory' },
     params: {

src/mol-plugin-state/actions/volume.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -75,8 +75,8 @@ const DownloadDensity = StateAction.build({
         case 'pdb-xray':
             downloadParams = src.params.provider.server === 'pdbe' ? {
                 url: Asset.Url(src.params.type === '2fofc'
-                    ? `http://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}.ccp4`
-                    : `http://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}_diff.ccp4`),
+                    ? `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}.ccp4`
+                    : `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}_diff.ccp4`),
                 isBinary: true,
                 label: `PDBe X-ray map: ${src.params.provider.id}`
             } : {

src/mol-plugin-state/animation/built-in/camera-rock.ts

@@ -0,0 +1,62 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Camera } from '../../../mol-canvas3d/camera';
+import { clamp } from '../../../mol-math/interpolate';
+import { Quat } from '../../../mol-math/linear-algebra/3d/quat';
+import { Vec3 } from '../../../mol-math/linear-algebra/3d/vec3';
+import { degToRad } from '../../../mol-math/misc';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginStateAnimation } from '../model';
+
+const _dir = Vec3(), _axis = Vec3(), _rot = Quat();
+
+type State = { snapshot: Camera.Snapshot };
+
+export const AnimateCameraRock = PluginStateAnimation.create({
+    name: 'built-in.animate-camera-rock',
+    display: { name: 'Camera Rock', description: 'Rock the 3D scene around the x-axis in view space' },
+    isExportable: true,
+    params: () => ({
+        durationInMs: PD.Numeric(4000, { min: 100, max: 20000, step: 100 }),
+        speed: PD.Numeric(1, { min: 1, max: 10, step: 1 }, { description: 'How many times to rock from side to side.' }),
+        angle: PD.Numeric(10, { min: 0, max: 180, step: 1 }, { description: 'How many degrees to rotate in each direction.' }),
+    }),
+    initialState: (p, ctx) => ({ snapshot: ctx.canvas3d!.camera.getSnapshot() }) as State,
+    getDuration: p => ({ kind: 'fixed', durationMs: p.durationInMs }),
+    teardown: (_, state: State, ctx) => {
+        ctx.canvas3d?.requestCameraReset({ snapshot: state.snapshot, durationMs: 0 });
+    },
+
+    async apply(animState: State, t, ctx) {
+        if (t.current === 0) {
+            return { kind: 'next', state: animState };
+        }
+
+        const snapshot = animState.snapshot;
+        if (snapshot.radiusMax < 0.0001) {
+            return { kind: 'finished' };
+        }
+
+        const phase = t.animation
+            ? t.animation?.currentFrame / (t.animation.frameCount + 1)
+            : clamp(t.current / ctx.params.durationInMs, 0, 1);
+        const angle = Math.sin(phase * ctx.params.speed * Math.PI * 2) * degToRad(ctx.params.angle);
+
+        Vec3.sub(_dir, snapshot.position, snapshot.target);
+        Vec3.normalize(_axis, snapshot.up);
+        Quat.setAxisAngle(_rot, _axis, angle);
+        Vec3.transformQuat(_dir, _dir, _rot);
+        const position = Vec3.add(Vec3(), snapshot.target, _dir);
+        ctx.plugin.canvas3d?.requestCameraReset({ snapshot: { ...snapshot, position }, durationMs: 0 });
+
+        if (phase >= 0.99999) {
+            return { kind: 'finished' };
+        }
+
+        return { kind: 'next', state: animState };
+    }
+});

src/mol-plugin-state/animation/built-in/camera-spin.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -17,11 +17,11 @@ type State = { snapshot: Camera.Snapshot };
 
 export const AnimateCameraSpin = PluginStateAnimation.create({
     name: 'built-in.animate-camera-spin',
-    display: { name: 'Camera Spin' },
+    display: { name: 'Camera Spin', description: 'Spin the 3D scene around the x-axis in view space' },
     isExportable: true,
     params: () => ({
         durationInMs: PD.Numeric(4000, { min: 100, max: 20000, step: 100 }),
-        speed: PD.Numeric(1, { min: 1, max: 10, step: 1 }, { description: 'How many times to spin in the specified dutation.' }),
+        speed: PD.Numeric(1, { min: 1, max: 10, step: 1 }, { description: 'How many times to spin in the specified duration.' }),
         direction: PD.Select<'cw' | 'ccw'>('cw', [['cw', 'Clockwise'], ['ccw', 'Counter Clockwise']], { cycle: true })
     }),
     initialState: (_, ctx) => ({ snapshot: ctx.canvas3d?.camera.getSnapshot()! }) as State,
@@ -39,13 +39,9 @@ export const AnimateCameraSpin = PluginStateAnimation.create({
             return { kind: 'finished' };
         }
 
-        const phase = clamp(t.current / ctx.params.durationInMs, 0, 1);
-
-        if (phase >= 0.99999) {
-            ctx.plugin.canvas3d?.requestCameraReset({ snapshot, durationMs: 0 });
-            return { kind: 'finished' };
-        }
-
+        const phase = t.animation
+            ? t.animation?.currentFrame / (t.animation.frameCount + 1)
+            : clamp(t.current / ctx.params.durationInMs, 0, 1);
         const angle = 2 * Math.PI * phase * ctx.params.speed * (ctx.params.direction === 'ccw' ? -1 : 1);
 
         Vec3.sub(_dir, snapshot.position, snapshot.target);
@@ -55,6 +51,10 @@ export const AnimateCameraSpin = PluginStateAnimation.create({
         const position = Vec3.add(Vec3(), snapshot.target, _dir);
         ctx.plugin.canvas3d?.requestCameraReset({ snapshot: { ...snapshot, position }, durationMs: 0 });
 
+        if (phase >= 0.99999) {
+            return { kind: 'finished' };
+        }
+
         return { kind: 'next', state: animState };
     }
 });

src/mol-plugin-state/animation/model.ts

@@ -51,7 +51,8 @@ namespace PluginStateAnimation {
 
     export interface Time {
         lastApplied: number,
-        current: number
+        current: number,
+        animation?: { currentFrame: number, frameCount: number }
     }
 
     export type ApplyResult<S> = { kind: 'finished' } | { kind: 'skip' } | { kind: 'next', state: S }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -24,6 +24,8 @@ import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bo
 import { StructConn } from '../../../mol-model-formats/structure/property/bonds/struct_conn';
 import { StructureRepresentationRegistry } from '../../../mol-repr/structure/registry';
 import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { Color } from '../../../mol-util/color';
+import { PostprocessingParams } from '../../../mol-canvas3d/passes/postprocessing';
 
 export interface StructureRepresentationPresetProvider<P = any, S extends _Result = _Result> extends PresetProvider<PluginStateObject.Molecule.Structure, P, S> { }
 export function StructureRepresentationPresetProvider<P, S extends _Result>(repr: StructureRepresentationPresetProvider<P, S>) { return repr; }
@@ -98,6 +100,15 @@ type CommonParams = StructureRepresentationPresetProvider.CommonParams
 const reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 const updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
 
+function resetPostprocessingProps(plugin: PluginContext) {
+    if (plugin.canvas3d) {
+        const p = PD.getDefaultValues(PostprocessingParams);
+        plugin.canvas3d.setProps({
+            postprocessing: { outline: p.outline, occlusion: p.occlusion }
+        });
+    }
+}
+
 const auto = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-auto',
     display: {
@@ -137,6 +148,7 @@ const empty = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-empty',
     display: { name: 'Empty', description: 'Removes all existing representations.' },
     async apply(ref, params, plugin) {
+        resetPostprocessingProps(plugin);
         return { };
     }
 });
@@ -191,6 +203,8 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: false });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
+        resetPostprocessingProps(plugin);
+
         return { components, representations };
     }
 });
@@ -230,6 +244,8 @@ const proteinAndNucleic = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
+        resetPostprocessingProps(plugin);
+
         return { components, representations };
     }
 });
@@ -282,6 +298,8 @@ const coarseSurface = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
+        resetPostprocessingProps(plugin);
+
         return { components, representations };
     }
 });
@@ -315,6 +333,8 @@ const polymerCartoon = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
+        resetPostprocessingProps(plugin);
+
         return { components, representations };
     }
 });
@@ -381,6 +401,56 @@ const atomicDetail = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params ?? colorParams);
 
+        resetPostprocessingProps(plugin);
+
+        return { components, representations };
+    }
+});
+
+const illustrative = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-illustrative',
+    display: {
+        name: 'Illustrative', group: 'Miscellaneous',
+        description: '...'
+    },
+    params: () => ({
+        ...CommonParams,
+        showCarbohydrateSymbol: PD.Boolean(false)
+    }),
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        if (!structureCell) return {};
+
+        const components = {
+            all: await presetStaticComponent(plugin, structureCell, 'all'),
+            branched: undefined
+        };
+
+        const structure = structureCell.obj!.data;
+
+        const { update, builder, typeParams, color } = reprBuilder(plugin, params, structure);
+
+        const representations = {
+            all: builder.buildRepresentation(update, components.all, { type: 'spacefill', typeParams: { ...typeParams, ignoreLight: true }, color: 'illustrative' }, { tag: 'all' }),
+        };
+        await update.commit({ revertOnError: true });
+        await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params);
+
+        if (plugin.canvas3d) {
+            plugin.canvas3d.setProps({
+                postprocessing: {
+                    outline: {
+                        name: 'on',
+                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
+                    },
+                    occlusion: {
+                        name: 'on',
+                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
+                    },
+                }
+            });
+        }
+
         return { components, representations };
     }
 });
@@ -400,6 +470,7 @@ export const PresetStructureRepresentations = {
     'polymer-cartoon': polymerCartoon,
     'polymer-and-ligand': polymerAndLigand,
     'protein-and-nucleic': proteinAndNucleic,
-    'coarse-surface': coarseSurface
+    'coarse-surface': coarseSurface,
+    'illustrative': illustrative,
 };
 export type PresetStructureRepresentations = typeof PresetStructureRepresentations;

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

@@ -18,7 +18,6 @@ import { objectForEach } from '../../mol-util/object';
 import { RecommendedIsoValue } from '../../mol-model-formats/volume/property';
 import { getContourLevelEmdb } from '../../mol-plugin/behavior/dynamic/volume-streaming/util';
 import { Task } from '../../mol-task';
-import { DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 export const VolumeFormatCategory = 'Volume';
 type Params = { entryId?: string };
@@ -42,19 +41,9 @@ async function tryObtainRecommendedIsoValue(plugin: PluginContext, volume?: Volu
 function tryGetRecomendedIsoValue(volume: Volume) {
     const recommendedIsoValue = RecommendedIsoValue.Provider.get(volume);
     if (!recommendedIsoValue) return;
-
     if (recommendedIsoValue.kind === 'relative') return recommendedIsoValue;
 
-    let stats = volume.grid.stats;
-    if (DscifFormat.is(volume.sourceData)) {
-        stats = {
-            min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
-            max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
-            mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
-            sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
-        };
-    }
-    return Volume.IsoValue.toRelative(recommendedIsoValue, stats);
+    return Volume.adjustedIsoValue(volume, recommendedIsoValue.absoluteValue, 'absolute');
 }
 
 async function defaultVisuals(plugin: PluginContext, data: { volume: StateObjectSelector<PluginStateObject.Volume.Data> }) {

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

@@ -99,12 +99,12 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
         await this.start();
     }
 
-    async tick(t: number, isSynchronous?: boolean) {
+    async tick(t: number, isSynchronous?: boolean, animation?: PluginAnimationManager.AnimationInfo) {
         this.currentTime = t;
         if (this.isStopped) return;
 
-        if (isSynchronous) {
-            await this.applyFrame();
+        if (isSynchronous || animation) {
+            await this.applyFrame(animation);
         } else {
             this.applyAsync();
         }
@@ -165,12 +165,12 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
         }
     }
 
-    private async applyFrame() {
+    private async applyFrame(animation?: PluginAnimationManager.AnimationInfo) {
         const t = this.currentTime;
         if (this._current.startedTime < 0) this._current.startedTime = t;
         const newState = await this._current.anim.apply(
             this._current.state,
-            { lastApplied: this._current.lastTime, current: t - this._current.startedTime },
+            { lastApplied: this._current.lastTime, current: t - this._current.startedTime, animation },
             { params: this._current.paramValues, plugin: this.context });
 
         if (newState.kind === 'finished') {
@@ -228,6 +228,11 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
 }
 
 namespace PluginAnimationManager {
+    export interface AnimationInfo {
+        currentFrame: number,
+        frameCount: number
+    }
+
     export interface Current {
         anim: PluginStateAnimation
         params: PD.Params,

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

@@ -84,7 +84,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         const from = this.getIndex(e);
         let to = (from + dir) % len;
         if (to < 0) to += len;
-        const f = this.state.entries.get(to);
+        const f = this.state.entries.get(to)!;
 
         const entries = this.state.entries.asMutable();
         entries.set(to, e);
@@ -115,7 +115,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         if (!id) {
             if (len === 0) return void 0;
             const idx = dir === -1 ? len - 1 : 0;
-            return this.state.entries.get(idx).snapshot.id;
+            return this.state.entries.get(idx)!.snapshot.id;
         }
 
         const e = this.getEntry(id);
@@ -126,7 +126,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         idx = (idx + dir) % len;
         if (idx < 0) idx += len;
 
-        return this.state.entries.get(idx).snapshot.id;
+        return this.state.entries.get(idx)!.snapshot.id;
     }
 
     async setStateSnapshot(snapshot: PluginStateSnapshotManager.StateSnapshot): Promise<PluginState.Snapshot | undefined> {

src/mol-plugin-state/transforms/model.ts

@@ -918,7 +918,7 @@ async function attachModelProps(model: Model, ctx: PluginContext, taskCtx: Runti
     const propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
     const { autoAttach, properties } = params;
     for (const name of Object.keys(properties)) {
-        const property = ctx.customModelProperties.get(name);
+        const property = ctx.customModelProperties.get(name)!;
         const props = properties[name];
         if (autoAttach.includes(name) || property.isHidden) {
             try {
@@ -973,7 +973,7 @@ async function attachStructureProps(structure: Structure, ctx: PluginContext, ta
     const propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
     const { autoAttach, properties } = params;
     for (const name of Object.keys(properties)) {
-        const property = ctx.customStructureProperties.get(name);
+        const property = ctx.customStructureProperties.get(name)!;
         const props = properties[name];
         if (autoAttach.includes(name) || property.isHidden) {
             try {

src/mol-plugin-ui/controls.tsx

@@ -125,7 +125,7 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
         } else if (e.keyCode === 38 || e.key === 'ArrowUp') {
             if (snapshots.state.isPlaying) snapshots.stop();
             if (snapshots.state.entries.size === 0) return;
-            const e = snapshots.state.entries.get(0);
+            const e = snapshots.state.entries.get(0)!;
             this.update(e.snapshot.id);
         } else if (e.keyCode === 39 || e.key === 'ArrowRight') {
             if (snapshots.state.isPlaying) snapshots.stop();
@@ -133,7 +133,7 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
         } else if (e.keyCode === 40 || e.key === 'ArrowDown') {
             if (snapshots.state.isPlaying) snapshots.stop();
             if (snapshots.state.entries.size === 0) return;
-            const e = snapshots.state.entries.get(snapshots.state.entries.size - 1);
+            const e = snapshots.state.entries.get(snapshots.state.entries.size - 1)!;
             this.update(e.snapshot.id);
         }
     };

src/mol-plugin-ui/structure/superposition.tsx

@@ -185,9 +185,9 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
             rmsd += xform.transform.rmsd;
         }
 
-        rmsd /= transforms.length - 1;
+        rmsd /= Math.max(transforms.length - 1, 1);
 
-        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)}.`);
+        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
         await new Promise(res => requestAnimationFrame(res));
         PluginCommands.Camera.Reset(this.plugin);
     };

src/mol-plugin-ui/viewport/simple-settings.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -46,10 +46,7 @@ const LayoutOptions = {
 type LayoutOptions = keyof typeof LayoutOptions
 
 const SimpleSettingsParams = {
-    spin: PD.Group({
-        spin: Canvas3DParams.trackball.params.spin,
-        speed: Canvas3DParams.trackball.params.spinSpeed
-    }, { pivot: 'spin' }),
+    animate: Canvas3DParams.trackball.params.animate,
     camera: Canvas3DParams.camera,
     background: PD.Group({
         color: PD.Color(Color(0xFCFBF9), { label: 'Background', description: 'Custom background color' }),
@@ -96,7 +93,7 @@ const SimpleSettingsMapping = ParamMapping({
 
         return {
             layout: props.layout,
-            spin: { spin: !!canvas.trackball.spin, speed: canvas.trackball.spinSpeed },
+            animate: canvas.trackball.animate,
             camera: canvas.camera,
             background: {
                 color: renderer.backgroundColor,
@@ -114,8 +111,7 @@ const SimpleSettingsMapping = ParamMapping({
     },
     update(s, props) {
         const canvas = props.canvas as Mutable<Canvas3DProps>;
-        canvas.trackball.spin = s.spin.spin;
-        canvas.trackball.spinSpeed = s.spin.speed;
+        canvas.trackball.animate = s.animate;
         canvas.camera = s.camera;
         canvas.transparentBackground = s.background.transparent;
         canvas.renderer.backgroundColor = s.background.color;

src/mol-plugin/animation-loop.ts

@@ -6,6 +6,7 @@
 
 import { PluginContext } from './context';
 import { now } from '../mol-util/now';
+import { PluginAnimationManager } from '../mol-plugin-state/manager/animation';
 
 export class PluginAnimationLoop {
     private currentFrame: any = void 0;
@@ -15,8 +16,8 @@ export class PluginAnimationLoop {
         return this._isAnimating;
     }
 
-    async tick(t: number, options?: { isSynchronous?: boolean, manualDraw?: boolean }) {
-        await this.plugin.managers.animation.tick(t, options?.isSynchronous);
+    async tick(t: number, options?: { isSynchronous?: boolean, manualDraw?: boolean, animation?: PluginAnimationManager.AnimationInfo }) {
+        await this.plugin.managers.animation.tick(t, options?.isSynchronous, options?.animation);
         this.plugin.canvas3d?.tick(t as now.Timestamp, options);
     }
 

src/mol-plugin/spec.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -23,6 +23,7 @@ import { StateTransforms } from '../mol-plugin-state/transforms';
 import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { AnimateStateInterpolation } from '../mol-plugin-state/animation/built-in/state-interpolation';
 import { AnimateStructureSpin } from '../mol-plugin-state/animation/built-in/spin-structure';
+import { AnimateCameraRock } from '../mol-plugin-state/animation/built-in/camera-rock';
 
 export { PluginSpec };
 
@@ -131,6 +132,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
     animations: [
         AnimateModelIndex,
         AnimateCameraSpin,
+        AnimateCameraRock,
         AnimateStateSnapshots,
         AnimateAssemblyUnwind,
         AnimateStructureSpin,

src/mol-plugin/util/toast.ts

@@ -72,7 +72,7 @@ export class PluginToastManager extends StatefulPluginComponent<{
 
         if (delay < 0) delay = 500;
         return <number><any>setTimeout(() => {
-            const e = this.state.entries.get(id);
+            const e = this.state.entries.get(id)!;
             e.timeout = void 0;
             this.hide(e);
         }, delay);

src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -101,6 +101,8 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
     return EmptyLoci;
 }
 
+const __linkIndicesSet = new Set<number>();
+
 function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
     let changed = false;
     if (!StructureElement.Loci.is(loci)) return false;
@@ -110,11 +112,14 @@ function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval
     for (const { unit, indices } of loci.elements) {
         if (!Unit.isAtomic(unit)) continue;
 
+        __linkIndicesSet.clear();
         OrderedSet.forEach(indices, v => {
-            // TODO avoid duplicate calls to apply
             const linkIndices = getLinkIndices(unit, unit.elements[v]);
             for (let i = 0, il = linkIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                }
             }
         });
     }

src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -29,8 +29,8 @@ import { getAltResidueLociFromId } from './util/common';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
 
 const t = Mat4.identity();
-const sVec = Vec3.zero();
-const pd = Vec3.zero();
+const sVec = Vec3();
+const pd = Vec3();
 
 const SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
 
@@ -212,6 +212,8 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
     return EmptyLoci;
 }
 
+const __elementIndicesSet = new Set<number>();
+
 /** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
 function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
     const { getElementIndices } = structure.carbohydrates;
@@ -222,11 +224,14 @@ function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: In
     for (const { unit, indices } of loci.elements) {
         if (!Unit.isAtomic(unit)) continue;
 
+        __elementIndicesSet.clear();
         OrderedSet.forEach(indices, v => {
-            // TODO avoid duplicate calls to apply
             const elementIndices = getElementIndices(unit, unit.elements[v]);
             for (let i = 0, il = elementIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(elementIndices[i] * 2))) changed = true;
+                if (!__elementIndicesSet.has(elementIndices[i])) {
+                    __elementIndicesSet.add(elementIndices[i]);
+                    if (apply(Interval.ofSingleton(elementIndices[i] * 2))) changed = true;
+                }
             }
         });
     }

src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -123,6 +123,8 @@ function getTerminalLinkLoci(pickingId: PickingId, structure: Structure, id: num
     return EmptyLoci;
 }
 
+const __linkIndicesSet = new Set<number>();
+
 function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
     let changed = false;
     if (!StructureElement.Loci.is(loci)) return false;
@@ -132,11 +134,14 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
     for (const { unit, indices } of loci.elements) {
         if (!Unit.isAtomic(unit)) continue;
 
+        __linkIndicesSet.clear();
         OrderedSet.forEach(indices, v => {
-            // TODO avoid duplicate calls to apply
             const linkIndices = getTerminalLinkIndices(unit, unit.elements[v]);
             for (let i = 0, il = linkIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                }
             }
         });
     }

src/mol-repr/structure/visual/util/bond.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -224,6 +224,8 @@ export function getInterBondLoci(pickingId: PickingId, structure: Structure, id:
     return EmptyLoci;
 }
 
+const __unitMap = new Map<number, OrderedSet<StructureElement.UnitIndex>>();
+
 export function eachInterBond(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean) {
     let changed = false;
     if (Bond.isLoci(loci)) {
@@ -238,14 +240,13 @@ export function eachInterBond(loci: Loci, structure: Structure, apply: (interval
         if (!Structure.areEquivalent(loci.structure, structure)) return false;
         if (isMarking && loci.elements.length === 1) return false; // only a single unit
 
-        const map = new Map<number, OrderedSet<StructureElement.UnitIndex>>();
-        for (const e of loci.elements) map.set(e.unit.id, e.indices);
+        for (const e of loci.elements) __unitMap.set(e.unit.id, e.indices);
 
         for (const e of loci.elements) {
             const { unit } = e;
             if (!Unit.isAtomic(unit)) continue;
             structure.interUnitBonds.getConnectedUnits(unit.id).forEach(b => {
-                const otherLociIndices = map.get(b.unitB);
+                const otherLociIndices = __unitMap.get(b.unitB);
                 if (!isMarking || otherLociIndices) {
                     OrderedSet.forEach(e.indices, v => {
                         if (!b.connectedIndices.includes(v)) return;
@@ -259,6 +260,8 @@ export function eachInterBond(loci: Loci, structure: Structure, apply: (interval
                 }
             });
         }
+
+        __unitMap.clear();
     }
     return changed;
 }

src/mol-repr/visual.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -88,6 +88,7 @@ namespace Visual {
         const currentStatus = markerStatus.ref.value as MarkerInfo['status'];
 
         if (!isEveryLoci(loci)) {
+            // assume that all interval are non-overlapping
             let intervalSize = 0;
             lociApply(loci, interval => {
                 intervalSize += Interval.size(interval);

src/mol-state/tree/immutable.ts

@@ -34,19 +34,38 @@ namespace StateTree {
         readonly forEach: OrderedSet<Ref>['forEach'],
         readonly map: OrderedSet<Ref>['map'],
         toArray(): Ref[],
-        first(): Ref
+        first(): Ref,
+        asMutable(): MutableChildSet
     }
 
+    export interface MutableChildSet extends ChildSet {
+        add(ref: Ref): MutableChildSet,
+        remove(ref: Ref): MutableChildSet,
+        asImmutable(): ChildSet
+    }
+
+
     interface _Map<T> {
         readonly size: number,
         has(ref: Ref): boolean,
-        get(ref: Ref): T
+        get(ref: Ref): T,
+        asImmutable(): _Map<T>,
+        asMutable(): MutableMap<T>
+    }
+
+    export interface MutableMap<T> extends _Map<T> {
+        set(ref: Ref, value: T): MutableMap<T>,
+        delete(ref: Ref): MutableMap<T>
     }
 
     export interface Transforms extends _Map<StateTransform> {}
     export interface Children extends _Map<ChildSet> { }
     export interface Dependencies extends _Map<ChildSet> { }
 
+    export interface MutableTransforms extends MutableMap<StateTransform> {}
+    export interface MutableChildren extends MutableMap<MutableChildSet> { }
+    export interface MutableDependencies extends MutableMap<MutableChildSet> { }
+
     class Impl implements StateTree {
         get root() { return this.transforms.get(StateTransform.RootRef)!; }
 
@@ -63,7 +82,10 @@ namespace StateTree {
      */
     export function createEmpty(customRoot?: StateTransform): StateTree {
         const root = customRoot || StateTransform.createRoot();
-        return create(ImmutableMap([[root.ref, root]]), ImmutableMap([[root.ref, OrderedSet()]]), ImmutableMap());
+        return create(
+            ImmutableMap([[root.ref, root] as [Ref, StateTransform]]) as Transforms,
+            ImmutableMap([[root.ref, OrderedSet()] as [Ref, ChildSet]]) as Children,
+            ImmutableMap() as Dependencies);
     }
 
     export function create(nodes: Transforms, children: Children, dependencies: Dependencies): StateTree {
@@ -148,13 +170,13 @@ namespace StateTree {
                 children.set(transform.ref, OrderedSet<Ref>().asMutable());
             }
 
-            if (transform.ref !== transform.parent) children.get(transform.parent).add(transform.ref);
+            if (transform.ref !== transform.parent) children.get(transform.parent)!.add(transform.ref);
         }
 
         const dependent = new Set<Ref>();
         for (const t of data.transforms) {
             const ref = t.ref;
-            children.set(ref, children.get(ref).asImmutable());
+            children.set(ref, children.get(ref)!.asImmutable());
 
             if (!t.dependsOn) continue;
 
@@ -163,16 +185,16 @@ namespace StateTree {
                 if (!dependencies.has(d)) {
                     dependencies.set(d, OrderedSet<Ref>([ref]).asMutable());
                 } else {
-                    dependencies.get(d).add(ref);
+                    dependencies.get(d)!.add(ref);
                 }
             }
         }
 
         dependent.forEach(d => {
-            dependencies.set(d, dependencies.get(d).asImmutable());
+            dependencies.set(d, dependencies.get(d)!.asImmutable());
         });
 
-        return create(nodes.asImmutable(), children.asImmutable(), dependencies.asImmutable());
+        return create(nodes.asImmutable() as Transforms, children.asImmutable() as Children, dependencies.asImmutable() as Dependencies);
     }
 
     export function dump(tree: StateTree) {

src/mol-state/tree/transient.ts

@@ -13,16 +13,16 @@ import { arrayEqual } from '../../mol-util/array';
 export { TransientTree };
 
 class TransientTree implements StateTree {
-    transforms = this.tree.transforms as ImmutableMap<StateTransform.Ref, StateTransform>;
-    children = this.tree.children as ImmutableMap<StateTransform.Ref, OrderedSet<StateTransform.Ref>>;
-    dependencies = this.tree.dependencies as ImmutableMap<StateTransform.Ref, OrderedSet<StateTransform.Ref>>;
+    transforms = this.tree.transforms as StateTree.MutableTransforms;
+    children = this.tree.children as StateTree.MutableChildren;
+    dependencies = this.tree.dependencies as StateTree.MutableDependencies;
 
     private changedNodes = false;
     private changedChildren = false;
     private changedDependencies = false;
 
     private _childMutations: Map<StateTransform.Ref, OrderedSet<StateTransform.Ref>> | undefined = void 0;
-    private _dependencyMutations: Map<StateTransform.Ref, OrderedSet<StateTransform.Ref>> | undefined = void 0;
+    private _dependencyMutations: Map<StateTransform.Ref, StateTree.MutableChildSet> | undefined = void 0;
     private _stateUpdates: Set<StateTransform.Ref> | undefined = void 0;
 
     private get childMutations() {
@@ -99,12 +99,11 @@ class TransientTree implements StateTree {
     }
 
     private mutateDependency(parent: StateTransform.Ref, child: StateTransform.Ref, action: 'add' | 'remove') {
-        let set = this.dependencyMutations.get(parent);
+        let set: StateTree.MutableChildSet | undefined = this.dependencyMutations.get(parent);
 
         if (!set) {
             const src = this.dependencies.get(parent);
             if (!src && action === 'remove') return;
-
             this.changeDependencies();
             set = src ? src.asMutable() : OrderedSet<string>().asMutable();
             this.dependencyMutations.set(parent, set);
@@ -275,7 +274,7 @@ class TransientTree implements StateTree {
     asImmutable() {
         if (!this.changedNodes && !this.changedChildren && !this._childMutations) return this.tree;
         if (this._childMutations) this._childMutations.forEach(fixChildMutations, this.children);
-        if (this._dependencyMutations) this._dependencyMutations.forEach(fixDependencyMutations, this.dependencies);
+        if (this._dependencyMutations) this._dependencyMutations.forEach(fixDependencyMutations as any, this.dependencies);
         return StateTree.create(
             this.changedNodes ? this.transforms.asImmutable() : this.transforms,
             this.changedChildren ? this.children.asImmutable() : this.children,

src/mol-theme/color/element-symbol.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -13,8 +13,12 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
 import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator-name';
+import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
 
 // from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
 export const ElementSymbolColors = ColorMap({
@@ -25,16 +29,20 @@ export type ElementSymbolColors = typeof ElementSymbolColors
 const DefaultElementSymbolColor = Color(0xFFFFFF);
 const Description = 'Assigns a color to every atom according to its chemical element.';
 
-// TODO generalise `carbonColor` param to all themes?
-
 export const ElementSymbolColorThemeParams = {
     carbonColor: PD.MappedStatic('chain-id', {
-        'chain-id': PD.Group({ ...ChainIdColorThemeParams }),
-        'operator-name': PD.Group({ ...OperatorNameColorThemeParams }),
-        'element-symbol': PD.Group({})
+        'chain-id': PD.Group(ChainIdColorThemeParams),
+        'entity-id': PD.Group(EntityIdColorThemeParams),
+        'entity-source': PD.Group(EntitySourceColorThemeParams),
+        'operator-name': PD.Group(OperatorNameColorThemeParams),
+        'element-symbol': PD.EmptyGroup()
     }, { description: 'Use chain-id coloring for carbon atoms.' }),
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ElementSymbolColors))
+    })
 };
 export type ElementSymbolColorThemeParams = typeof ElementSymbolColorThemeParams
 export function getElementSymbolColorThemeParams(ctx: ThemeDataContext) {
@@ -47,13 +55,16 @@ export function elementSymbolColor(colorMap: ElementSymbolColors, element: Eleme
 }
 
 export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<ElementSymbolColorThemeParams>): ColorTheme<ElementSymbolColorThemeParams> {
-    const colorMap = getAdjustedColorMap(ElementSymbolColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ElementSymbolColors : props.colors.params, props.saturation, props.lightness);
 
-    const carbonColor = props.carbonColor.name === 'chain-id'
-        ? ChainIdColorTheme(ctx, props.carbonColor.params).color
-        : props.carbonColor.name === 'operator-name'
-            ? OperatorNameColorTheme(ctx, props.carbonColor.params).color
-            : undefined;
+    const pcc = props.carbonColor;
+    const carbonColor =
+        pcc.name === 'chain-id' ? ChainIdColorTheme(ctx, pcc.params).color :
+            pcc.name === 'entity-id' ? EntityIdColorTheme(ctx, pcc.params).color :
+                pcc.name === 'entity-source' ? EntitySourceColorTheme(ctx, pcc.params).color :
+                    pcc.name === 'operator-name' ? OperatorNameColorTheme(ctx, pcc.params).color :
+                        pcc.name === 'element-symbol' ? undefined :
+                            assertUnreachable(pcc);
 
     function elementColor(element: ElementSymbol, location: Location) {
         return (carbonColor && element === 'C')
@@ -86,8 +97,8 @@ export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<
         color,
         props,
         description: Description,
-        legend: TableLegend(Object.keys(ElementSymbolColors).map(name => {
-            return [name, (ElementSymbolColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
         }))
     };
 }

src/mol-theme/color/entity-id.ts

@@ -1,10 +1,10 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { StructureProperties, StructureElement, Bond, Structure } from '../../mol-model/structure';
+import { StructureProperties, StructureElement, Bond, Structure, Unit } from '../../mol-model/structure';
 import { Color } from '../../mol-util/color';
 import { Location } from '../../mol-model/location';
 import { ColorTheme, LocationColor } from '../color';
@@ -38,10 +38,33 @@ function getEntityIdSerialMap(structure: Structure) {
             const k = key(label_entity_id.value(j), i);
             if (!map.has(k)) map.set(k, map.size);
         }
+        const { coarseHierarchy } = structure.models[i];
+        if (coarseHierarchy.isDefined) {
+            const { entity_id: spheres_entity_id } = coarseHierarchy.spheres;
+            for (let j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
+                const k = key(spheres_entity_id.value(j), i);
+                if (!map.has(k)) map.set(k, map.size);
+            }
+            const { entity_id: gaussians_entity_id } = coarseHierarchy.gaussians;
+            for (let j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
+                const k = key(gaussians_entity_id.value(j), i);
+                if (!map.has(k)) map.set(k, map.size);
+            }
+        }
     }
     return map;
 }
 
+function getEntityId(location: StructureElement.Location): string {
+    switch (location.unit.kind) {
+        case Unit.Kind.Atomic:
+            return StructureProperties.chain.label_entity_id(location);
+        case Unit.Kind.Spheres:
+        case Unit.Kind.Gaussians:
+            return StructureProperties.coarse.entity_id(location);
+    }
+}
+
 export function EntityIdColorTheme(ctx: ThemeDataContext, props: PD.Values<EntityIdColorThemeParams>): ColorTheme<EntityIdColorThemeParams> {
     let color: LocationColor;
     let legend: ScaleLegend | TableLegend | undefined;
@@ -59,16 +82,16 @@ export function EntityIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Entit
         color = (location: Location): Color => {
             let serial: number | undefined = undefined;
             if (StructureElement.Location.is(location)) {
-                const atomId = StructureProperties.chain.label_entity_id(location);
+                const entityId = getEntityId(location);
                 const modelIndex = location.structure.models.indexOf(location.unit.model);
-                const k = key(atomId, modelIndex);
+                const k = key(entityId, modelIndex);
                 serial = entityIdSerialMap.get(k);
             } else if (Bond.isLocation(location)) {
                 l.unit = location.aUnit;
                 l.element = location.aUnit.elements[location.aIndex];
-                const atomId = StructureProperties.chain.label_entity_id(l);
+                const entityId = getEntityId(l);
                 const modelIndex = l.structure.models.indexOf(l.unit.model);
-                const k = key(atomId, modelIndex);
+                const k = key(entityId, modelIndex);
                 serial = entityIdSerialMap.get(k);
             }
             return serial === undefined ? DefaultColor : palette.color(serial);

src/mol-theme/color/illustrative.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,24 +12,42 @@ import { ColorTheme } from '../color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
+import { UniformColorTheme, UniformColorThemeParams } from './uniform';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
+import { MoleculeTypeColorTheme, MoleculeTypeColorThemeParams } from './molecule-type';
+import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
 
 const DefaultIllustrativeColor = Color(0xEEEEEE);
-const Description = `Assigns an illustrative color that gives every chain a unique color with lighter carbons (inspired by David Goodsell's Molecule of the Month style).`;
+const Description = `Assigns an illustrative color that gives every chain a color based on the choosen style but with lighter carbons (inspired by David Goodsell's Molecule of the Month style).`;
 
 export const IllustrativeColorThemeParams = {
-    ...ChainIdColorThemeParams,
+    style: PD.MappedStatic('entity-id', {
+        uniform: PD.Group(UniformColorThemeParams),
+        'chain-id': PD.Group(ChainIdColorThemeParams),
+        'entity-id': PD.Group(EntityIdColorThemeParams),
+        'entity-source': PD.Group(EntitySourceColorThemeParams),
+        'molecule-type': PD.Group(MoleculeTypeColorThemeParams),
+    }),
     carbonLightness: PD.Numeric(0.8, { min: -6, max: 6, step: 0.1 })
 };
 export type IllustrativeColorThemeParams = typeof IllustrativeColorThemeParams
 export function getIllustrativeColorThemeParams(ctx: ThemeDataContext) {
-    return IllustrativeColorThemeParams; // TODO return copy
+    const params = PD.clone(IllustrativeColorThemeParams);
+    return params;
 }
 
 export function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<IllustrativeColorThemeParams>): ColorTheme<IllustrativeColorThemeParams> {
-    const { color: chainIdColor, legend } = ChainIdColorTheme(ctx, props);
+    const { color: styleColor, legend } =
+        props.style.name === 'uniform' ? UniformColorTheme(ctx, props.style.params) :
+            props.style.name === 'chain-id' ? ChainIdColorTheme(ctx, props.style.params) :
+                props.style.name === 'entity-id' ? EntityIdColorTheme(ctx, props.style.params) :
+                    props.style.name === 'entity-source' ? EntitySourceColorTheme(ctx, props.style.params) :
+                        props.style.name === 'molecule-type' ? MoleculeTypeColorTheme(ctx, props.style.params) :
+                            assertUnreachable(props.style);
 
     function illustrativeColor(location: Location, typeSymbol: ElementSymbol) {
-        const baseColor = chainIdColor(location, false);
+        const baseColor = styleColor(location, false);
         return typeSymbol === 'C' ? Color.lighten(baseColor, props.carbonLightness) : baseColor;
     }
 

src/mol-theme/color/molecule-type.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,6 +14,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 
 export const MoleculeTypeColors = ColorMap({
     water: 0x386cb0,
@@ -31,7 +32,11 @@ const Description = 'Assigns a color based on the molecule type of a residue.';
 
 export const MoleculeTypeColorThemeParams = {
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(MoleculeTypeColors))
+    })
 };
 export type MoleculeTypeColorThemeParams = typeof MoleculeTypeColorThemeParams
 export function getMoleculeTypeColorThemeParams(ctx: ThemeDataContext) {
@@ -53,7 +58,7 @@ export function moleculeTypeColor(colorMap: MoleculeTypeColors, unit: Unit, elem
 }
 
 export function MoleculeTypeColorTheme(ctx: ThemeDataContext, props: PD.Values<MoleculeTypeColorThemeParams>): ColorTheme<MoleculeTypeColorThemeParams> {
-    const colorMap = getAdjustedColorMap(MoleculeTypeColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? MoleculeTypeColors : props.colors.params, props.saturation, props.lightness);
 
     function color(location: Location): Color {
         if (StructureElement.Location.is(location)) {
@@ -70,8 +75,8 @@ export function MoleculeTypeColorTheme(ctx: ThemeDataContext, props: PD.Values<M
         color,
         props,
         description: Description,
-        legend: TableLegend(Object.keys(MoleculeTypeColors).map(name => {
-            return [name, (MoleculeTypeColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
         }).concat([['Other/unknown', DefaultMoleculeTypeColor]]))
     };
 }

src/mol-theme/color/residue-name.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,6 +12,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 
 // protein colors from Jmol http://jmol.sourceforge.net/jscolors/
 export const ResidueNameColors = ColorMap({
@@ -66,7 +67,11 @@ const Description = 'Assigns a color to every residue according to its name.';
 
 export const ResidueNameColorThemeParams = {
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ResidueNameColors))
+    })
 };
 export type ResidueNameColorThemeParams = typeof ResidueNameColorThemeParams
 export function getResidueNameColorThemeParams(ctx: ThemeDataContext) {
@@ -93,7 +98,7 @@ export function residueNameColor(colorMap: ResidueNameColors, residueName: strin
 }
 
 export function ResidueNameColorTheme(ctx: ThemeDataContext, props: PD.Values<ResidueNameColorThemeParams>): ColorTheme<ResidueNameColorThemeParams> {
-    const colorMap = getAdjustedColorMap(ResidueNameColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ResidueNameColors : props.colors.params, props.saturation, props.lightness);
 
     function color(location: Location): Color {
         if (StructureElement.Location.is(location)) {
@@ -123,8 +128,8 @@ export function ResidueNameColorTheme(ctx: ThemeDataContext, props: PD.Values<Re
         color,
         props,
         description: Description,
-        legend: TableLegend(Object.keys(ResidueNameColors).map(name => {
-            return [name, (ResidueNameColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
         }).concat([['Unknown', DefaultResidueNameColor]]))
     };
 }

src/mol-theme/color/secondary-structure.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -15,6 +15,7 @@ import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { SecondaryStructureProvider, SecondaryStructureValue } from '../../mol-model-props/computed/secondary-structure';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { hash2 } from '../../mol-data/util';
 
@@ -41,7 +42,11 @@ const Description = 'Assigns a color based on the type of secondary structure an
 
 export const SecondaryStructureColorThemeParams = {
     saturation: PD.Numeric(-1, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(SecondaryStructureColors))
+    })
 };
 export type SecondaryStructureColorThemeParams = typeof SecondaryStructureColorThemeParams
 export function getSecondaryStructureColorThemeParams(ctx: ThemeDataContext) {
@@ -88,7 +93,7 @@ export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Va
     const computedSecondaryStructure = ctx.structure && SecondaryStructureProvider.get(ctx.structure);
     const contextHash = computedSecondaryStructure ? hash2(computedSecondaryStructure.id, computedSecondaryStructure.version) : -1;
 
-    const colorMap = getAdjustedColorMap(SecondaryStructureColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? SecondaryStructureColors : props.colors.params, props.saturation, props.lightness);
 
     function color(location: Location): Color {
         if (StructureElement.Location.is(location)) {
@@ -107,8 +112,8 @@ export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Va
         props,
         contextHash,
         description: Description,
-        legend: TableLegend(Object.keys(SecondaryStructureColors).map(name => {
-            return [name, (SecondaryStructureColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
         }).concat([['Other', DefaultSecondaryStructureColor]]))
     };
 }

src/mol-util/color/color.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

src/mol-util/color/params.ts

@@ -0,0 +1,17 @@
+/**
+ * Copyright (c) 2022 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 { objectForEach } from '../object';
+import { ColorMap } from './color';
+
+export function getColorMapParams<T extends { [k: string]: number }>(map: ColorMap<T>) {
+    const colors: Record<string, PD.Color> = {};
+    objectForEach(map, (_, k) => {
+        colors[k] = PD.Color(map[k]);
+    });
+    return colors as { [k in keyof T]: PD.Color };
+}

src/servers/volume/config.ts

@@ -197,13 +197,13 @@ export function configureLocal() {
         description: VOLUME_SERVER_HEADER
     });
     parser.add_argument('--jobs', { help: `Path to a JSON file with job specification.`, required: false });
-    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });
+    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, action: 'store_true' });
     addJsonConfigArgs(parser);
     addLimitsArgs(parser);
 
     const config = parser.parse_args() as LimitsConfig & ServerJsonConfig;
 
-    if (config.cfgTemplate !== null) {
+    if (config.cfgTemplate) {
         console.log(JSON.stringify(DefaultLimitsConfig, null, 2));
         process.exit(0);
     }
@@ -216,7 +216,7 @@ export function configureLocal() {
             setLimitsConfig(cfg);
         }
 
-        if (config.printCfg !== null) {
+        if (config.printCfg) {
             console.log(JSON.stringify(LimitsConfig, null, 2));
             process.exit(0);
         }

src/servers/volume/query.ts

@@ -14,7 +14,7 @@ import * as LocalApi from './server/local-api';
 
 const config = configureLocal();
 
-if (config.jobsTemplate !== null) {
+if (config.jobsTemplate) {
     const exampleJobs: LocalApi.JobEntry[] = [{
         source: {
             filename: `g:/test/mdb/xray-1tqn.mdb`,