2.0.4

Fix incorrect deflate progress

.npmignore

@@ -1 +1 @@
-tsconfig.commonjs.buildinfo
+tsconfig.commonjs.tsbuildinfo

CHANGELOG.md

@@ -0,0 +1,39 @@
+# Change Log
+All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/) for its most widely used - and defacto - public interfaces.
+
+Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
+
+## [v2.0.4] - 2021-04-20
+
+- [WIP] Mesh export extension
+- ``Structure.eachAtomicHierarchyElement`` (#161)
+- Fixed reading multi-line values in SDF format
+- Fixed Measurements UI labels (#166)
+
+## [v2.0.3] - 2021-04-09
+### Added
+- Support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
+
+### Changed
+- [Breaking] The `zip` function is now asynchronous and expects a `RuntimeContext`. Also added `Zip()` returning a `Task`.
+- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
+
+## [v2.0.2] - 2021-03-29
+### Added
+- `Canvas3D.getRenderObjects`.
+- [WIP] Animate state interpolating, including model trajectories
+
+### Changed
+- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
+
+### Fixed
+- VolumeFromDensityServerCif transform label
+
+
+## [v2.0.1] - 2021-03-23
+### Fixed
+- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
+
+
+## [v2.0.0] - 2021-03-23
+Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.

README.md

@@ -5,15 +5,12 @@
 
 # Mol*
 
-The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as a basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open-source and available to anyone who wants to use it for developing visualization tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
 
-This particular project is the implementation of this technology (still under development).
 
-*If you are looking for the "MOLeculAR structure annoTator", that package is now available on NPM as [MolArt](https://www.npmjs.com/package/molart).*
+## Project Structure Overview
 
-## Project Overview
-
-The core of Mol* currently consists of these modules (see under `src/`):
+The core of Mol* consists of these modules (see under `src/`):
 
 - `mol-task` Computation abstraction with progress tracking and cancellation support.
 - `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
@@ -29,7 +26,6 @@ The core of Mol* currently consists of these modules (see under `src/`):
 - `mol-gl` A wrapper around WebGL.
 - `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
 - `mol-state` State representation tree with state saving and automatic updates.
-- `mol-app` Components for building UIs.
 - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
 - `mol-plugin-state` State transformations, builders, and managers.
 - `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
@@ -41,7 +37,7 @@ Moreover, the project contains the implementation of `servers`, including
 - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
 - `servers/plugin-state` A basic server to store Mol* Plugin states.
 
-The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
 
 ## Previous Work
 This project builds on experience from previous solutions:
@@ -169,9 +165,6 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 ## Contributing
 Just open an issue or make a pull request. All contributions are welcome.
 
-## Roadmap
-Continually develop this prototype project. As individual modules become stable, make them into standalone libraries.
-
 ## Funding
 Funding sources include but are not limited to:
 * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE

docs/interesting-pdb-entries.md

@@ -27,3 +27,4 @@
     * DNA (5D3G)
 * Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
 * Long linear sugar chain (4HG6)
+* Anisotropic B-factors/Ellipsoids (1EJG)

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.8",
+  "version": "2.0.4",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -14,6 +14,7 @@
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
     "test": "npm run lint && jest",
+    "jest": "jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
     "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",

src/apps/docking-viewer/viewport.tsx

@@ -4,24 +4,23 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as React from 'react';
-import { PluginUIComponent } from '../../mol-plugin-ui/base';
-import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
-import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
-import { LociLabels } from '../../mol-plugin-ui/controls';
-import { Toasts } from '../../mol-plugin-ui/toast';
-import { Button } from '../../mol-plugin-ui/controls/common';
-import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { StateObjectRef } from '../../mol-state';
-import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { InteractionsRepresentationProvider } from '../../mol-model-props/computed/representations/interactions';
 import { InteractionTypeColorThemeProvider } from '../../mol-model-props/computed/themes/interaction-type';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
+import { presetStaticComponent, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
 import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
-import { Color } from '../../mol-util/color';
+import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import { LociLabels } from '../../mol-plugin-ui/controls';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
+import { Toasts } from '../../mol-plugin-ui/toast';
+import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginConfig } from '../../mol-plugin/config';
+import { PluginContext } from '../../mol-plugin/context';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { StateObjectRef } from '../../mol-state';
+import { Color } from '../../mol-util/color';
 
 function shinyStyle(plugin: PluginContext) {
     return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {

src/apps/viewer/index.html

@@ -49,11 +49,13 @@
             if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
                 pdbProvider: pdbProvider || 'pdbe',
                 emdbProvider: emdbProvider || 'pdbe',
             });

src/apps/viewer/index.ts

@@ -10,6 +10,7 @@ import { CellPack } from '../../extensions/cellpack';
 import { DnatcoConfalPyramids } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
 import { Mp4Export } from '../../extensions/mp4-export';
+import { GeometryExport } from '../../extensions/geo-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
@@ -55,7 +56,8 @@ const Extensions = {
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
     'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
     'g3d': PluginSpec.Behavior(G3DFormat),
-    'mp4-export': PluginSpec.Behavior(Mp4Export)
+    'mp4-export': PluginSpec.Behavior(Mp4Export),
+    'geo-export': PluginSpec.Behavior(GeometryExport)
 };
 
 const DefaultViewerOptions = {
@@ -68,6 +70,7 @@ const DefaultViewerOptions = {
     layoutShowSequence: true,
     layoutShowLog: true,
     layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
     disableAntialiasing: false,
     pixelScale: 1,
     enableWboit: true,
@@ -106,6 +109,12 @@ export class Viewer {
                     isExpanded: o.layoutIsExpanded,
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: 'full',
+                        top: 'full',
+                    }
                 },
             },
             components: {

src/examples/alpha-orbitals/controls.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as React from 'react';
 import * as ReactDOM from 'react-dom';
 import { AlphaOrbitalsExample } from '.';
 import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';

src/examples/alpha-orbitals/index.ts

@@ -174,7 +174,8 @@ export class AlphaOrbitalsExample {
             kind,
             relativeIsovalue: this.state.value.isoValue,
             pickable: false,
-            xrayShaded: true
+            xrayShaded: true,
+            tryUseGpu: false
         };
     }
 

src/examples/basic-wrapper/controls.tsx

@@ -5,7 +5,6 @@
  */
 
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
-import * as React from 'react';
 
 export class CustomToastMessage extends PluginUIComponent {
     render() {

src/examples/basic-wrapper/custom-theme.ts

@@ -0,0 +1,51 @@
+import { isPositionLocation } from '../../mol-geo/util/location-iterator';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { ColorTheme } from '../../mol-theme/color';
+import { ThemeDataContext } from '../../mol-theme/theme';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+export function CustomColorTheme(
+    ctx: ThemeDataContext,
+    props: PD.Values<{}>
+): ColorTheme<{}> {
+    const { radius, center } = ctx.structure?.boundary.sphere!;
+    const radiusSq = Math.max(radius * radius, 0.001);
+    const scale = ColorTheme.PaletteScale;
+
+    return {
+        factory: CustomColorTheme,
+        granularity: 'vertex',
+        color: location => {
+            if (!isPositionLocation(location)) return ColorNames.black;
+            const dist = Vec3.squaredDistance(location.position, center);
+            const t = Math.min(dist / radiusSq, 1);
+            return ((t * scale) | 0) as Color;
+        },
+        palette: {
+            filter: 'nearest',
+            colors: [
+                ColorNames.red,
+                ColorNames.pink,
+                ColorNames.violet,
+                ColorNames.orange,
+                ColorNames.yellow,
+                ColorNames.green,
+                ColorNames.blue
+            ]
+        },
+        props: props,
+        description: '',
+    };
+}
+
+export const CustomColorThemeProvider: ColorTheme.Provider<{}, 'basic-wrapper-custom-color-theme'> = {
+    name: 'basic-wrapper-custom-color-theme',
+    label: 'Custom Color Theme',
+    category: ColorTheme.Category.Misc,
+    factory: CustomColorTheme,
+    getParams: () => ({}),
+    defaultValues: { },
+    isApplicable: (ctx: ThemeDataContext) => true,
+};

src/examples/basic-wrapper/index.html

@@ -97,6 +97,7 @@
             addHeader('Misc');
 
             addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
+            addControl('Apply Custom Theme', () => BasicMolStarWrapper.coloring.applyCustomTheme());
             addControl('Default Coloring', () => BasicMolStarWrapper.coloring.applyDefault());
 
             addHeader('Interactivity');

src/examples/basic-wrapper/index.ts

@@ -18,6 +18,7 @@ import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import { StripedResidues } from './coloring';
 import { CustomToastMessage } from './controls';
+import { CustomColorThemeProvider } from './custom-theme';
 import './index.html';
 import { buildStaticSuperposition, dynamicSuperpositionTest, StaticSuperpositionTestData } from './superposition';
 require('mol-plugin-ui/skin/light.scss');
@@ -42,6 +43,7 @@ class BasicWrapper {
         });
 
         this.plugin.representation.structure.themes.colorThemeRegistry.add(StripedResidues.colorThemeProvider!);
+        this.plugin.representation.structure.themes.colorThemeRegistry.add(CustomColorThemeProvider);
         this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider!);
         this.plugin.customModelProperties.register(StripedResidues.propertyProvider, true);
     }
@@ -103,6 +105,13 @@ class BasicWrapper {
                 }
             });
         },
+        applyCustomTheme: async () => {
+            this.plugin.dataTransaction(async () => {
+                for (const s of this.plugin.managers.structure.hierarchy.current.structures) {
+                    await this.plugin.managers.structure.component.updateRepresentationsTheme(s.components, { color: CustomColorThemeProvider.name as any });
+                }
+            });
+        },
         applyDefault: async () => {
             this.plugin.dataTransaction(async () => {
                 for (const s of this.plugin.managers.structure.hierarchy.current.structures) {

src/examples/proteopedia-wrapper/ui/controls.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as React from 'react';
 import * as ReactDOM from 'react-dom';
 import { PluginUIContext } from '../../../mol-plugin-ui/context';
 import { PluginContextContainer } from '../../../mol-plugin-ui/plugin';

src/extensions/alpha-orbitals/data-model.ts

@@ -9,6 +9,7 @@ import { Grid } from '../../mol-model/volume';
 import { SphericalBasisOrder } from './spherical-functions';
 import { Box3D, RegularGrid3d } from '../../mol-math/geometry';
 import { arrayMin, arrayMax, arrayRms, arrayMean } from '../../mol-util/array';
+import { ModelFormat } from '../../mol-model-formats/format';
 
 // Note: generally contracted gaussians are currently not supported.
 export interface SphericalElectronShell {
@@ -59,6 +60,17 @@ export interface CubeGrid {
     isovalues?: { negative?: number; positive?: number };
 }
 
+export type CubeGridFormat = ModelFormat<CubeGrid>;
+
+// eslint-disable-next-line
+export function CubeGridFormat(grid: CubeGrid): CubeGridFormat {
+    return { name: 'custom grid', kind: 'cube-grid', data: grid };
+}
+
+export function isCubeGridData(f: ModelFormat): f is CubeGridFormat {
+    return f.kind === 'cube-grid';
+}
+
 export function initCubeGrid(params: CubeGridComputationParams): CubeGridInfo {
     const geometry = params.basis.atoms.map(a => a.center);
     const { gridSpacing: spacing, boxExpand: expand } = params;

src/extensions/alpha-orbitals/transforms.ts

@@ -17,7 +17,7 @@ import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers
 import { StateTransformer } from '../../mol-state';
 import { Theme } from '../../mol-theme/theme';
 import { VolumeRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
-import { AlphaOrbital, Basis, CubeGrid } from './data-model';
+import { AlphaOrbital, Basis, CubeGrid, CubeGridFormat, isCubeGridData } from './data-model';
 import { createSphericalCollocationDensityGrid } from './density';
 import { Tensor } from '../../mol-math/linear-algebra';
 
@@ -114,7 +114,7 @@ export const CreateOrbitalVolume = PluginStateTransform.BuiltIn({
             }, a.data.orbitals[params.index], plugin.canvas3d?.webgl).runInContext(ctx);
             const volume: Volume = {
                 grid: data.grid,
-                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
+                sourceData: CubeGridFormat(data),
                 customProperties: new CustomProperties(),
                 _propertyData: Object.create(null),
             };
@@ -146,7 +146,7 @@ export const CreateOrbitalDensityVolume = PluginStateTransform.BuiltIn({
             }, a.data.orbitals, plugin.canvas3d?.webgl).runInContext(ctx);
             const volume: Volume = {
                 grid: data.grid,
-                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
+                sourceData: CubeGridFormat(data),
                 customProperties: new CustomProperties(),
                 _propertyData: Object.create(null),
             };
@@ -172,7 +172,8 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
         color: PD.Color(ColorNames.blue),
         alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
         xrayShaded: PD.Boolean(false),
-        pickable: PD.Boolean(true)
+        pickable: PD.Boolean(true),
+        tryUseGpu: PD.Boolean(true)
     }
 })({
     canAutoUpdate() {
@@ -190,7 +191,7 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
             repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
             await repr.createOrUpdate(props, a.data).runInContext(ctx);
             repr.setState({ pickable: srcParams.pickable });
-            return new PluginStateObject.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
+            return new PluginStateObject.Volume.Representation3D({ repr, sourceData: a.data }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
         });
     },
     update({ a, b, newParams: srcParams }, plugin: PluginContext) {
@@ -200,6 +201,7 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams.type.params };
             b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            b.data.sourceData = a.data;
             b.data.repr.setState({ pickable: srcParams.pickable });
             b.description = VolumeRepresentation3DHelpers.getDescription(props);
             return StateTransformer.UpdateResult.Updated;
@@ -208,9 +210,9 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
 });
 
 function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Data, params: StateTransformer.Params<typeof CreateOrbitalRepresentation3D>) {
-    if (volume.data.sourceData.kind !== 'alpha-orbitals') throw new Error('Invalid data source kind.');
+    if (!isCubeGridData(volume.data.sourceData)) throw new Error('Invalid data source kind.');
 
-    const { isovalues } = volume.data.sourceData.data as CubeGrid;
+    const { isovalues } = volume.data.sourceData.data;
     if (!isovalues) throw new Error('Isovalues are not computed.');
 
     const value = isovalues[params.kind];
@@ -229,7 +231,7 @@ function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Da
         colorParams: { value: params.color }
     } : {
         type: 'isosurface',
-        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded },
+        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded, tryUseGpu: params.tryUseGpu },
         color: 'uniform',
         colorParams: { value: params.color }
     });

src/extensions/anvil/behavior.ts

@@ -121,7 +121,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
             await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
             const repr = MembraneOrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => MembraneOrientationParams);
             await repr.createOrUpdate(params, a.data).runInContext(ctx);
-            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: 'Membrane Orientation' });
+            return new PluginStateObject.Shape.Representation3D({ repr, sourceData: a.data }, { label: 'Membrane Orientation' });
         });
     },
     update({ a, b, newParams }, plugin: PluginContext) {
@@ -129,6 +129,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
             await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            b.data.sourceData = a.data;
             return StateTransformer.UpdateResult.Updated;
         });
     },

src/extensions/cellpack/model.ts

@@ -414,7 +414,7 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
         }
 
         if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
-        const structure = new Structure(units);
+        const structure = Structure.create(units);
         for( let i = 0, il = structure.models.length; i < il; ++i) {
             Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
         }

src/extensions/geo-export/controls.ts

@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ */
+
+import { PluginComponent } from '../../mol-plugin-state/component';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { ObjExporter } from './export';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateSelection } from '../../mol-state';
+import { SetUtils } from '../../mol-util/set';
+import { zip } from '../../mol-util/zip/zip';
+
+export class GeometryControls extends PluginComponent {
+    getFilename() {
+        const models = this.plugin.state.data.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Model)).map(s => s.obj!.data);
+        const uniqueIds = new Set<string>();
+        models.forEach(m => uniqueIds.add(m.entryId.toUpperCase()));
+        const idString = SetUtils.toArray(uniqueIds).join('-');
+        return `${idString || 'molstar-model'}`;
+    }
+
+    exportObj() {
+        const task = Task.create('Export OBJ', async ctx => {
+            try {
+                const renderObjects = this.plugin.canvas3d?.getRenderObjects()!;
+
+                const filename = this.getFilename();
+                const objExporter = new ObjExporter(filename);
+                for (let i = 0, il = renderObjects.length; i < il; ++i) {
+                    await ctx.update({ message: `Exporting object ${i}/${il}` });
+                    await objExporter.add(renderObjects[i], ctx);
+                }
+                const { obj, mtl } = objExporter.getData();
+
+                const asciiWrite = (data: Uint8Array, str: string) => {
+                    for (let i = 0, il = str.length; i < il; ++i) {
+                        data[i] = str.charCodeAt(i);
+                    }
+                };
+                const objData = new Uint8Array(obj.length);
+                asciiWrite(objData, obj);
+                const mtlData = new Uint8Array(mtl.length);
+                asciiWrite(mtlData, mtl);
+
+                const zipDataObj = {
+                    [filename + '.obj']: objData,
+                    [filename + '.mtl']: mtlData
+                };
+                const zipData = await zip(ctx, zipDataObj);
+                return {
+                    zipData,
+                    filename: filename + '.zip'
+                };
+            } catch (e) {
+                this.plugin.log.error('' + e);
+                throw e;
+            }
+        });
+
+        return this.plugin.runTask(task, { useOverlay: true });
+    }
+
+    constructor(private plugin: PluginContext) {
+        super();
+    }
+}

src/extensions/geo-export/export.ts

@@ -0,0 +1,321 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ */
+
+import { GraphicsRenderObject } from '../../mol-gl/render-object';
+import { MeshValues } from '../../mol-gl/renderable/mesh';
+import { LinesValues } from '../../mol-gl/renderable/lines';
+import { PointsValues } from '../../mol-gl/renderable/points';
+import { SpheresValues } from '../../mol-gl/renderable/spheres';
+import { CylindersValues } from '../../mol-gl/renderable/cylinders';
+import { BaseValues, SizeValues } from '../../mol-gl/renderable/schema';
+import { TextureImage } from '../../mol-gl/renderable/util';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
+import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
+import { Vec3, Mat3, Mat4 } from '../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../mol-task';
+import { StringBuilder } from '../../mol-util';
+import { Color } from '../../mol-util/color/color';
+import { decodeFloatRGB } from '../../mol-util/float-packing';
+
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3fromArray = Vec3.fromArray;
+const v3transformMat4 = Vec3.transformMat4;
+const v3transformMat3 = Vec3.transformMat3;
+const mat3directionTransform = Mat3.directionTransform;
+
+type RenderObjectExportData = {
+    [k: string]: string | Uint8Array | undefined
+}
+
+interface RenderObjectExporter<D extends RenderObjectExportData> {
+    add(renderObject: GraphicsRenderObject, ctx: RuntimeContext): Promise<void> | undefined
+    getData(): D
+}
+
+// http://paulbourke.net/dataformats/obj/
+// http://paulbourke.net/dataformats/mtl/
+
+export type ObjData = {
+    obj: string
+    mtl: string
+}
+
+export class ObjExporter implements RenderObjectExporter<ObjData> {
+    private obj = StringBuilder.create();
+    private mtl = StringBuilder.create();
+    private vertexOffset = 0;
+    private currentColor: Color | undefined;
+    private currentAlpha: number | undefined;
+    private materialSet = new Set<string>();
+
+    private static getSizeFromTexture(tSize: TextureImage<Uint8Array>, i: number): number {
+        const r = tSize.array[i * 3];
+        const g = tSize.array[i * 3 + 1];
+        const b = tSize.array[i * 3 + 2];
+        return decodeFloatRGB(r, g, b);
+    }
+
+    private static getSize(values: BaseValues & SizeValues, instanceIndex: number, group: number): number {
+        const tSize = values.tSize.ref.value;
+        let size = 0;
+        switch (values.dSizeType.ref.value) {
+            case 'uniform':
+                size = values.uSize.ref.value;
+                break;
+            case 'instance':
+                size = ObjExporter.getSizeFromTexture(tSize, instanceIndex) / 100;
+                break;
+            case 'group':
+                size = ObjExporter.getSizeFromTexture(tSize, group) / 100;
+                break;
+            case 'groupInstance':
+                const groupCount = values.uGroupCount.ref.value;
+                size = ObjExporter.getSizeFromTexture(tSize, instanceIndex * groupCount + group) / 100;
+                break;
+        }
+        return size * values.uSizeFactor.ref.value;
+    }
+
+    private updateMaterial(color: Color, alpha: number) {
+        if (this.currentColor === color && this.currentAlpha === alpha) return;
+
+        this.currentColor = color;
+        this.currentAlpha = alpha;
+        const material = Color.toHexString(color) + alpha;
+        StringBuilder.writeSafe(this.obj, `usemtl ${material}`);
+        StringBuilder.newline(this.obj);
+        if (!this.materialSet.has(material)) {
+            this.materialSet.add(material);
+            const [r, g, b] = Color.toRgbNormalized(color);
+            const mtl = this.mtl;
+            StringBuilder.writeSafe(mtl, `newmtl ${material}\n`);
+            StringBuilder.writeSafe(mtl, 'illum 2\n'); // illumination model
+            StringBuilder.writeSafe(mtl, 'Ns 163\n'); // specular exponent
+            StringBuilder.writeSafe(mtl, 'Ni 0.001\n'); // optical density a.k.a. index of refraction
+            StringBuilder.writeSafe(mtl, 'Ka 0 0 0\n'); // ambient reflectivity
+            StringBuilder.writeSafe(mtl, 'Kd '); // diffuse reflectivity
+            StringBuilder.writeFloat(mtl, r, 1000);
+            StringBuilder.whitespace1(mtl);
+            StringBuilder.writeFloat(mtl, g, 1000);
+            StringBuilder.whitespace1(mtl);
+            StringBuilder.writeFloat(mtl, b, 1000);
+            StringBuilder.newline(mtl);
+            StringBuilder.writeSafe(mtl, 'Ks 0.25 0.25 0.25\n'); // specular reflectivity
+            StringBuilder.writeSafe(mtl, 'd '); // dissolve
+            StringBuilder.writeFloat(mtl, alpha, 1000);
+            StringBuilder.newline(mtl);
+        }
+    }
+
+    private async addMeshWithColors(vertices: Float32Array, normals: Float32Array, indices: Uint32Array, groups: Float32Array, vertexCount: number, drawCount: number, values: BaseValues, instanceIndex: number, ctx: RuntimeContext) {
+        const obj = this.obj;
+        const t = Mat4();
+        const n = Mat3();
+        const tmpV = Vec3();
+
+        const colorType = values.dColorType.ref.value;
+        const tColor = values.tColor.ref.value.array;
+        const uAlpha = values.uAlpha.ref.value;
+        const aTransform = values.aTransform.ref.value;
+
+        Mat4.fromArray(t, aTransform, instanceIndex * 16);
+        mat3directionTransform(n, t);
+
+        const currentProgress = (vertexCount * 2 + drawCount) * instanceIndex;
+        await ctx.update({ isIndeterminate: false, current: currentProgress, max: (vertexCount * 2 + drawCount) * values.uInstanceCount.ref.value });
+
+        // position
+        for (let i = 0; i < vertexCount; ++i) {
+            if (i % 1000 === 0 && ctx.shouldUpdate) await ctx.update({ current: currentProgress + i });
+            v3transformMat4(tmpV, v3fromArray(tmpV, vertices, i * 3), t);
+            StringBuilder.writeSafe(obj, 'v ');
+            StringBuilder.writeFloat(obj, tmpV[0], 1000);
+            StringBuilder.whitespace1(obj);
+            StringBuilder.writeFloat(obj, tmpV[1], 1000);
+            StringBuilder.whitespace1(obj);
+            StringBuilder.writeFloat(obj, tmpV[2], 1000);
+            StringBuilder.newline(obj);
+        }
+
+        // normal
+        for (let i = 0; i < vertexCount; ++i) {
+            if (i % 1000 === 0 && ctx.shouldUpdate) await ctx.update({ current: currentProgress + vertexCount + i });
+            v3transformMat3(tmpV, v3fromArray(tmpV, normals, i * 3), n);
+            StringBuilder.writeSafe(obj, 'vn ');
+            StringBuilder.writeFloat(obj, tmpV[0], 100);
+            StringBuilder.whitespace1(obj);
+            StringBuilder.writeFloat(obj, tmpV[1], 100);
+            StringBuilder.whitespace1(obj);
+            StringBuilder.writeFloat(obj, tmpV[2], 100);
+            StringBuilder.newline(obj);
+        }
+
+        // face
+        for (let i = 0; i < drawCount; i += 3) {
+            if (i % 3000 === 0 && ctx.shouldUpdate) await ctx.update({ current: currentProgress + vertexCount * 2 + i });
+            let color: Color;
+            switch (colorType) {
+                case 'uniform':
+                    color = Color.fromNormalizedArray(values.uColor.ref.value, 0);
+                    break;
+                case 'instance':
+                    color = Color.fromArray(tColor, instanceIndex * 3);
+                    break;
+                case 'group':
+                    color = Color.fromArray(tColor, groups[indices[i]] * 3);
+                    break;
+                case 'groupInstance':
+                    const groupCount = values.uGroupCount.ref.value;
+                    const group = groups[indices[i]];
+                    color = Color.fromArray(tColor, (instanceIndex * groupCount + group) * 3);
+                    break;
+                case 'vertex':
+                    color = Color.fromArray(tColor, i * 3);
+                    break;
+                case 'vertexInstance':
+                    color = Color.fromArray(tColor, (instanceIndex * drawCount + i) * 3);
+                    break;
+                default: throw new Error('Unsupported color type.');
+            }
+            this.updateMaterial(color, uAlpha);
+
+            const v1 = this.vertexOffset + indices[i] + 1;
+            const v2 = this.vertexOffset + indices[i + 1] + 1;
+            const v3 = this.vertexOffset + indices[i + 2] + 1;
+            StringBuilder.writeSafe(obj, 'f ');
+            StringBuilder.writeInteger(obj, v1);
+            StringBuilder.writeSafe(obj, '//');
+            StringBuilder.writeIntegerAndSpace(obj, v1);
+            StringBuilder.writeInteger(obj, v2);
+            StringBuilder.writeSafe(obj, '//');
+            StringBuilder.writeIntegerAndSpace(obj, v2);
+            StringBuilder.writeInteger(obj, v3);
+            StringBuilder.writeSafe(obj, '//');
+            StringBuilder.writeInteger(obj, v3);
+            StringBuilder.newline(obj);
+        }
+
+        this.vertexOffset += vertexCount;
+    }
+
+    private async addMesh(values: MeshValues, ctx: RuntimeContext) {
+        const aPosition = values.aPosition.ref.value;
+        const aNormal = values.aNormal.ref.value;
+        const elements = values.elements.ref.value;
+        const aGroup = values.aGroup.ref.value;
+        const instanceCount = values.instanceCount.ref.value;
+        const vertexCount = values.uVertexCount.ref.value;
+        const drawCount = values.drawCount.ref.value;
+
+        for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
+            await this.addMeshWithColors(aPosition, aNormal, elements, aGroup, vertexCount, drawCount, values, instanceIndex, ctx);
+        }
+    }
+
+    private async addLines(values: LinesValues, ctx: RuntimeContext) {
+        // TODO
+    }
+
+    private async addPoints(values: PointsValues, ctx: RuntimeContext) {
+        // TODO
+    }
+
+    private async addSpheres(values: SpheresValues, ctx: RuntimeContext) {
+        const center = Vec3();
+
+        const aPosition = values.aPosition.ref.value;
+        const aGroup = values.aGroup.ref.value;
+        const instanceCount = values.instanceCount.ref.value;
+        const vertexCount = values.uVertexCount.ref.value;
+
+        for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
+            const state = MeshBuilder.createState(512, 256);
+
+            for (let i = 0; i < vertexCount; i += 4) {
+                v3fromArray(center, aPosition, i * 3);
+
+                const group = aGroup[i];
+                const radius = ObjExporter.getSize(values, instanceIndex, group);
+                state.currentGroup = group;
+                addSphere(state, center, radius, 2);
+            }
+
+            const mesh = MeshBuilder.getMesh(state);
+            const vertices = mesh.vertexBuffer.ref.value;
+            const normals = mesh.normalBuffer.ref.value;
+            const indices = mesh.indexBuffer.ref.value;
+            const groups = mesh.groupBuffer.ref.value;
+            await this.addMeshWithColors(vertices, normals, indices, groups, vertices.length / 3, indices.length, values, instanceIndex, ctx);
+        }
+    }
+
+    private async addCylinders(values: CylindersValues, ctx: RuntimeContext) {
+        const start = Vec3();
+        const end = Vec3();
+
+        const aStart = values.aStart.ref.value;
+        const aEnd = values.aEnd.ref.value;
+        const aScale = values.aScale.ref.value;
+        const aCap = values.aCap.ref.value;
+        const aGroup = values.aGroup.ref.value;
+        const instanceCount = values.instanceCount.ref.value;
+        const vertexCount = values.uVertexCount.ref.value;
+
+        for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
+            const state = MeshBuilder.createState(512, 256);
+
+            for (let i = 0; i < vertexCount; i += 6) {
+                v3fromArray(start, aStart, i * 3);
+                v3fromArray(end, aEnd, i * 3);
+
+                const group = aGroup[i];
+                const radius = ObjExporter.getSize(values, instanceIndex, group) * aScale[i];
+                const cap = aCap[i];
+                const topCap = cap === 1 || cap === 3;
+                const bottomCap = cap >= 2;
+                const cylinderProps = { radiusTop: radius, radiusBottom: radius, topCap, bottomCap, radialSegments: 32 };
+                state.currentGroup = aGroup[i];
+                addCylinder(state, start, end, 1, cylinderProps);
+            }
+
+            const mesh = MeshBuilder.getMesh(state);
+            const vertices = mesh.vertexBuffer.ref.value;
+            const normals = mesh.normalBuffer.ref.value;
+            const indices = mesh.indexBuffer.ref.value;
+            const groups = mesh.groupBuffer.ref.value;
+            await this.addMeshWithColors(vertices, normals, indices, groups, vertices.length / 3, indices.length, values, instanceIndex, ctx);
+        }
+    }
+
+    add(renderObject: GraphicsRenderObject, ctx: RuntimeContext) {
+        if (!renderObject.state.visible) return;
+
+        switch (renderObject.type) {
+            case 'mesh':
+                return this.addMesh(renderObject.values as MeshValues, ctx);
+            case 'lines':
+                return this.addLines(renderObject.values as LinesValues, ctx);
+            case 'points':
+                return this.addPoints(renderObject.values as PointsValues, ctx);
+            case 'spheres':
+                return this.addSpheres(renderObject.values as SpheresValues, ctx);
+            case 'cylinders':
+                return this.addCylinders(renderObject.values as CylindersValues, ctx);
+        }
+    }
+
+    getData() {
+        return {
+            obj: StringBuilder.getString(this.obj),
+            mtl: StringBuilder.getString(this.mtl)
+        };
+    }
+
+    constructor(filename: string) {
+        StringBuilder.writeSafe(this.obj, `mtllib ${filename}.mtl\n`);
+    }
+}

src/extensions/geo-export/index.ts

@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { GeometryExporterUI } from './ui';
+
+export const GeometryExport = PluginBehavior.create<{ }>({
+    name: 'extension-geo-export',
+    category: 'misc',
+    display: {
+        name: 'Geometry Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.customStructureControls.set('geo-export', GeometryExporterUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customStructureControls.delete('geo-export');
+        }
+    },
+    params: () => ({ })
+});

src/extensions/geo-export/ui.tsx

@@ -0,0 +1,64 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ */
+
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { GetAppSvg, CubeSendSvg } from '../../mol-plugin-ui/controls/icons';
+import { download } from '../../mol-util/download';
+import { GeometryControls } from './controls';
+
+interface State {
+    busy?: boolean
+}
+
+export class GeometryExporterUI extends CollapsableControls<{}, State> {
+    private _controls: GeometryControls | undefined;
+
+    get controls() {
+        return this._controls || (this._controls = new GeometryControls(this.plugin));
+    }
+
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Export Geometries',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: CubeSendSvg }
+        };
+    }
+
+    protected renderControls(): JSX.Element {
+        return <>
+            <Button icon={GetAppSvg}
+                onClick={this.saveObj} style={{ marginTop: 1 }}
+                disabled={this.state.busy || !this.plugin.canvas3d?.reprCount.value}>
+                Save OBJ + MTL
+            </Button>
+        </>;
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.canvas3d!.reprCount, () => {
+            if (!this.state.isCollapsed) this.forceUpdate();
+        });
+    }
+
+    componentWillUnmount() {
+        this._controls?.dispose();
+        this._controls = void 0;
+    }
+
+    saveObj = async () => {
+        try {
+            this.setState({ busy: true });
+            const data = await this.controls.exportObj();
+            this.setState({ busy: false });
+
+            download(new Blob([data.zipData]), data.filename);
+        } catch {
+            this.setState({ busy: false });
+        }
+    }
+}

src/extensions/mp4-export/ui.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import React from 'react';
 import { merge } from 'rxjs';
 import { debounceTime } from 'rxjs/operators';
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';

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

@@ -124,7 +124,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
             const repr = AssemblySymmetryRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => AssemblySymmetryParams);
             await repr.createOrUpdate(params, a.data).runInContext(ctx);
             const { type, kind, symbol } = assemblySymmetry;
-            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: kind, description: `${type} (${symbol})` });
+            return new PluginStateObject.Shape.Representation3D({ repr, sourceData: a.data }, { label: kind, description: `${type} (${symbol})` });
         });
     },
     update({ a, b, newParams }, plugin: PluginContext) {
@@ -138,6 +138,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
             }
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            b.data.sourceData = a.data;
             const { type, kind, symbol } = assemblySymmetry;
             b.label = kind;
             b.description = `${type} (${symbol})`;

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

@@ -4,7 +4,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as React from 'react';
 import { CollapsableState, CollapsableControls } from '../../../mol-plugin-ui/base';
 import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
 import { InitAssemblySymmetry3D, AssemblySymmetry3D, AssemblySymmetryPreset, tryCreateAssemblySymmetry } from './behavior';

src/mol-canvas3d/camera.ts

@@ -9,6 +9,7 @@ import { Mat4, Vec3, Vec4, EPSILON } from '../mol-math/linear-algebra';
 import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
+import { Scene } from '../mol-gl/scene';
 
 export { ICamera, Camera };
 
@@ -126,6 +127,23 @@ class Camera implements ICamera {
         return state;
     }
 
+    getInvariantFocus(target: Vec3, radius: number, up: Vec3, dir: Vec3): Partial<Camera.Snapshot> {
+        const r = Math.max(radius, 0.01);
+        const targetDistance = this.getTargetDistance(r);
+
+        Vec3.copy(this.deltaDirection, dir);
+        Vec3.setMagnitude(this.deltaDirection, this.deltaDirection, targetDistance);
+        Vec3.sub(this.newPosition, target, this.deltaDirection);
+
+        const state = Camera.copySnapshot(Camera.createDefaultSnapshot(), this.state);
+        state.target = Vec3.clone(target);
+        state.radius = r;
+        state.position = Vec3.clone(this.newPosition);
+        Vec3.copy(state.up, up);
+
+        return state;
+    }
+
     focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3) {
         if (radius > 0) {
             this.setState(this.getFocus(target, radius, up, dir), durationMs);
@@ -150,6 +168,8 @@ class Camera implements ICamera {
 namespace Camera {
     export type Mode = 'perspective' | 'orthographic'
 
+    export type SnapshotProvider = Partial<Snapshot> | ((scene: Scene, camera: Camera) => Partial<Snapshot>)
+
     /**
      * Sets an offseted view in a larger frustum. This is useful for
      * - multi-window or multi-monitor/multi-machine setups

src/mol-canvas3d/canvas3d.ts

@@ -229,11 +229,12 @@ interface Canvas3D {
     /** performs handleResize on the next animation frame */
     requestResize(): void
     /** Focuses camera on scene's bounding sphere, centered and zoomed. */
-    requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
+    requestCameraReset(options?: { durationMs?: number, snapshot?: Camera.SnapshotProvider }): void
     readonly camera: Camera
     readonly boundingSphere: Readonly<Sphere3D>
     setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void), doNotRequestDraw?: boolean /* = false */): void
     getImagePass(props: Partial<ImageProps>): ImagePass
+    getRenderObjects(): GraphicsRenderObject[]
 
     /** Returns a copy of the current Canvas3D instance props */
     readonly props: Readonly<Canvas3DProps>
@@ -296,7 +297,7 @@ namespace Canvas3D {
         let drawPending = false;
         let cameraResetRequested = false;
         let nextCameraResetDuration: number | undefined = void 0;
-        let nextCameraResetSnapshot: Partial<Camera.Snapshot> | undefined = void 0;
+        let nextCameraResetSnapshot: Camera.SnapshotProvider | undefined = void 0;
         let resizeRequested = false;
 
         let notifyDidDraw = true;
@@ -305,7 +306,11 @@ namespace Canvas3D {
             let loci: Loci = EmptyLoci;
             let repr: Representation.Any = Representation.Empty;
             if (pickingId) {
+                const cameraHelperLoci = helper.camera.getLoci(pickingId);
+                if (cameraHelperLoci !== EmptyLoci) return { loci: cameraHelperLoci, repr };
+
                 loci = helper.handle.getLoci(pickingId);
+
                 reprRenderObjects.forEach((_, _repr) => {
                     const _loci = _repr.getLoci(pickingId);
                     if (!isEmptyLoci(_loci)) {
@@ -327,11 +332,13 @@ namespace Canvas3D {
                 changed = repr.mark(loci, action);
             } else {
                 changed = helper.handle.mark(loci, action);
+                changed = helper.camera.mark(loci, action) || changed;
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
             if (changed) {
                 scene.update(void 0, true);
                 helper.handle.scene.update(void 0, true);
+                helper.camera.scene.update(void 0, true);
                 const prevPickDirty = pickHelper.dirty;
                 draw(true);
                 pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
@@ -453,11 +460,21 @@ namespace Canvas3D {
         function resolveCameraReset() {
             if (!cameraResetRequested) return;
 
-            const { center, radius } = scene.boundingSphereVisible;
+            const boundingSphere = scene.boundingSphereVisible;
+            const { center, radius } = boundingSphere;
+
+            const autoAdjustControls = controls.props.autoAdjustMinMaxDistance;
+            if (autoAdjustControls.name === 'on') {
+                const minDistance = autoAdjustControls.params.minDistanceFactor * radius + autoAdjustControls.params.minDistancePadding;
+                const maxDistance = Math.max(autoAdjustControls.params.maxDistanceFactor * radius, autoAdjustControls.params.maxDistanceMin);
+                controls.setProps({ minDistance, maxDistance });
+            }
+
             if (radius > 0) {
                 const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration;
                 const focus = camera.getFocus(center, radius);
-                const snapshot = nextCameraResetSnapshot ? { ...focus, ...nextCameraResetSnapshot } : focus;
+                const next = typeof nextCameraResetSnapshot === 'function' ? nextCameraResetSnapshot(scene, camera) : nextCameraResetSnapshot;
+                const snapshot = next ? { ...focus, ...next } : focus;
                 camera.setState({ ...snapshot, radiusMax: scene.boundingSphere.radius }, duration);
             }
 
@@ -753,6 +770,11 @@ namespace Canvas3D {
             getImagePass: (props: Partial<ImageProps> = {}) => {
                 return new ImagePass(webgl, renderer, scene, camera, helper, passes.draw.wboitEnabled, props);
             },
+            getRenderObjects(): GraphicsRenderObject[] {
+                const renderObjects: GraphicsRenderObject[] = [];
+                scene.forEach((_, ro) => renderObjects.push(ro));
+                return renderObjects;
+            },
 
             get props() {
                 return getProps();

src/mol-canvas3d/controls/trackball.ts

@@ -49,7 +49,21 @@ export const TrackballControlsParams = {
     minDistance: PD.Numeric(0.01, {}, { isHidden: true }),
     maxDistance: PD.Numeric(1e150, {}, { isHidden: true }),
 
-    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true })
+    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true }),
+
+    /**
+     * minDistance = minDistanceFactor * boundingSphere.radius + minDistancePadding
+     * maxDistance = max(maxDistanceFactor * boundingSphere.radius, maxDistanceMin)
+     */
+    autoAdjustMinMaxDistance: PD.MappedStatic('on', {
+        off: PD.EmptyGroup(),
+        on: PD.Group({
+            minDistanceFactor: PD.Numeric(0),
+            minDistancePadding: PD.Numeric(5),
+            maxDistanceFactor: PD.Numeric(10),
+            maxDistanceMin: PD.Numeric(20)
+        })
+    }, { isHidden: true })
 };
 export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 

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

@@ -1,30 +1,35 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { WebGLContext } from '../../mol-gl/webgl/context';
-import { Scene } from '../../mol-gl/scene';
-import { Camera, ICamera } from '../camera';
-import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
-import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
-import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
-import { GraphicsRenderObject } from '../../mol-gl/render-object';
-import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
-import { ColorNames } from '../../mol-util/color/names';
-import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
-import { Viewport } from '../camera/util';
-import { Sphere3D } from '../../mol-math/geometry';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import produce from 'immer';
+import { Interval } from '../../mol-data/int/interval';
+import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
+import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+import { PickingId } from '../../mol-geo/geometry/picking';
+import { GraphicsRenderObject } from '../../mol-gl/render-object';
+import { Scene } from '../../mol-gl/scene';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Sphere3D } from '../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { DataLoci, EmptyLoci, Loci } from '../../mol-model/loci';
 import { Shape } from '../../mol-model/shape';
+import { Visual } from '../../mol-repr/visual';
+import { ColorNames } from '../../mol-util/color/names';
+import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Camera, ICamera } from '../camera';
+import { Viewport } from '../camera/util';
 
 // TODO add scale line/grid
 
 const AxesParams = {
     ...Mesh.Params,
-    alpha: { ...Mesh.Params.alpha, defaultValue: 0.33 },
+    alpha: { ...Mesh.Params.alpha, defaultValue: 0.51 },
     ignoreLight: { ...Mesh.Params.ignoreLight, defaultValue: true },
     colorX: PD.Color(ColorNames.red, { isEssential: true }),
     colorY: PD.Color(ColorNames.green, { isEssential: true }),
@@ -87,6 +92,32 @@ export class CameraHelper {
         return this.props.axes.name === 'on';
     }
 
+    getLoci(pickingId: PickingId) {
+        const { objectId, groupId, instanceId } = pickingId;
+        if (!this.renderObject || objectId !== this.renderObject.id || groupId === CameraHelperAxis.None) return EmptyLoci;
+        return CameraAxesLoci(this, groupId, instanceId);
+    }
+
+    private eachGroup = (loci: Loci, apply: (interval: Interval) => boolean): boolean => {
+        if (!this.renderObject) return false;
+        if (!isCameraAxesLoci(loci)) return false;
+        let changed = false;
+        const groupCount = this.renderObject.values.uGroupCount.ref.value;
+        const { elements } = loci;
+        for (const { groupId, instanceId } of elements) {
+            const idx = instanceId * groupCount + groupId;
+            if (apply(Interval.ofSingleton(idx))) changed = true;
+        }
+        return changed;
+    }
+
+    mark(loci: Loci, action: MarkerAction) {
+        if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
+        if (!isCameraAxesLoci(loci)) return false;
+        if (loci.data !== this) return false;
+        return Visual.mark(this.renderObject, loci, action, this.eachGroup);
+    }
+
     update(camera: ICamera) {
         if (!this.renderObject) return;
 
@@ -102,6 +133,38 @@ export class CameraHelper {
     }
 }
 
+export const enum CameraHelperAxis {
+    None = 0,
+    X,
+    Y,
+    Z,
+    XY,
+    XZ,
+    YZ
+}
+
+function getAxisLabel(axis: number) {
+    switch (axis) {
+        case CameraHelperAxis.X: return 'X Axis';
+        case CameraHelperAxis.Y: return 'Y Axis';
+        case CameraHelperAxis.Z: return 'Z Axis';
+        case CameraHelperAxis.XY: return 'XY Plane';
+        case CameraHelperAxis.XZ: return 'XZ Plane';
+        case CameraHelperAxis.YZ: return 'YZ Plane';
+        default: return 'Axes';
+    }
+}
+
+function CameraAxesLoci(cameraHelper: CameraHelper, groupId: number, instanceId: number) {
+    return DataLoci('camera-axes', cameraHelper, [{ groupId, instanceId }],
+        void 0 /** bounding sphere */,
+        () => getAxisLabel(groupId));
+}
+export type CameraAxesLoci = ReturnType<typeof CameraAxesLoci>
+export function isCameraAxesLoci(x: Loci): x is CameraAxesLoci {
+    return x.kind === 'data-loci' && x.tag === 'camera-axes';
+}
+
 function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.ViewOffset) {
     const { near, far } = camera;
 
@@ -134,27 +197,52 @@ function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.Vie
 
 function createAxesMesh(scale: number, mesh?: Mesh) {
     const state = MeshBuilder.createState(512, 256, mesh);
-    const radius = 0.05 * scale;
+    const radius = 0.075 * scale;
     const x = Vec3.scale(Vec3(), Vec3.unitX, scale);
     const y = Vec3.scale(Vec3(), Vec3.unitY, scale);
     const z = Vec3.scale(Vec3(), Vec3.unitZ, scale);
     const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments: 32 };
 
-    state.currentGroup = 0;
+    state.currentGroup = CameraHelperAxis.None;
     addSphere(state, Vec3.origin, radius, 2);
 
-    state.currentGroup = 1;
+    state.currentGroup = CameraHelperAxis.X;
     addSphere(state, x, radius, 2);
     addCylinder(state, Vec3.origin, x, 1, cylinderProps);
 
-    state.currentGroup = 2;
+    state.currentGroup = CameraHelperAxis.Y;
     addSphere(state, y, radius, 2);
     addCylinder(state, Vec3.origin, y, 1, cylinderProps);
 
-    state.currentGroup = 3;
+    state.currentGroup = CameraHelperAxis.Z;
     addSphere(state, z, radius, 2);
     addCylinder(state, Vec3.origin, z, 1, cylinderProps);
 
+    Vec3.scale(x, x, 0.5);
+    Vec3.scale(y, y, 0.5);
+    Vec3.scale(z, z, 0.5);
+
+    state.currentGroup = CameraHelperAxis.XY;
+    MeshBuilder.addTriangle(state, Vec3.origin, x, y);
+    MeshBuilder.addTriangle(state, Vec3.origin, y, x);
+    const xy = Vec3.add(Vec3(), x, y);
+    MeshBuilder.addTriangle(state, xy, x, y);
+    MeshBuilder.addTriangle(state, xy, y, x);
+
+    state.currentGroup = CameraHelperAxis.XZ;
+    MeshBuilder.addTriangle(state, Vec3.origin, x, z);
+    MeshBuilder.addTriangle(state, Vec3.origin, z, x);
+    const xz = Vec3.add(Vec3(), x, z);
+    MeshBuilder.addTriangle(state, xz, x, z);
+    MeshBuilder.addTriangle(state, xz, z, x);
+
+    state.currentGroup = CameraHelperAxis.YZ;
+    MeshBuilder.addTriangle(state, Vec3.origin, y, z);
+    MeshBuilder.addTriangle(state, Vec3.origin, z, y);
+    const yz = Vec3.add(Vec3(), y, z);
+    MeshBuilder.addTriangle(state, yz, y, z);
+    MeshBuilder.addTriangle(state, yz, z, y);
+
     return MeshBuilder.getMesh(state);
 }
 

src/mol-canvas3d/passes/pick.ts

@@ -66,14 +66,20 @@ export class PickPass {
     private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: GraphicsRenderVariant) {
         const depth = this.drawPass.depthTexturePrimitives;
         renderer.clear(false);
+
+        renderer.update(camera);
         renderer.renderPick(scene.primitives, camera, variant, null);
         renderer.renderPick(scene.volumes, camera, variant, depth);
         renderer.renderPick(helper.handle.scene, camera, variant, null);
+
+        if (helper.camera.isEnabled) {
+            helper.camera.update(camera);
+            renderer.update(helper.camera.camera);
+            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null);
+        }
     }
 
     render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper) {
-        renderer.update(camera);
-
         this.objectPickTarget.bind();
         this.renderVariant(renderer, camera, scene, helper, 'pickObject');
 

src/mol-canvas3d/util.ts

@@ -12,13 +12,13 @@ export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height:
 }
 
 /** Resize canvas to container element taking `devicePixelRatio` into account */
-export function resizeCanvas (canvas: HTMLCanvasElement, container: Element, scale = 1) {
+export function resizeCanvas (canvas: HTMLCanvasElement, container: HTMLElement, scale = 1) {
     let width = window.innerWidth;
     let height = window.innerHeight;
     if (container !== document.body) {
-        let bounds = container.getBoundingClientRect();
-        width = bounds.right - bounds.left;
-        height = bounds.bottom - bounds.top;
+        // fixes issue #molstar/molstar#147, offsetWidth/offsetHeight is correct size when css transform:scale is used
+        width = container.offsetWidth;
+        height = container.offsetHeight;
     }
     setCanvasSize(canvas, width, height, scale);
 }

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

@@ -18,11 +18,24 @@ export type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance' | 've
 export type ColorData = {
     uColor: ValueCell<Vec3>,
     tColor: ValueCell<TextureImage<Uint8Array>>,
+    tPalette: ValueCell<TextureImage<Uint8Array>>,
     uColorTexDim: ValueCell<Vec2>,
     dColorType: ValueCell<string>,
+    dUsePalette: ValueCell<boolean>,
 }
 
 export function createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any>, colorData?: ColorData): ColorData {
+    const data = _createColors(locationIt, positionIt, colorTheme, colorData);
+    if (colorTheme.palette) {
+        ValueCell.updateIfChanged(data.dUsePalette, true);
+        updatePaletteTexture(colorTheme.palette, data.tPalette);
+    } else {
+        ValueCell.updateIfChanged(data.dUsePalette, false);
+    }
+    return data;
+}
+
+function _createColors(locationIt: LocationIterator, positionIt: LocationIterator, colorTheme: ColorTheme<any>, colorData?: ColorData): ColorData {
     switch (Geometry.getGranularity(locationIt, colorTheme.granularity)) {
         case 'uniform': return createUniformColor(locationIt, colorTheme.color, colorData);
         case 'instance': return createInstanceColor(locationIt, colorTheme.color, colorData);
@@ -42,18 +55,20 @@ export function createValueColor(value: Color, colorData?: ColorData): ColorData
         return {
             uColor: ValueCell.create(Color.toVec3Normalized(Vec3(), value)),
             tColor: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
+            tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             uColorTexDim: ValueCell.create(Vec2.create(1, 1)),
             dColorType: ValueCell.create('uniform'),
+            dUsePalette: ValueCell.create(false),
         };
     }
 }
 
 /** Creates color uniform */
-export function createUniformColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
+function createUniformColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
     return createValueColor(color(NullLocation, false), colorData);
 }
 
-export function createTextureColor(colors: TextureImage<Uint8Array>, type: ColorType, colorData?: ColorData): ColorData {
+function createTextureColor(colors: TextureImage<Uint8Array>, type: ColorType, colorData?: ColorData): ColorData {
     if (colorData) {
         ValueCell.update(colorData.tColor, colors);
         ValueCell.update(colorData.uColorTexDim, Vec2.create(colors.width, colors.height));
@@ -63,14 +78,16 @@ export function createTextureColor(colors: TextureImage<Uint8Array>, type: Color
         return {
             uColor: ValueCell.create(Vec3()),
             tColor: ValueCell.create(colors),
+            tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             uColorTexDim: ValueCell.create(Vec2.create(colors.width, colors.height)),
             dColorType: ValueCell.create(type),
+            dUsePalette: ValueCell.create(false),
         };
     }
 }
 
 /** Creates color texture with color for each instance */
-export function createInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
+function createInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
     const { instanceCount } = locationIt;
     const colors = createTextureImage(Math.max(1, instanceCount), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
     locationIt.reset();
@@ -83,7 +100,7 @@ export function createInstanceColor(locationIt: LocationIterator, color: Locatio
 }
 
 /** Creates color texture with color for each group (i.e. shared across instances) */
-export function createGroupColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
+function createGroupColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
     const { groupCount } = locationIt;
     const colors = createTextureImage(Math.max(1, groupCount), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
     locationIt.reset();
@@ -95,7 +112,7 @@ export function createGroupColor(locationIt: LocationIterator, color: LocationCo
 }
 
 /** Creates color texture with color for each group in each instance */
-export function createGroupInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
+function createGroupInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
     const { groupCount, instanceCount } = locationIt;
     const count = instanceCount * groupCount;
     const colors = createTextureImage(Math.max(1, count), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
@@ -108,7 +125,7 @@ export function createGroupInstanceColor(locationIt: LocationIterator, color: Lo
 }
 
 /** Creates color texture with color for each vertex (i.e. shared across instances) */
-export function createVertexColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
+function createVertexColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
     const { groupCount, stride } = locationIt;
     const colors = createTextureImage(Math.max(1, groupCount), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
     locationIt.reset();
@@ -124,7 +141,7 @@ export function createVertexColor(locationIt: LocationIterator, color: LocationC
 }
 
 /** Creates color texture with color for each vertex in each instance */
-export function createVertexInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
+function createVertexInstanceColor(locationIt: LocationIterator, color: LocationColor, colorData?: ColorData): ColorData {
     const { groupCount, instanceCount, stride } = locationIt;
     const count = instanceCount * groupCount;
     const colors = createTextureImage(Math.max(1, count), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
@@ -138,3 +155,34 @@ export function createVertexInstanceColor(locationIt: LocationIterator, color: L
     }
     return createTextureColor(colors, 'vertexInstance', colorData);
 }
+
+function updatePaletteTexture(palette: ColorTheme.Palette, cell: ValueCell<TextureImage<Uint8Array>>) {
+    let isSynced = true;
+    const texture = cell.ref.value;
+    if (palette.colors.length !== texture.width || texture.filter !== palette.filter) {
+        isSynced = false;
+    } else {
+        const data = texture.array;
+        let o = 0;
+        for (const c of palette.colors) {
+            const [r, g, b] = Color.toRgb(c);
+            if (data[o++] !== r || data[o++] !== g || data[o++] !== b) {
+                isSynced = false;
+                break;
+            }
+        }
+    }
+
+    if (isSynced) return;
+
+    const array = new Uint8Array(palette.colors.length * 3);
+    let o = 0;
+    for (const c of palette.colors) {
+        const [r, g, b] = Color.toRgb(c);
+        array[o++] = r;
+        array[o++] = g;
+        array[o++] = b;
+    }
+
+    ValueCell.update(cell, { array, height: 1, width: palette.colors.length, filter: palette.filter });
+}

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

@@ -177,7 +177,7 @@ export namespace Spheres {
 
         const counts = { drawCount: spheres.sphereCount * 2 * 3, vertexCount: spheres.sphereCount * 4, groupCount, instanceCount };
 
-        const padding = getMaxSize(size) * props.sizeFactor;
+        const padding = spheres.boundingSphere.radius ? getMaxSize(size) * props.sizeFactor : 0;
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), spheres.boundingSphere, padding);
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
 
@@ -222,7 +222,9 @@ export namespace Spheres {
     }
 
     function updateBoundingSphere(values: SpheresValues, spheres: Spheres) {
-        const padding = getMaxSize(values) * values.uSizeFactor.ref.value;
+        const padding = spheres.boundingSphere.radius
+            ? getMaxSize(values) * values.uSizeFactor.ref.value
+            : 0;
         const invariantBoundingSphere = Sphere3D.expand(Sphere3D(), spheres.boundingSphere, padding);
         const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
 

src/mol-gl/_spec/renderer.spec.ts

@@ -133,7 +133,7 @@ describe('renderer', () => {
         scene.add(points);
         scene.commit();
         expect(ctx.stats.resourceCounts.attribute).toBe(ctx.isWebGL2 ? 4 : 5);
-        expect(ctx.stats.resourceCounts.texture).toBe(6);
+        expect(ctx.stats.resourceCounts.texture).toBe(7);
         expect(ctx.stats.resourceCounts.vertexArray).toBe(6);
         expect(ctx.stats.resourceCounts.program).toBe(6);
         expect(ctx.stats.resourceCounts.shader).toBe(12);

src/mol-gl/compute/marching-cubes/isosurface.ts

@@ -32,6 +32,7 @@ const IsosurfaceSchema = {
     uSize: UniformSpec('f'),
     uLevels: UniformSpec('f'),
     uCount: UniformSpec('f'),
+    uInvert: UniformSpec('b'),
 
     uGridDim: UniformSpec('v3'),
     uGridTexDim: UniformSpec('v3'),
@@ -44,7 +45,7 @@ type IsosurfaceValues = Values<typeof IsosurfaceSchema>
 
 const IsosurfaceName = 'isosurface';
 
-function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, packedGroup: boolean): ComputeRenderable<IsosurfaceValues> {
+function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, invert: boolean, packedGroup: boolean): ComputeRenderable<IsosurfaceValues> {
     if (ctx.namedComputeRenderables[IsosurfaceName]) {
         const v = ctx.namedComputeRenderables[IsosurfaceName].values as IsosurfaceValues;
 
@@ -56,6 +57,7 @@ function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture
         ValueCell.updateIfChanged(v.uSize, Math.pow(2, levels));
         ValueCell.updateIfChanged(v.uLevels, levels);
         ValueCell.updateIfChanged(v.uCount, count);
+        ValueCell.updateIfChanged(v.uInvert, invert);
 
         ValueCell.update(v.uGridDim, gridDim);
         ValueCell.update(v.uGridTexDim, gridTexDim);
@@ -66,12 +68,12 @@ function getIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture
 
         ctx.namedComputeRenderables[IsosurfaceName].update();
     } else {
-        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, packedGroup);
+        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
     }
     return ctx.namedComputeRenderables[IsosurfaceName];
 }
 
-function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, packedGroup: boolean) {
+function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Texture, activeVoxelsBase: Texture, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, levels: number, scale: Vec2, count: number, invert: boolean, packedGroup: boolean) {
     // console.log('uSize', Math.pow(2, levels))
     const values: IsosurfaceValues = {
         ...QuadValues,
@@ -85,6 +87,7 @@ function createIsosurfaceRenderable(ctx: WebGLContext, activeVoxelsPyramid: Text
         uSize: ValueCell.create(Math.pow(2, levels)),
         uLevels: ValueCell.create(levels),
         uCount: ValueCell.create(count),
+        uInvert: ValueCell.create(invert),
 
         uGridDim: ValueCell.create(gridDim),
         uGridTexDim: ValueCell.create(gridTexDim),
@@ -112,7 +115,7 @@ function setRenderingDefaults(ctx: WebGLContext) {
     state.clearColor(0, 0, 0, 0);
 }
 
-export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
+export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     const { gl, resources, extensions } = ctx;
     const { pyramidTex, height, levels, scale, count } = histogramPyramid;
     const width = pyramidTex.getWidth();
@@ -167,7 +170,7 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
     groupTexture.attachFramebuffer(framebuffer, 1);
     normalTexture.attachFramebuffer(framebuffer, 2);
 
-    const renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, packedGroup);
+    const renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
     ctx.state.currentRenderItemId = -1;
 
     const { drawBuffers } = ctx.extensions;
@@ -192,7 +195,16 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
 
 //
 
-export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
+/**
+ * GPU isosurface extraction
+ *
+ * Algorithm from "High‐speed Marching Cubes using HistoPyramids"
+ * by C Dyken, G Ziegler, C Theobalt, HP Seidel
+ * https://doi.org/10.1111/j.1467-8659.2008.01182.x
+ *
+ * Implementation based on http://www.miaumiau.cat/2016/10/stream-compaction-in-webgl/
+ */
+export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     // console.time('calcActiveVoxels');
     const activeVoxelsTex = calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);
     // ctx.waitForGpuCommandsCompleteSync();
@@ -204,7 +216,7 @@ export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDi
     // console.timeEnd('createHistogramPyramid');
 
     // console.time('createIsosurfaceBuffers');
-    const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, packedGroup, vertexTexture, groupTexture, normalTexture);
+    const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, vertexTexture, groupTexture, normalTexture);
     // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createIsosurfaceBuffers');
 

src/mol-gl/renderable/schema.ts

@@ -185,7 +185,9 @@ export const ColorSchema = {
     uColor: UniformSpec('v3', 'material'),
     uColorTexDim: UniformSpec('v2'),
     tColor: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
+    tPalette: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
     dColorType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'group', 'groupInstance', 'vertex', 'vertexInstance']),
+    dUsePalette: DefineSpec('boolean'),
 } as const;
 export type ColorSchema = typeof ColorSchema
 export type ColorValues = Values<ColorSchema>

src/mol-gl/renderable/util.ts

@@ -7,6 +7,7 @@
 import { Sphere3D } from '../../mol-math/geometry';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
+import { TextureFilter } from '../webgl/texture';
 
 export function calculateTextureInfo (n: number, itemSize: number) {
     n = Math.max(n, 2); // observed issues with 1 pixel textures
@@ -22,6 +23,7 @@ export interface TextureImage<T extends Uint8Array | Float32Array | Int32Array>
     readonly width: number
     readonly height: number
     readonly flipY?: boolean
+    readonly filter?: TextureFilter
 }
 
 export interface TextureVolume<T extends Uint8Array | Float32Array> {

src/mol-gl/shader/chunks/assign-color-varying.glsl.ts

@@ -14,6 +14,10 @@ export const assign_color_varying = `
         vColor.rgb = readFromTexture(tColor, int(aInstance) * uVertexCount + VertexID, uColorTexDim).rgb;
     #endif
 
+    #ifdef dUsePalette
+        vPaletteV = ((vColor.r * 256.0 * 256.0 * 255.0 + vColor.g * 256.0 * 255.0 + vColor.b * 255.0) - 1.0) / 16777215.0;
+    #endif
+
     #ifdef dOverpaint
         vOverpaint = readFromTexture(tOverpaint, aInstance * float(uGroupCount) + group, uOverpaintTexDim);
     #endif

src/mol-gl/shader/chunks/assign-material-color.glsl.ts

@@ -1,6 +1,8 @@
 export const assign_material_color = `
 #if defined(dRenderVariant_color)
-    #if defined(dColorType_uniform)
+    #if defined(dUsePalette)
+        vec4 material = vec4(texture2D(tPalette, vec2(vPaletteV, 0.5)).rgb, uAlpha);
+    #elif defined(dColorType_uniform)
         vec4 material = vec4(uColor, uAlpha);
     #elif defined(dColorType_varying)
         vec4 material = vec4(vColor.rgb, uAlpha);

src/mol-gl/shader/chunks/color-frag-params.glsl.ts

@@ -21,4 +21,9 @@ export const color_frag_params = `
     varying float vGroup;
     varying float vTransparency;
 #endif
+
+#ifdef dUsePalette
+    uniform sampler2D tPalette;
+    varying float vPaletteV;
+#endif
 `;

src/mol-gl/shader/chunks/color-vert-params.glsl.ts

@@ -30,4 +30,8 @@ export const color_vert_params = `
     uniform vec2 uTransparencyTexDim;
     uniform sampler2D tTransparency;
 #endif
+
+#ifdef dUsePalette
+    varying float vPaletteV;
+#endif
 `;

src/mol-gl/shader/marching-cubes/isosurface.frag.ts

@@ -18,6 +18,7 @@ uniform float uIsoValue;
 uniform float uLevels;
 uniform float uSize;
 uniform float uCount;
+uniform bool uInvert;
 
 uniform vec3 uGridDim;
 uniform vec3 uGridTexDim;
@@ -163,6 +164,13 @@ void main(void) {
     // current vertex for the up to 15 MC cases
     int currentVertex = vI - idot4(m, starts);
 
+    // ensure winding-order is the same for negative and positive iso-levels
+    if (uInvert) {
+        int v = imod(currentVertex + 1, 3);
+        if (v == 1) currentVertex += 2;
+        else if (v == 0) currentVertex -= 2;
+    }
+
     // get index into triIndices table
     int mcIndex = 16 * int(edgeIndex) + currentVertex;
     vec4 mcData = texture2D(tTriIndices, vec2(imod(mcIndex, 64), mcIndex / 64) / 64.);
@@ -273,11 +281,18 @@ void main(void) {
         voxelPadded(b1 - c3).a - voxelPadded(b1 + c3).a,
         voxelPadded(b1 - c4).a - voxelPadded(b1 + c4).a
     ));
-    mat3 normalMatrix = transpose3(inverse3(mat3(uGridTransform)));
-    gl_FragData[2].xyz = normalMatrix * -vec3(
+    gl_FragData[2].xyz = -vec3(
         n0.x + t * (n0.x - n1.x),
         n0.y + t * (n0.y - n1.y),
         n0.z + t * (n0.z - n1.z)
     );
+
+    // ensure normal-direction is the same for negative and positive iso-levels
+    if (uInvert) {
+        gl_FragData[2].xyz *= -1.0;
+    }
+
+    // apply normal matrix
+    gl_FragData[2].xyz *= transpose3(inverse3(mat3(uGridTransform)));
 }
 `;

src/mol-gl/webgl/texture.ts

@@ -283,6 +283,9 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
             gl.bindTexture(gl.TEXTURE_2D, texture);
             gl.texImage2D(gl.TEXTURE_2D, 0, internalFormat, format, type, data);
         } else if (isTexture2d(data, target, gl)) {
+            const _filter = data.filter ? getFilter(gl, data.filter) : filter;
+            gl.texParameteri(target, gl.TEXTURE_MAG_FILTER, _filter);
+            gl.texParameteri(target, gl.TEXTURE_MIN_FILTER, _filter);
             gl.pixelStorei(gl.UNPACK_FLIP_Y_WEBGL, !!data.flipY);
             if (sub) {
                 gl.texSubImage2D(target, 0, 0, 0, data.width, data.height, format, type, data.array);

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

@@ -2,7 +2,7 @@
 import { parseSdf } from '../sdf/parser';
 
 const SdfString = `
-  Mrv1718007121815122D          
+  Mrv1718007121815122D
 
   5  4  0  0  0  0            999 V2000
     0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
@@ -17,7 +17,7 @@ const SdfString = `
 M  CHG  3   1  -1   3  -1   5  -1
 M  END
 > <DATABASE_ID>
-DB14523
+0
 
 > <DATABASE_NAME>
 drugbank
@@ -112,7 +112,225 @@ Phosphate ion
 > <SYNONYMS>
 Orthophosphate; Phosphate
 
-$$$$`;
+$$$$
+
+Comp 2
+
+5  4  0  0  0  0            999 V2000
+  0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+ -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  0.0000   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+  0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+  0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+4  1  1  0  0  0  0
+4  2  2  0  0  0  0
+4  3  1  0  0  0  0
+4  5  1  0  0  0  0
+M  CHG  3   1  -1   3  -1   5  -1
+M  END
+> <DATABASE_ID>
+1
+
+$$$$
+
+2244
+  -OEChem-04122119123D
+
+ 21 21  0     0  0  0  0  0  0999 V2000
+    1.2333    0.5540    0.7792 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6952   -2.7148   -0.7502 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7958   -2.1843    0.8685 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7813    0.8105   -1.4821 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0857    0.6088    0.4403 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7927   -0.5515    0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7288    1.8464    0.4133 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.1426   -0.4741   -0.2184 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.0787    1.9238    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7855    0.7636   -0.2453 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1409   -1.8536    0.1477 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1094    0.6715   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.5305    0.5996    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1851    2.7545    0.6593 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7247   -1.3605   -0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5797    2.8872    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8374    0.8238   -0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7290    1.4184    0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.2045    0.6969   -0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7105   -0.3659    0.6426 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2555   -3.5916   -0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  5  1  0  0  0  0
+  1 12  1  0  0  0  0
+  2 11  1  0  0  0  0
+  2 21  1  0  0  0  0
+  3 11  2  0  0  0  0
+  4 12  2  0  0  0  0
+  5  6  1  0  0  0  0
+  5  7  2  0  0  0  0
+  6  8  2  0  0  0  0
+  6 11  1  0  0  0  0
+  7  9  1  0  0  0  0
+  7 14  1  0  0  0  0
+  8 10  1  0  0  0  0
+  8 15  1  0  0  0  0
+  9 10  2  0  0  0  0
+  9 16  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 18  1  0  0  0  0
+ 13 19  1  0  0  0  0
+ 13 20  1  0  0  0  0
+M  END
+> <PUBCHEM_COMPOUND_CID>
+2244
+
+> <PUBCHEM_CONFORMER_RMSD>
+0.6
+
+> <PUBCHEM_CONFORMER_DIVERSEORDER>
+1
+11
+10
+3
+15
+17
+13
+5
+16
+7
+14
+9
+8
+4
+18
+6
+12
+2
+
+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
+18
+1 -0.23
+10 -0.15
+11 0.63
+12 0.66
+13 0.06
+14 0.15
+15 0.15
+16 0.15
+17 0.15
+2 -0.65
+21 0.5
+3 -0.57
+4 -0.57
+5 0.08
+6 0.09
+7 -0.15
+8 -0.15
+9 -0.15
+
+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
+3
+
+> <PUBCHEM_PHARMACOPHORE_FEATURES>
+5
+1 2 acceptor
+1 3 acceptor
+1 4 acceptor
+3 2 3 11 anion
+6 5 6 7 8 9 10 rings
+
+> <PUBCHEM_HEAVY_ATOM_COUNT>
+13
+
+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+1
+
+> <PUBCHEM_CONFORMER_ID>
+000008C400000001
+
+> <PUBCHEM_MMFF94_ENERGY>
+39.5952
+
+> <PUBCHEM_FEATURE_SELFOVERLAP>
+25.432
+
+> <PUBCHEM_SHAPE_FINGERPRINT>
+1 1 18265615372930943622
+100427 49 16967750034970055351
+12138202 97 18271247217817981012
+12423570 1 16692715976000295083
+12524768 44 16753525617747228747
+12716758 59 18341332292274886536
+13024252 1 17968377969333732145
+14181834 199 17830728755827362645
+14614273 12 18262232214645093005
+15207287 21 17703787037639964108
+15775835 57 18340488876329928641
+16945 1 18271533103414939405
+193761 8 17907860604865584321
+20645476 183 17677348215414174190
+20871998 184 18198632231250704846
+21040471 1 18411412921197846465
+21501502 16 18123463883164380929
+23402539 116 18271795865171824860
+23419403 2 13539898140662769886
+23552423 10 18048876295495619569
+23559900 14 18272369794190581304
+241688 4 16179044415907240795
+257057 1 17478316999871287486
+2748010 2 18339085878070479087
+305870 269 18263645056784260212
+528862 383 18117272558388284091
+53812653 8 18410289211719108569
+7364860 26 17910392788380644719
+81228 2 18050568744116491203
+
+> <PUBCHEM_SHAPE_MULTIPOLES>
+244.06
+3.86
+2.45
+0.89
+1.95
+1.58
+0.15
+-1.85
+0.38
+-0.61
+-0.02
+0.29
+0.01
+-0.33
+
+> <PUBCHEM_SHAPE_SELFOVERLAP>
+513.037
+
+> <PUBCHEM_SHAPE_VOLUME>
+136
+
+> <PUBCHEM_COORDINATE_TYPE>
+2
+5
+10
+
+$$$$
+`;
 
 describe('sdf reader', () => {
     it('basic', async () => {
@@ -120,14 +338,21 @@ describe('sdf reader', () => {
         if (parsed.isError) {
             throw new Error(parsed.message);
         }
-        const compound = parsed.result.compounds[0];
-        const { molFile, dataItems } = compound;
+        const compound1 = parsed.result.compounds[0];
+        const compound2 = parsed.result.compounds[1];
+        const compound3 = parsed.result.compounds[2];
+        const { molFile, dataItems } = compound1;
         const { atoms, bonds } = molFile;
 
+        expect(parsed.result.compounds.length).toBe(3);
+
         // number of structures
         expect(atoms.count).toBe(5);
         expect(bonds.count).toBe(4);
 
+        expect(compound2.molFile.atoms.count).toBe(5);
+        expect(compound2.molFile.bonds.count).toBe(4);
+
         expect(atoms.x.value(0)).toBeCloseTo(0, 0.001);
         expect(atoms.y.value(0)).toBeCloseTo(0.8250, 0.0001);
         expect(atoms.z.value(0)).toBeCloseTo(0, 0.0001);
@@ -138,12 +363,21 @@ describe('sdf reader', () => {
         expect(bonds.order.value(3)).toBe(1);
 
         expect(dataItems.dataHeader.value(0)).toBe('DATABASE_ID');
-        expect(dataItems.data.value(0)).toBe('DB14523');
+        expect(dataItems.data.value(0)).toBe('0');
 
         expect(dataItems.dataHeader.value(1)).toBe('DATABASE_NAME');
         expect(dataItems.data.value(1)).toBe('drugbank');
 
         expect(dataItems.dataHeader.value(31)).toBe('SYNONYMS');
         expect(dataItems.data.value(31)).toBe('Orthophosphate; Phosphate');
+
+        expect(compound1.dataItems.data.value(0)).toBe('0');
+        expect(compound2.dataItems.data.value(0)).toBe('1');
+
+        expect(compound3.dataItems.dataHeader.value(2)).toBe('PUBCHEM_CONFORMER_DIVERSEORDER');
+        expect(compound3.dataItems.data.value(2)).toBe('1\n11\n10\n3\n15\n17\n13\n5\n16\n7\n14\n9\n8\n4\n18\n6\n12\n2');
+
+        expect(compound3.dataItems.dataHeader.value(21)).toBe('PUBCHEM_COORDINATE_TYPE');
+        expect(compound3.dataItems.data.value(21)).toBe('2\n5\n10');
     });
 });

src/mol-io/reader/common/text/tokenizer.ts

@@ -91,12 +91,21 @@ namespace Tokenizer {
         return eatLine(state);
     }
 
-    /** Advance the state by the given number of lines and return line as string. */
+    /** Advance the state and return line as string. */
     export function readLine(state: Tokenizer): string {
         markLine(state);
         return getTokenString(state);
     }
 
+    /** Advance the state and return trimmed line as string. */
+    export function readLineTrim(state: Tokenizer): string {
+        markLine(state);
+        const position = state.position;
+        trim(state, state.tokenStart, state.tokenEnd);
+        state.position = position;
+        return getTokenString(state);
+    }
+
     function readLinesChunk(state: Tokenizer, count: number, tokens: Tokens) {
         let read = 0;
         for (let i = 0; i < count; i++) {

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

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column } from '../../../mol-data/db';
@@ -22,24 +23,36 @@ 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);
 
-    let sawHeaderToken = false;
     while (tokenizer.position < tokenizer.length) {
         const line = Tokenizer.readLine(tokenizer);
-        if (!!line) {
-            if (line.startsWith('> <')) {
-                TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
-                sawHeaderToken = true;
-            } else if (sawHeaderToken) {
-                TokenBuilder.add(data, tokenizer.tokenStart, tokenizer.tokenEnd);
-                sawHeaderToken = false;
-                // TODO can there be multiline values?
+        if (line.startsWith(delimiter)) break;
+        if (!line) continue;
+
+        if (line.startsWith('> <')) {
+            TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
+
+            Tokenizer.markLine(tokenizer);
+            const start = tokenizer.tokenStart;
+            let end = tokenizer.tokenEnd;
+            let added = false;
+            while (tokenizer.position < tokenizer.length) {
+                const line2 = Tokenizer.readLine(tokenizer);
+                if (!line2 || line2.startsWith(delimiter) || line2.startsWith('> <')) {
+                    TokenBuilder.add(data, start, end);
+                    added = true;
+                    break;
+                }
+                end = tokenizer.tokenEnd;
+            }
+
+            if (!added) {
+                TokenBuilder.add(data, start, end);
             }
-        } else {
-            sawHeaderToken = false;
         }
     }
 
@@ -49,9 +62,7 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
     };
 }
 
-function handleMolFile(data: string) {
-    const tokenizer = Tokenizer(data);
-
+function handleMolFile(tokenizer: Tokenizer) {
     const title = Tokenizer.readLine(tokenizer).trim();
     const program = Tokenizer.readLine(tokenizer).trim();
     const comment = Tokenizer.readLine(tokenizer).trim();
@@ -60,6 +71,15 @@ function handleMolFile(data: string) {
 
     const atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
 
+    if (Number.isNaN(atomCount) || Number.isNaN(bondCount)) {
+        // try to skip to next molecule
+        while (tokenizer.position < tokenizer.length) {
+            const line = Tokenizer.readLine(tokenizer);
+            if (line.startsWith(delimiter)) break;
+        }
+        return;
+    }
+
     const atoms = handleAtoms(tokenizer, atomCount);
     const bonds = handleBonds(tokenizer, bondCount);
     const dataItems = handleDataItems(tokenizer);
@@ -70,10 +90,16 @@ function handleMolFile(data: string) {
     };
 }
 
-const delimiter = '$$$$';
 function parseInternal(data: string): Result<SdfFile> {
-    const result: SdfFile = { compounds: data.split(delimiter).map(d => handleMolFile(d)) };
-    return Result.success(result);
+    const tokenizer = Tokenizer(data);
+
+    const compounds: SdfFile['compounds'] = [];
+    while (tokenizer.position < tokenizer.length) {
+        const c = handleMolFile(tokenizer);
+        if (c) compounds.push(c);
+    }
+
+    return Result.success({ compounds });
 }
 
 export function parseSdf(data: string) {

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

@@ -32,7 +32,7 @@ function handleMolecule(tokenizer: Tokenizer): XyzFile['molecules'][number] {
     const type_symbol = new Array<string>(count);
 
     for (let i = 0; i < count; ++i) {
-        const line = Tokenizer.readLine(tokenizer);
+        const line = Tokenizer.readLineTrim(tokenizer);
         const fields = line.split(/\s+/g);
         type_symbol[i] = fields[0];
         x[i] = +fields[1];

src/mol-math/geometry/spacegroup/construction.ts

@@ -111,33 +111,41 @@ namespace Spacegroup {
 
     const _translationRef = Vec3();
     const _translationRefSymop = Vec3();
+    const _translationRefOffset = Vec3();
     const _translationSymop = Vec3();
-    export function setOperatorMatrixRef(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, ref: Vec3, target: Mat4) {
-        Vec3.set(_ijkVec, i, j, k);
-        Vec3.floor(_translationRef, ref);
-
-        Mat4.copy(target, spacegroup.operators[index]);
-
-        Vec3.floor(_translationRefSymop, Vec3.transformMat4(_translationRefSymop, ref, target));
-
-        Mat4.getTranslation(_translationSymop, target);
-        Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop);
-        Vec3.add(_translationSymop, _translationSymop, _translationRef);
-        Vec3.add(_translationSymop, _translationSymop, _ijkVec);
-
-        Mat4.setTranslation(target, _translationSymop);
-        Mat4.mul(target, spacegroup.cell.fromFractional, target);
-        Mat4.mul(target, target, spacegroup.cell.toFractional);
-        return target;
-    }
 
     /**
      * Get Symmetry operator for transformation around the given
      * reference point `ref` in fractional coordinates
      */
     export function getSymmetryOperatorRef(spacegroup: Spacegroup, spgrOp: number, i: number, j: number, k: number, ref: Vec3) {
-        const operator = setOperatorMatrixRef(spacegroup, spgrOp, i, j, k, ref, Mat4.zero());
-        return SymmetryOperator.create(`${spgrOp + 1}_${5 + i}${5 + j}${5 + k}`, operator, { hkl: Vec3.create(i, j, k), spgrOp });
+
+        const operator =  Mat4.zero();
+
+        Vec3.set(_ijkVec, i, j, k);
+        Vec3.floor(_translationRef, ref);
+
+        Mat4.copy(operator, spacegroup.operators[spgrOp]);
+
+        Vec3.floor(_translationRefSymop, Vec3.transformMat4(_translationRefSymop, ref, operator));
+
+        Mat4.getTranslation(_translationSymop, operator);
+        Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop);
+        Vec3.add(_translationSymop, _translationSymop, _translationRef);
+        Vec3.add(_translationSymop, _translationSymop, _ijkVec);
+
+        Mat4.setTranslation(operator, _translationSymop);
+        Mat4.mul(operator, spacegroup.cell.fromFractional, operator);
+        Mat4.mul(operator, operator, spacegroup.cell.toFractional);
+
+        Vec3.sub(_translationRefOffset, _translationRefSymop, _translationRef);
+
+        const _i = i - _translationRefOffset[0];
+        const _j = j - _translationRefOffset[1];
+        const _k = k - _translationRefOffset[2];
+
+        // const operator = setOperatorMatrixRef(spacegroup, spgrOp, i, j, k, ref, Mat4.zero());
+        return SymmetryOperator.create(`${spgrOp + 1}_${5 + _i}${5 + _j}${5 + _k}`, operator, { hkl: Vec3.create(_i, _j, _k), spgrOp });
     }
 
     function getOperatorMatrix(ids: number[]) {

src/mol-math/linear-algebra/3d/vec3.ts

@@ -590,6 +590,9 @@ namespace Vec3 {
     export const unitX: ReadonlyVec3 = create(1, 0, 0);
     export const unitY: ReadonlyVec3 = create(0, 1, 0);
     export const unitZ: ReadonlyVec3 = create(0, 0, 1);
+    export const negUnitX: ReadonlyVec3 = create(-1, 0, 0);
+    export const negUnitY: ReadonlyVec3 = create(0, -1, 0);
+    export const negUnitZ: ReadonlyVec3 = create(0, 0, -1);
 }
 
 export { Vec3 };

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

@@ -54,6 +54,12 @@ const StandardComponents = (function() {
         { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
         { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
 
+        { id: 'MSE', name: 'SELENOMETHIONINE', type: 'L-peptide linking' },
+        { id: 'SEP', name: 'PHOSPHOSERINE', type: 'L-peptide linking' },
+        { id: 'TPO', name: 'PHOSPHOTHREONINE', type: 'L-peptide linking' },
+        { id: 'PTR', name: 'O-PHOSPHOTYROSINE', type: 'L-peptide linking' },
+        { id: 'PCA', name: 'PYROGLUTAMIC ACID', type: 'L-peptide linking' },
+
         { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
         { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
         { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },

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

@@ -61,7 +61,7 @@ namespace CustomElementProperty {
             type: builder.type || 'dynamic',
             defaultParams: {},
             getParams: (data: Model) => ({}),
-            isApplicable: (data: Model) => !!builder.isApplicable?.(data),
+            isApplicable: (data: Model) => !builder.isApplicable || !!builder.isApplicable(data),
             obtain: async (ctx: CustomProperty.Context, data: Model) => {
                 return await builder.getData(data, ctx);
             }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -15,7 +15,7 @@ import { ComplexMeshParams, ComplexVisual, ComplexMeshVisual } from '../../../mo
 import { VisualUpdateState } from '../../../mol-repr/util';
 import { PickingId } from '../../../mol-geo/geometry/picking';
 import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Interval, OrderedSet } from '../../../mol-data/int';
+import { Interval, OrderedSet, SortedArray } from '../../../mol-data/int';
 import { Interactions } from '../interactions/interactions';
 import { InteractionsProvider } from '../interactions';
 import { LocationIterator } from '../../../mol-geo/util/location-iterator';
@@ -35,6 +35,8 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
 
     if (!edgeCount) return Mesh.createEmpty(mesh);
 
+    const { child } = structure;
+
     const builderProps = {
         linkCount: edgeCount,
         position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
@@ -63,12 +65,28 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
             const sizeB = theme.size.size(l);
             return Math.min(sizeA, sizeB) * sizeFactor;
         },
-        ignore: (edgeIndex: number) => edges[edgeIndex].props.flag === InteractionFlag.Filtered
+        ignore: (edgeIndex: number) => {
+            if (edges[edgeIndex].props.flag === InteractionFlag.Filtered) return true;
+
+            if (child) {
+                const b = edges[edgeIndex];
+                const childUnitA = child.unitMap.get(b.unitA);
+                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;
+            }
+
+            return false;
+        }
     };
 
     const m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
 
-    const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * sizeFactor);
+    const sphere = Sphere3D.expand(Sphere3D(), (child ?? structure).boundary.sphere, 1 * sizeFactor);
     m.setBoundingSphere(sphere);
 
     return m;
@@ -80,6 +98,7 @@ export const InteractionsInterUnitParams = {
     sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
     dashCount: PD.Numeric(6, { min: 2, max: 10, step: 2 }),
     dashScale: PD.Numeric(0.4, { min: 0, max: 2, step: 0.1 }),
+    includeParent: PD.Boolean(false),
 };
 export type InteractionsInterUnitParams = typeof InteractionsInterUnitParams
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -7,7 +7,7 @@
 import { Unit, Structure, StructureElement } from '../../../mol-model/structure';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { Loci, EmptyLoci } from '../../../mol-model/loci';
-import { Interval, OrderedSet } from '../../../mol-data/int';
+import { Interval, OrderedSet, SortedArray } from '../../../mol-data/int';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { PickingId } from '../../../mol-geo/geometry/picking';
@@ -25,6 +25,10 @@ import { Sphere3D } from '../../../mol-math/geometry';
 async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<InteractionsIntraUnitParams>, mesh?: Mesh) {
     if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
 
+    const { child } = structure;
+    const childUnit = child?.unitMap.get(unit.id);
+    if (child && !childUnit) return Mesh.createEmpty(mesh);
+
     const location = StructureElement.Location.create(structure, unit);
 
     const interactions = InteractionsProvider.get(structure).value!;
@@ -51,12 +55,16 @@ 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
+        ignore: (edgeIndex: number) => (
+            flag[edgeIndex] === InteractionFlag.Filtered ||
+            // TODO: check all members
+            (!!childUnit && !SortedArray.has(childUnit.elements, unit.elements[members[offsets[a[edgeIndex]]]]))
+        )
     };
 
     const m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
 
-    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * sizeFactor);
+    const sphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, 1 * sizeFactor);
     m.setBoundingSphere(sphere);
 
     return m;
@@ -68,6 +76,7 @@ export const InteractionsIntraUnitParams = {
     sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
     dashCount: PD.Numeric(6, { min: 2, max: 10, step: 2 }),
     dashScale: PD.Numeric(0.4, { min: 0, max: 2, step: 0.1 }),
+    includeParent: PD.Boolean(false),
 };
 export type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams
 
@@ -147,7 +156,7 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int
         const { offset } = contacts;
         const { offsets: fOffsets, indices: fIndices } = features.elementsIndex;
 
-        // TODO when isMarking, all elements of contact features need to be in the loci
+        // 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;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -50,5 +50,11 @@ export const InteractionsRepresentationProvider = StructureRepresentationProvide
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, structure: Structure) => InteractionsProvider.attach(ctx, structure, void 0, true),
         detach: (data) => InteractionsProvider.ref(data, false)
+    },
+    getData: (structure: Structure, props: PD.Values<InteractionsParams>) => {
+        return props.includeParent ? structure.asParent() : structure;
+    },
+    mustRecreate: (oldProps: PD.Values<InteractionsParams>, newProps: PD.Values<InteractionsParams>) => {
+        return oldProps.includeParent !== newProps.includeParent;
     }
 });

src/mol-model/loci.ts

@@ -37,9 +37,10 @@ export interface DataLoci<T = unknown, E = unknown> {
     readonly kind: 'data-loci',
     readonly tag: string
     readonly data: T,
-    readonly elements: ReadonlyArray<E>
+    readonly elements: ReadonlyArray<E>,
 
-    getBoundingSphere(boundingSphere: Sphere3D): Sphere3D
+    /** if undefined, won't zoom */
+    getBoundingSphere?(boundingSphere: Sphere3D): Sphere3D
     getLabel(): string
 }
 export function isDataLoci(x?: Loci): x is DataLoci {
@@ -159,7 +160,7 @@ namespace Loci {
         } else if (loci.kind === 'group-loci') {
             return ShapeGroup.getBoundingSphere(loci, boundingSphere);
         } else if (loci.kind === 'data-loci') {
-            return loci.getBoundingSphere(boundingSphere);
+            return loci.getBoundingSphere?.(boundingSphere);
         } else if (loci.kind === 'volume-loci') {
             return Volume.getBoundingSphere(loci.volume, boundingSphere);
         } else if (loci.kind === 'isosurface-loci') {

src/mol-model/structure/model/properties/utils/residue-set.ts

@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureElement } from '../../../structure/element';
+import { StructureProperties } from '../../../structure/properties';
+
+export interface ResidueSetEntry {
+    label_asym_id: string,
+    label_comp_id: string,
+    label_seq_id: number,
+    label_alt_id: string,
+    ins_code: string,
+    // 1_555 by default
+    operator_name?: string
+}
+
+export class ResidueSet {
+    private index = new Map<string, Map<number, ResidueSetEntry[]>>();
+    private checkOperator: boolean = false;
+
+    add(entry: ResidueSetEntry) {
+        let root = this.index.get(entry.label_asym_id);
+        if (!root) {
+            root = new Map();
+            this.index.set(entry.label_asym_id, root);
+        }
+
+        let entries = root.get(entry.label_seq_id);
+        if (!entries) {
+            entries = [];
+            root.set(entry.label_seq_id, entries);
+        }
+
+        const exists = this._find(entry, entries);
+        if (!exists) {
+            entries.push(entry);
+            return true;
+        }
+
+        return false;
+    }
+
+    hasLabelAsymId(asym_id: string) {
+        return this.index.has(asym_id);
+    }
+
+    has(loc: StructureElement.Location) {
+        const asym_id = _asym_id(loc);
+        if (!this.index.has(asym_id)) return;
+        const root = this.index.get(asym_id)!;
+        const seq_id = _seq_id(loc);
+        if (!root.has(seq_id)) return;
+        const entries = root.get(seq_id)!;
+
+        const comp_id = _comp_id(loc);
+        const alt_id = _alt_id(loc);
+        const ins_code = _ins_code(loc);
+        const op_name = _op_name(loc) ?? '1_555';
+
+        for (const e of entries) {
+            if (e.label_comp_id !== comp_id || e.label_alt_id !== alt_id || e.ins_code !== ins_code) continue;
+            if (this.checkOperator && (e.operator_name ?? '1_555') !== op_name) continue;
+
+            return e;
+        }
+    }
+
+    static getLabel(entry: ResidueSetEntry, checkOperator = false) {
+        return `${entry.label_asym_id} ${entry.label_comp_id} ${entry.label_seq_id}:${entry.ins_code}:${entry.label_alt_id}${checkOperator ? ' ' + (entry.operator_name ?? '1_555') : ''}`;
+    }
+
+    static getEntryFromLocation(loc: StructureElement.Location): ResidueSetEntry {
+        return {
+            label_asym_id: _asym_id(loc),
+            label_comp_id: _comp_id(loc),
+            label_seq_id: _seq_id(loc),
+            label_alt_id: _alt_id(loc),
+            ins_code: _ins_code(loc),
+            operator_name: _op_name(loc) ?? '1_555'
+        };
+    }
+
+    private _find(entry: ResidueSetEntry, xs: ResidueSetEntry[]) {
+        for (const e of xs) {
+            if (e.label_comp_id !== entry.label_comp_id || e.label_alt_id !== entry.label_alt_id || e.ins_code !== entry.ins_code) continue;
+            if (this.checkOperator && (e.operator_name ?? '1_555') !== (entry.operator_name ?? '1_555')) continue;
+
+            return true;
+        }
+
+        return false;
+    }
+
+    constructor(options?: { checkOperator?: boolean }) {
+        this.checkOperator = options?.checkOperator ?? false;
+    }
+}
+
+const _asym_id = StructureProperties.chain.label_asym_id;
+const _seq_id = StructureProperties.residue.label_seq_id;
+const _comp_id = StructureProperties.atom.label_comp_id;
+const _alt_id = StructureProperties.atom.label_alt_id;
+const _ins_code = StructureProperties.residue.pdbx_PDB_ins_code;
+const _op_name = StructureProperties.unit.operator_name;

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

@@ -245,7 +245,9 @@ export const WaterNames = new Set([
 export const AminoAcidNamesL = new Set([
     'HIS', 'ARG', 'LYS', 'ILE', 'PHE', 'LEU', 'TRP', 'ALA', 'MET', 'PRO', 'CYS',
     'ASN', 'VAL', 'GLY', 'SER', 'GLN', 'TYR', 'ASP', 'GLU', 'THR', 'SEC', 'PYL',
-    'UNK' // unknown amino acid from CCD
+    'UNK', // unknown amino acid from CCD
+    'MSE', 'SEP', 'TPO', 'PTR', 'PCA' // common
+
 ]);
 export const AminoAcidNamesD = new Set([
     'DAL', // D-ALANINE

src/mol-model/structure/query/queries/internal.ts

@@ -43,7 +43,7 @@ export function atomicSequence(): StructureQuery {
 
             units.push(unit);
         }
-        return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
+        return StructureSelection.Singletons(inputStructure, Structure.create(units, { parent: inputStructure }));
     };
 }
 
@@ -62,7 +62,7 @@ export function water(): StructureQuery {
             if (P.entity.type(l) !== 'water') continue;
             units.push(unit);
         }
-        return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
+        return StructureSelection.Singletons(inputStructure, Structure.create(units, { parent: inputStructure }));
     };
 }
 
@@ -92,7 +92,7 @@ export function atomicHet(): StructureQuery {
 
             units.push(unit);
         }
-        return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
+        return StructureSelection.Singletons(inputStructure, Structure.create(units, { parent: inputStructure }));
     };
 }
 
@@ -105,7 +105,7 @@ export function spheres(): StructureQuery {
             if (unit.kind !== Unit.Kind.Spheres) continue;
             units.push(unit);
         }
-        return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
+        return StructureSelection.Singletons(inputStructure, Structure.create(units, { parent: inputStructure }));
     };
 }
 

src/mol-model/structure/query/queries/modifiers.ts

@@ -11,10 +11,14 @@ import { StructureSelection } from '../selection';
 import { UniqueStructuresBuilder } from '../utils/builders';
 import { StructureUniqueSubsetBuilder } from '../../structure/util/unique-subset-builder';
 import { QueryContext, QueryFn } from '../context';
-import { structureIntersect, structureSubtract } from '../utils/structure-set';
+import { structureIntersect, structureSubtract, structureUnion } from '../utils/structure-set';
 import { UniqueArray } from '../../../../mol-data/generic';
 import { StructureSubsetBuilder } from '../../structure/util/subset-builder';
 import { StructureElement } from '../../structure/element';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { ResidueSet, ResidueSetEntry } from '../../model/properties/utils/residue-set';
+import { StructureProperties } from '../../structure/properties';
+import { arraySetAdd } from '../../../../mol-util/array';
 
 function getWholeResidues(ctx: QueryContext, source: Structure, structure: Structure) {
     const builder = source.subsetBuilder(true);
@@ -435,4 +439,252 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
     return builder.getStructure();
 }
 
+export interface SurroundingLigandsParams {
+    query: StructureQuery,
+    radius: number,
+    includeWater: boolean
+}
+
+/**
+ * Includes expanded surrounding ligands based on radius from the source, struct_conn entries & pdbx_molecule entries.
+ */
+export function surroundingLigands({ query, radius, includeWater }: SurroundingLigandsParams): StructureQuery {
+    return function query_surroundingLigands(ctx) {
+
+        const inner = StructureSelection.unionStructure(query(ctx));
+        const surroundings = getWholeResidues(ctx, ctx.inputStructure, getIncludeSurroundings(ctx, ctx.inputStructure, inner, { radius }));
+
+        const prd = getPrdAsymIdx(ctx.inputStructure);
+        const graph = getStructConnInfo(ctx.inputStructure);
+
+        const l = StructureElement.Location.create(surroundings);
+
+        const includedPrdChains = new Map<string, string[]>();
+
+        const componentResidues = new ResidueSet({ checkOperator: true });
+
+        for (const unit of surroundings.units) {
+            if (unit.kind !== Unit.Kind.Atomic) continue;
+
+            l.unit = unit;
+
+            const { elements } = unit;
+            const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+            const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+
+            while (chainsIt.hasNext) {
+                const chainSegment = chainsIt.move();
+                l.element = elements[chainSegment.start];
+
+                const asym_id = StructureProperties.chain.label_asym_id(l);
+                const op_name = StructureProperties.unit.operator_name(l);
+
+                // check for PRD molecules
+                if (prd.has(asym_id)) {
+                    if (includedPrdChains.has(asym_id)) {
+                        arraySetAdd(includedPrdChains.get(asym_id)!, op_name);
+                    } else {
+                        includedPrdChains.set(asym_id, [op_name]);
+                    }
+                    continue;
+                }
+
+                const entityType = StructureProperties.entity.type(l);
+
+                // test entity and chain
+                if (entityType === 'water' || entityType === 'polymer') continue;
+
+                residuesIt.setSegment(chainSegment);
+                while (residuesIt.hasNext) {
+                    const residueSegment = residuesIt.move();
+                    l.element = elements[residueSegment.start];
+                    graph.addComponent(ResidueSet.getEntryFromLocation(l), componentResidues);
+                }
+            }
+
+            ctx.throwIfTimedOut();
+        }
+
+        // assemble the core structure
+
+        const builder = ctx.inputStructure.subsetBuilder(true);
+        for (const unit of ctx.inputStructure.units) {
+            if (unit.kind !== Unit.Kind.Atomic) continue;
+
+            l.unit = unit;
+            const { elements } = unit;
+            const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+            const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+
+            builder.beginUnit(unit.id);
+
+            while (chainsIt.hasNext) {
+                const chainSegment = chainsIt.move();
+                l.element = elements[chainSegment.start];
+
+                const asym_id = StructureProperties.chain.label_asym_id(l);
+                const op_name = StructureProperties.unit.operator_name(l);
+
+                if (includedPrdChains.has(asym_id) && includedPrdChains.get(asym_id)!.indexOf(op_name) >= 0) {
+                    builder.addElementRange(elements, chainSegment.start, chainSegment.end);
+                    continue;
+                }
+
+                if (!componentResidues.hasLabelAsymId(asym_id)) {
+                    continue;
+                }
+
+                residuesIt.setSegment(chainSegment);
+                while (residuesIt.hasNext) {
+                    const residueSegment = residuesIt.move();
+                    l.element = elements[residueSegment.start];
+
+                    if (!componentResidues.has(l)) continue;
+                    builder.addElementRange(elements, residueSegment.start, residueSegment.end);
+                }
+            }
+            builder.commitUnit();
+
+            ctx.throwIfTimedOut();
+        }
+
+        const components = structureUnion(ctx.inputStructure, [builder.getStructure(), inner]);
+
+        // add water
+        if (includeWater) {
+            const finalBuilder = new StructureUniqueSubsetBuilder(ctx.inputStructure);
+            const lookup = ctx.inputStructure.lookup3d;
+            for (const unit of components.units) {
+                const { x, y, z } = unit.conformation;
+                const elements = unit.elements;
+                for (let i = 0, _i = elements.length; i < _i; i++) {
+                    const e = elements[i];
+                    lookup.findIntoBuilderIf(x(e), y(e), z(e), radius, finalBuilder, testIsWater);
+                    finalBuilder.addToUnit(unit.id, e);
+                }
+
+                ctx.throwIfTimedOut();
+            }
+
+            return StructureSelection.Sequence(ctx.inputStructure, [finalBuilder.getStructure()]);
+        } else {
+            return StructureSelection.Sequence(ctx.inputStructure, [components]);
+        }
+    };
+}
+
+const _entity_type = StructureProperties.entity.type;
+function testIsWater(l: StructureElement.Location) {
+    return _entity_type(l) === 'water';
+}
+
+function getPrdAsymIdx(structure: Structure) {
+    const model = structure.models[0];
+    const ids = new Set<string>();
+    if (!MmcifFormat.is(model.sourceData)) return ids;
+    const { _rowCount, asym_id } = model.sourceData.data.db.pdbx_molecule;
+    for (let i = 0; i < _rowCount; i++) {
+        ids.add(asym_id.value(i));
+    }
+    return ids;
+}
+
+function getStructConnInfo(structure: Structure) {
+    const model = structure.models[0];
+    const graph = new StructConnGraph();
+
+    if (!MmcifFormat.is(model.sourceData)) return graph;
+
+    const struct_conn = model.sourceData.data.db.struct_conn;
+    const { conn_type_id } = struct_conn;
+    const { ptnr1_label_asym_id, ptnr1_label_comp_id, ptnr1_label_seq_id, ptnr1_symmetry, pdbx_ptnr1_label_alt_id, pdbx_ptnr1_PDB_ins_code } = struct_conn;
+    const { ptnr2_label_asym_id, ptnr2_label_comp_id, ptnr2_label_seq_id, ptnr2_symmetry, pdbx_ptnr2_label_alt_id, pdbx_ptnr2_PDB_ins_code } = struct_conn;
+
+    for (let i = 0; i < struct_conn._rowCount; i++) {
+        const bondType = conn_type_id.value(i);
+        if (bondType !== 'covale' && bondType !== 'metalc') continue;
+
+        const a: ResidueSetEntry = {
+            label_asym_id: ptnr1_label_asym_id.value(i),
+            label_comp_id: ptnr1_label_comp_id.value(i),
+            label_seq_id: ptnr1_label_seq_id.value(i),
+            label_alt_id: pdbx_ptnr1_label_alt_id.value(i),
+            ins_code: pdbx_ptnr1_PDB_ins_code.value(i),
+            operator_name: ptnr1_symmetry.value(i) ?? '1_555'
+        };
+
+        const b: ResidueSetEntry = {
+            label_asym_id: ptnr2_label_asym_id.value(i),
+            label_comp_id: ptnr2_label_comp_id.value(i),
+            label_seq_id: ptnr2_label_seq_id.value(i),
+            label_alt_id: pdbx_ptnr2_label_alt_id.value(i),
+            ins_code: pdbx_ptnr2_PDB_ins_code.value(i),
+            operator_name: ptnr2_symmetry.value(i) ?? '1_555'
+        };
+
+        graph.addEdge(a, b);
+    }
+
+    return graph;
+}
+
+class StructConnGraph {
+    vertices = new Map<string, ResidueSetEntry>();
+    edges = new Map<string, string[]>();
+
+    private addVertex(e: ResidueSetEntry, label: string) {
+        if (this.vertices.has(label)) return;
+        this.vertices.set(label, e);
+        this.edges.set(label, []);
+    }
+
+    addEdge(a: ResidueSetEntry, b: ResidueSetEntry) {
+        const al = ResidueSet.getLabel(a);
+        const bl = ResidueSet.getLabel(b);
+        this.addVertex(a, al);
+        this.addVertex(b, bl);
+        arraySetAdd(this.edges.get(al)!, bl);
+        arraySetAdd(this.edges.get(bl)!, al);
+    }
+
+    addComponent(start: ResidueSetEntry, set: ResidueSet) {
+        const startLabel = ResidueSet.getLabel(start);
+
+        if (!this.vertices.has(startLabel)) {
+            set.add(start);
+            return;
+        }
+
+        const visited = new Set<string>();
+        const added = new Set<string>();
+        const stack = [startLabel];
+
+        added.add(startLabel);
+        set.add(start);
+
+        while (stack.length > 0) {
+            const a = stack.pop()!;
+            visited.add(a);
+
+            const u = this.vertices.get(a)!;
+
+            for (const b of this.edges.get(a)!) {
+                if (visited.has(b)) continue;
+                stack.push(b);
+
+                if (added.has(b)) continue;
+                added.add(b);
+
+                const v = this.vertices.get(b)!;
+                if (u.operator_name === v.operator_name) {
+                    set.add({ ...v, operator_name: start.operator_name });
+                } else {
+                    set.add(v);
+                }
+
+            }
+        }
+    }
+}
+
 // TODO: unionBy (skip this one?), cluster

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

@@ -23,6 +23,9 @@ import { StructureProperties } from '../properties';
 import { BoundaryHelper } from '../../../../mol-math/geometry/boundary-helper';
 import { Boundary } from '../../../../mol-math/geometry/boundary';
 
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const osSize = OrderedSet.size;
+
 /** Represents multiple structure element index locations */
 export interface Loci {
     readonly kind: 'element-loci',
@@ -71,7 +74,7 @@ export namespace Loci {
 
     export function size(loci: Loci) {
         let s = 0;
-        for (const u of loci.elements) s += OrderedSet.size(u.indices);
+        for (const u of loci.elements) s += osSize(u.indices);
         return s;
     }
 

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

@@ -98,12 +98,12 @@ const residue = {
     microheterogeneityCompIds: p(microheterogeneityCompIds),
     secondary_structure_type: p(l => {
         if (!Unit.isAtomic(l.unit)) notAtomic();
-        const secStruc = SecondaryStructureProvider.get(l.structure).value?.get(l.unit.id);
+        const secStruc = SecondaryStructureProvider.get(l.structure).value?.get(l.unit.invariantId);
         return secStruc?.type[l.unit.residueIndex[l.element]] ?? SecondaryStructureType.Flag.NA;
     }),
     secondary_structure_key: p(l => {
         if (!Unit.isAtomic(l.unit)) notAtomic();
-        const secStruc = SecondaryStructureProvider.get(l.structure).value?.get(l.unit.id);
+        const secStruc = SecondaryStructureProvider.get(l.structure).value?.get(l.unit.invariantId);
         return secStruc?.key[l.unit.residueIndex[l.element]] ?? -1;
     }),
     chem_comp_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l))!.type),

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

@@ -23,7 +23,7 @@ import { Carbohydrates } from './carbohydrates/data';
 import { computeCarbohydrates } from './carbohydrates/compute';
 import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
 import { idFactory } from '../../../mol-util/id-factory';
-import { Box3D, GridLookup3D } from '../../../mol-math/geometry';
+import { GridLookup3D } from '../../../mol-math/geometry';
 import { UUID } from '../../../mol-util';
 import { CustomProperties } from '../../custom-property';
 import { AtomicHierarchy } from '../model/properties/atomic';
@@ -35,90 +35,73 @@ import { Trajectory } from '../trajectory';
 import { RuntimeContext, Task } from '../../../mol-task';
 import { computeStructureBoundary } from './util/boundary';
 
+/** Internal structure state */
+type State = {
+    parent?: Structure,
+    boundary?: Boundary,
+    lookup3d?: StructureLookup3D,
+    interUnitBonds?: InterUnitBonds,
+    unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
+    unitSymmetryGroupsIndexMap?: IntMap<number>,
+    unitsSortedByVolume?: ReadonlyArray<Unit>;
+    carbohydrates?: Carbohydrates,
+    models?: ReadonlyArray<Model>,
+    model?: Model,
+    masterModel?: Model,
+    representativeModel?: Model,
+    uniqueResidueNames?: Set<string>,
+    uniqueElementSymbols?: Set<ElementSymbol>,
+    entityIndices?: ReadonlyArray<EntityIndex>,
+    uniqueAtomicResidueIndices?: ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>>,
+    serialMapping?: SerialMapping,
+    hashCode: number,
+    transformHash: number,
+    elementCount: number,
+    bondCount: number,
+    uniqueElementCount: number,
+    atomicResidueCount: number,
+    polymerResidueCount: number,
+    polymerGapCount: number,
+    polymerUnitCount: number,
+    coordinateSystem: SymmetryOperator,
+    label: string,
+    propertyData?: any,
+    customProps?: CustomProperties
+}
+
 class Structure {
-    /** Maps unit.id to unit */
-    readonly unitMap: IntMap<Unit>;
-    /** Maps unit.id to index of unit in units array */
-    readonly unitIndexMap: IntMap<number>;
-    /** Array of all units in the structure, sorted by unit.id */
-    readonly units: ReadonlyArray<Unit>;
-
-    private _props: {
-        parent?: Structure,
-        boundary?: Boundary,
-        lookup3d?: StructureLookup3D,
-        interUnitBonds?: InterUnitBonds,
-        unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
-        unitSymmetryGroupsIndexMap?: IntMap<number>,
-        unitsSortedByVolume?: ReadonlyArray<Unit>;
-        carbohydrates?: Carbohydrates,
-        models?: ReadonlyArray<Model>,
-        model?: Model,
-        masterModel?: Model,
-        representativeModel?: Model,
-        uniqueResidueNames?: Set<string>,
-        uniqueElementSymbols?: Set<ElementSymbol>,
-        entityIndices?: ReadonlyArray<EntityIndex>,
-        uniqueAtomicResidueIndices?: ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>>,
-        serialMapping?: SerialMapping,
-        hashCode: number,
-        /** Hash based on all unit.id values in the structure, reflecting the units transformation */
-        transformHash: number,
-        elementCount: number,
-        bondCount: number,
-        uniqueElementCount: number,
-        atomicResidueCount: number,
-        polymerResidueCount: number,
-        polymerUnitCount: number,
-        coordinateSystem: SymmetryOperator,
-        label: string,
-        propertyData?: any,
-        customProps?: CustomProperties
-    } = {
-        hashCode: -1,
-        transformHash: -1,
-        elementCount: -1,
-        bondCount: -1,
-        uniqueElementCount: -1,
-        atomicResidueCount: -1,
-        polymerResidueCount: -1,
-        polymerUnitCount: -1,
-        coordinateSystem: SymmetryOperator.Default,
-        label: ''
-    };
-
     subsetBuilder(isSorted: boolean) {
         return new StructureSubsetBuilder(this, isSorted);
     }
 
     /** Count of all elements in the structure, i.e. the sum of the elements in the units */
     get elementCount() {
-        return this._props.elementCount;
+        return this.state.elementCount;
     }
 
     /** Count of all bonds (intra- and inter-unit) in the structure */
     get bondCount() {
-        if (this._props.bondCount === -1) {
-            this._props.bondCount = this.interUnitBonds.edgeCount + Bond.getIntraUnitBondCount(this);
+        if (this.state.bondCount === -1) {
+            this.state.bondCount = this.interUnitBonds.edgeCount + Bond.getIntraUnitBondCount(this);
         }
-        return this._props.bondCount;
+        return this.state.bondCount;
     }
 
     get hasCustomProperties() {
-        return !!this._props.customProps && this._props.customProps.all.length > 0;
+        return !!this.state.customProps && this.state.customProps.all.length > 0;
     }
 
     get customPropertyDescriptors() {
-        if (!this._props.customProps) this._props.customProps = new CustomProperties();
-        return this._props.customProps;
+        if (!this.state.customProps) this.state.customProps = new CustomProperties();
+        return this.state.customProps;
     }
 
     /**
      * Property data unique to this instance of the structure.
      */
     get currentPropertyData() {
-        if (!this._props.propertyData) this._props.propertyData = Object.create(null);
-        return this._props.propertyData;
+        if (!this.state.propertyData) this.state.propertyData = Object.create(null);
+        return this.state.propertyData;
     }
 
     /**
@@ -130,31 +113,39 @@ class Structure {
 
     /** Count of all polymer residues in the structure */
     get polymerResidueCount() {
-        if (this._props.polymerResidueCount === -1) {
-            this._props.polymerResidueCount = getPolymerResidueCount(this);
+        if (this.state.polymerResidueCount === -1) {
+            this.state.polymerResidueCount = getPolymerResidueCount(this);
         }
-        return this._props.polymerResidueCount;
+        return this.state.polymerResidueCount;
+    }
+
+    /** Count of all polymer gaps in the structure */
+    get polymerGapCount() {
+        if (this.state.polymerGapCount === -1) {
+            this.state.polymerGapCount = getPolymerGapCount(this);
+        }
+        return this.state.polymerGapCount;
     }
 
     get polymerUnitCount() {
-        if (this._props.polymerUnitCount === -1) {
-            this._props.polymerUnitCount = getPolymerUnitCount(this);
+        if (this.state.polymerUnitCount === -1) {
+            this.state.polymerUnitCount = getPolymerUnitCount(this);
         }
-        return this._props.polymerUnitCount;
+        return this.state.polymerUnitCount;
     }
 
     get uniqueElementCount() {
-        if (this._props.uniqueElementCount === -1) {
-            this._props.uniqueElementCount = getUniqueElementCount(this);
+        if (this.state.uniqueElementCount === -1) {
+            this.state.uniqueElementCount = getUniqueElementCount(this);
         }
-        return this._props.uniqueElementCount;
+        return this.state.uniqueElementCount;
     }
 
     get atomicResidueCount() {
-        if (this._props.atomicResidueCount === -1) {
-            this._props.atomicResidueCount = getAtomicResidueCount(this);
+        if (this.state.atomicResidueCount === -1) {
+            this.state.atomicResidueCount = getAtomicResidueCount(this);
         }
-        return this._props.atomicResidueCount;
+        return this.state.atomicResidueCount;
     }
 
     /**
@@ -170,15 +161,15 @@ class Structure {
     }
 
     get hashCode() {
-        if (this._props.hashCode !== -1) return this._props.hashCode;
+        if (this.state.hashCode !== -1) return this.state.hashCode;
         return this.computeHash();
     }
 
     /** Hash based on all unit.id values in the structure, reflecting the units transformation */
     get transformHash() {
-        if (this._props.transformHash !== -1) return this._props.transformHash;
-        this._props.transformHash = hashFnv32a(this.units.map(u => u.id));
-        return this._props.transformHash;
+        if (this.state.transformHash !== -1) return this.state.transformHash;
+        this.state.transformHash = hashFnv32a(this.units.map(u => u.id));
+        return this.state.transformHash;
     }
 
     private computeHash() {
@@ -191,7 +182,7 @@ class Structure {
         hash = (31 * hash + this.elementCount) | 0;
         hash = hash1(hash);
         if (hash === -1) hash = 0;
-        this._props.hashCode = hash;
+        this.state.hashCode = hash;
         return hash;
     }
 
@@ -202,12 +193,12 @@ class Structure {
 
     /** The parent or itself in case this is the root */
     get root() {
-        return this._props.parent || this;
+        return this.state.parent || this;
     }
 
     /** The root/top-most parent or `undefined` in case this is the root */
     get parent() {
-        return this._props.parent;
+        return this.state.parent;
     }
 
     /**
@@ -218,81 +209,74 @@ class Structure {
      * by the consumer.
      */
     get coordinateSystem(): SymmetryOperator {
-        return this._props.coordinateSystem;
+        return this.state.coordinateSystem;
     }
 
     get label() {
-        return this._props.label;
+        return this.state.label;
     }
 
     get boundary() {
-        if (this._props.boundary) return this._props.boundary;
-        this._props.boundary = computeStructureBoundary(this);
-        return this._props.boundary;
+        if (this.state.boundary) return this.state.boundary;
+        this.state.boundary = computeStructureBoundary(this);
+        return this.state.boundary;
     }
 
     get lookup3d() {
-        if (this._props.lookup3d) return this._props.lookup3d;
-        this._props.lookup3d = new StructureLookup3D(this);
-        return this._props.lookup3d;
+        if (this.state.lookup3d) return this.state.lookup3d;
+        this.state.lookup3d = new StructureLookup3D(this);
+        return this.state.lookup3d;
     }
 
     get interUnitBonds() {
-        if (this._props.interUnitBonds) return this._props.interUnitBonds;
-        this._props.interUnitBonds = computeInterUnitBonds(this);
-        return this._props.interUnitBonds;
+        if (this.state.interUnitBonds) return this.state.interUnitBonds;
+        this.state.interUnitBonds = computeInterUnitBonds(this);
+        return this.state.interUnitBonds;
     }
 
     get unitSymmetryGroups(): ReadonlyArray<Unit.SymmetryGroup> {
-        if (this._props.unitSymmetryGroups) return this._props.unitSymmetryGroups;
-        this._props.unitSymmetryGroups = StructureSymmetry.computeTransformGroups(this);
-        return this._props.unitSymmetryGroups;
+        if (this.state.unitSymmetryGroups) return this.state.unitSymmetryGroups;
+        this.state.unitSymmetryGroups = StructureSymmetry.computeTransformGroups(this);
+        return this.state.unitSymmetryGroups;
     }
 
     /** Maps unit.id to index of SymmetryGroup in unitSymmetryGroups array */
     get unitSymmetryGroupsIndexMap(): IntMap<number> {
-        if (this._props.unitSymmetryGroupsIndexMap) return this._props.unitSymmetryGroupsIndexMap;
-        this._props.unitSymmetryGroupsIndexMap = Unit.SymmetryGroup.getUnitSymmetryGroupsIndexMap(this.unitSymmetryGroups);
-        return this._props.unitSymmetryGroupsIndexMap;
-    }
-
-    /** Array of all units in the structure, sorted by their boundary volume */
-    get unitsSortedByVolume(): ReadonlyArray<Unit> {
-        if (this._props.unitsSortedByVolume) return this._props.unitsSortedByVolume;
-        this._props.unitsSortedByVolume = getUnitsSortedByVolume(this);
-        return this._props.unitsSortedByVolume;
+        if (this.state.unitSymmetryGroupsIndexMap) return this.state.unitSymmetryGroupsIndexMap;
+        this.state.unitSymmetryGroupsIndexMap = Unit.SymmetryGroup.getUnitSymmetryGroupsIndexMap(this.unitSymmetryGroups);
+        return this.state.unitSymmetryGroupsIndexMap;
     }
 
     get carbohydrates(): Carbohydrates {
-        if (this._props.carbohydrates) return this._props.carbohydrates;
-        this._props.carbohydrates = computeCarbohydrates(this);
-        return this._props.carbohydrates;
+        if (this.state.carbohydrates) return this.state.carbohydrates;
+        this.state.carbohydrates = computeCarbohydrates(this);
+        return this.state.carbohydrates;
     }
 
     get models(): ReadonlyArray<Model> {
-        if (this._props.models) return this._props.models;
-        this._props.models = getModels(this);
-        return this._props.models;
+        if (this.state.models) return this.state.models;
+        this.state.models = getModels(this);
+        return this.state.models;
     }
 
     get uniqueResidueNames() {
-        return this._props.uniqueResidueNames
-            || (this._props.uniqueResidueNames = getUniqueResidueNames(this));
+        return this.state.uniqueResidueNames
+            || (this.state.uniqueResidueNames = getUniqueResidueNames(this));
     }
 
     get uniqueElementSymbols() {
-        return this._props.uniqueElementSymbols
-            || (this._props.uniqueElementSymbols = getUniqueElementSymbols(this));
+        return this.state.uniqueElementSymbols
+            || (this.state.uniqueElementSymbols = getUniqueElementSymbols(this));
     }
 
     get entityIndices() {
-        return this._props.entityIndices
-            || (this._props.entityIndices = getEntityIndices(this));
+        return this.state.entityIndices
+            || (this.state.entityIndices = getEntityIndices(this));
     }
 
     get uniqueAtomicResidueIndices() {
-        return this._props.uniqueAtomicResidueIndices
-            || (this._props.uniqueAtomicResidueIndices = getUniqueAtomicResidueIndices(this));
+        return this.state.uniqueAtomicResidueIndices
+            || (this.state.uniqueAtomicResidueIndices = getUniqueAtomicResidueIndices(this));
     }
 
     /** Contains only atomic units */
@@ -327,7 +311,7 @@ class Structure {
      * to address elements in a structure.
      */
     get serialMapping() {
-        return this._props.serialMapping || (this._props.serialMapping = getSerialMapping(this));
+        return this.state.serialMapping || (this.state.serialMapping = getSerialMapping(this));
     }
 
     /**
@@ -335,25 +319,25 @@ class Structure {
      * Otherwise throw an exception.
      */
     get model(): Model {
-        if (this._props.model) return this._props.model;
-        if (this._props.representativeModel) return this._props.representativeModel;
-        if (this._props.masterModel) return this._props.masterModel;
+        if (this.state.model) return this.state.model;
+        if (this.state.representativeModel) return this.state.representativeModel;
+        if (this.state.masterModel) return this.state.masterModel;
         const models = this.models;
         if (models.length > 1) {
             throw new Error('The structure is based on multiple models and has neither a master- nor a representative-model.');
         }
-        this._props.model = models[0];
-        return this._props.model;
+        this.state.model = models[0];
+        return this.state.model;
     }
 
     /** The master-model, other models can have bonds to it  */
     get masterModel(): Model | undefined {
-        return this._props.masterModel;
+        return this.state.masterModel;
     }
 
     /** A representative model, e.g. the first model of a trajectory */
     get representativeModel(): Model | undefined {
-        return this._props.representativeModel;
+        return this.state.representativeModel;
     }
 
     hasElement(e: StructureElement.Location) {
@@ -377,51 +361,39 @@ class Structure {
         }
         return Structure.create(units, {
             label: this.label,
-            interUnitBonds: this._props.interUnitBonds,
+            interUnitBonds: this.state.interUnitBonds,
         });
     }
 
-    private initUnits(units: ArrayLike<Unit>) {
-        const unitMap = IntMap.Mutable<Unit>();
-        const unitIndexMap = IntMap.Mutable<number>();
-        let elementCount = 0;
-        let isSorted = true;
-        let lastId = units.length > 0 ? units[0].id : 0;
-        for (let i = 0, _i = units.length; i < _i; i++) {
-            const u = units[i];
-            unitMap.set(u.id, u);
-            elementCount += u.elements.length;
-            if (u.id < lastId) isSorted = false;
-            lastId = u.id;
-        }
-        if (!isSorted) sort(units, 0, units.length, cmpUnits, arraySwap);
-        for (let i = 0, _i = units.length; i < _i; i++) {
-            unitIndexMap.set(units[i].id, i);
-        }
-        this._props.elementCount = elementCount;
-        return { unitMap, unitIndexMap };
+    private _child: Structure | undefined;
+    private _target: Structure | undefined;
+
+    /**
+     * For `structure` with `parent` this returns a proxy that
+     * targets `parent` and has `structure` attached as a child.
+     */
+    asParent(): Structure {
+        return this.parent ? new Structure(this.parent.units, this.parent.unitMap, this.parent.unitIndexMap, this.parent.state, { child: this, target: this.parent }) : this;
     }
 
-    constructor(units: ArrayLike<Unit>, props: Structure.Props = {}) {
-        const { unitMap, unitIndexMap } = this.initUnits(units);
-        this.unitMap = unitMap;
-        this.unitIndexMap = unitIndexMap;
-        this.units = units as ReadonlyArray<Unit>;
+    get child(): Structure | undefined {
+        return this._child;
+    }
 
-        if (props.parent) this._props.parent = props.parent.parent || props.parent;
-        if (props.interUnitBonds) this._props.interUnitBonds = props.interUnitBonds;
+    /** Get the proxy target. Usefull for equality checks. */
+    get target(): Structure {
+        return this._target ?? this;
+    }
 
-        if (props.coordinateSystem) this._props.coordinateSystem = props.coordinateSystem;
-        else if (props.parent) this._props.coordinateSystem = props.parent.coordinateSystem;
-
-        if (props.label) this._props.label = props.label;
-        else if (props.parent) this._props.label = props.parent.label;
-
-        if (props.masterModel) this._props.masterModel = props.masterModel;
-        else if (props.parent) this._props.masterModel = props.parent.masterModel;
-
-        if (props.representativeModel) this._props.representativeModel = props.representativeModel;
-        else if (props.parent) this._props.representativeModel = props.parent.representativeModel;
+    /**
+     * @param units Array of all units in the structure, sorted by unit.id
+     * @param unitMap Maps unit.id to index of unit in units array
+     * @param unitIndexMap Array of all units in the structure, sorted by unit.id
+     */
+    constructor(readonly units: ReadonlyArray<Unit>, readonly unitMap: IntMap<Unit>, readonly unitIndexMap: IntMap<number>, private readonly state: State, asParent?: { child: Structure, target: Structure }) {
+        // always assign to ensure object shape
+        this._child = asParent?.child;
+        this._target = asParent?.target;
     }
 }
 
@@ -429,24 +401,6 @@ function cmpUnits(units: ArrayLike<Unit>, i: number, j: number) {
     return units[i].id - units[j].id;
 
 }
-function cmpUnitGroupVolume(units: ArrayLike<[index: number, volume: number]>, i: number, j: number) {
-    const d = units[i][1] - units[j][1];
-    if (d === 0) return units[i][0] - units[j][0];
-    return d;
-}
-
-function getUnitsSortedByVolume(structure: Structure) {
-    const { unitSymmetryGroups } = structure;
-    const groups = unitSymmetryGroups.map((g, i) => [i, Box3D.volume(g.units[0].lookup3d.boundary.box)] as [number, number]);
-    sort(groups, 0, groups.length, cmpUnitGroupVolume, arraySwap);
-    const ret: Unit[] = [];
-    for (const [i] of groups) {
-        for (const u of unitSymmetryGroups[i].units) {
-            ret.push(u);
-        }
-    }
-    return ret;
-}
 
 function getModels(s: Structure) {
     const { units } = s;
@@ -568,6 +522,15 @@ function getPolymerResidueCount(structure: Structure): number {
     return polymerResidueCount;
 }
 
+function getPolymerGapCount(structure: Structure): number {
+    const { units } = structure;
+    let polymerGapCount = 0;
+    for (let i = 0, _i = units.length; i < _i; i++) {
+        polymerGapCount += units[i].gapElements.length / 2;
+    }
+    return polymerGapCount;
+}
+
 function getPolymerUnitCount(structure: Structure): number {
     const { units } = structure;
     let polymerUnitCount = 0;
@@ -632,7 +595,7 @@ function getSerialMapping(structure: Structure): SerialMapping {
 }
 
 namespace Structure {
-    export const Empty = new Structure([]);
+    export const Empty = create([]);
 
     export interface Props {
         parent?: Structure
@@ -645,7 +608,7 @@ namespace Structure {
         representativeModel?: Model
     }
 
-    /** Serial index of an element in the structure accross all units */
+    /** Serial index of an element in the structure across all units */
     export type SerialIndex = { readonly '@type': 'serial-index' } & number
 
     /** Represents a single structure */
@@ -686,8 +649,57 @@ namespace Structure {
         return Loci(structure);
     }
 
-    export function create(units: ReadonlyArray<Unit>, props?: Props): Structure {
-        return new Structure(units, props);
+    export function create(units: ReadonlyArray<Unit>, props: Props = {}): Structure {
+        // init units
+        const unitMap = IntMap.Mutable<Unit>();
+        const unitIndexMap = IntMap.Mutable<number>();
+        let elementCount = 0;
+        let isSorted = true;
+        let lastId = units.length > 0 ? units[0].id : 0;
+        for (let i = 0, _i = units.length; i < _i; i++) {
+            const u = units[i];
+            unitMap.set(u.id, u);
+            elementCount += u.elements.length;
+            if (u.id < lastId) isSorted = false;
+            lastId = u.id;
+        }
+        if (!isSorted) sort(units, 0, units.length, cmpUnits, arraySwap);
+        for (let i = 0, _i = units.length; i < _i; i++) {
+            unitIndexMap.set(units[i].id, i);
+        }
+
+        // initial state
+        const state: State = {
+            hashCode: -1,
+            transformHash: -1,
+            elementCount,
+            bondCount: -1,
+            uniqueElementCount: -1,
+            atomicResidueCount: -1,
+            polymerResidueCount: -1,
+            polymerGapCount: -1,
+            polymerUnitCount: -1,
+            coordinateSystem: SymmetryOperator.Default,
+            label: ''
+        };
+
+        // handle props
+        if (props.parent) state.parent = props.parent.parent || props.parent;
+        if (props.interUnitBonds) state.interUnitBonds = props.interUnitBonds;
+
+        if (props.coordinateSystem) state.coordinateSystem = props.coordinateSystem;
+        else if (props.parent) state.coordinateSystem = props.parent.coordinateSystem;
+
+        if (props.label) state.label = props.label;
+        else if (props.parent) state.label = props.parent.label;
+
+        if (props.masterModel) state.masterModel = props.masterModel;
+        else if (props.parent) state.masterModel = props.parent.masterModel;
+
+        if (props.representativeModel) state.representativeModel = props.representativeModel;
+        else if (props.parent) state.representativeModel = props.parent.representativeModel;
+
+        return new Structure(units, unitMap, unitIndexMap, state);
     }
 
     export async function ofTrajectory(trajectory: Trajectory, ctx: RuntimeContext): Promise<Structure> {
@@ -893,7 +905,7 @@ namespace Structure {
 
         const cs = s.coordinateSystem;
         const newCS = SymmetryOperator.compose(SymmetryOperator.create(cs.name, transform, cs), cs);
-        return new Structure(units, { parent: s, coordinateSystem: newCS });
+        return create(units, { parent: s, coordinateSystem: newCS });
     }
 
     export class StructureBuilder {
@@ -1155,6 +1167,57 @@ namespace Structure {
         }
     }
 
+    export interface ForEachAtomicHierarchyElementParams {
+        // Called for 1st element of each chain
+        // Note that chains can be split, meaning each chain would be called multiple times.
+        chain?: (e: StructureElement.Location<Unit.Atomic>) => void,
+        // Called for 1st element of each residue
+        residue?: (e: StructureElement.Location<Unit.Atomic>) => void,
+        // Called for each element
+        atom?: (e: StructureElement.Location<Unit.Atomic>) => void,
+    };
+
+    export function eachAtomicHierarchyElement(structure: Structure, { chain, residue, atom }: ForEachAtomicHierarchyElementParams) {
+        const l = StructureElement.Location.create<Unit.Atomic>(structure);
+        for (const unit of structure.units) {
+            if (unit.kind !== Unit.Kind.Atomic) continue;
+
+            l.unit = unit;
+
+            const { elements } = unit;
+            const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+            const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+
+            while (chainsIt.hasNext) {
+                const chainSegment = chainsIt.move();
+
+                if (chain) {
+                    l.element = elements[chainSegment.start];
+                    chain(l);
+                }
+
+                if (!residue && !atom) continue;
+
+                residuesIt.setSegment(chainSegment);
+                while (residuesIt.hasNext) {
+                    const residueSegment = residuesIt.move();
+
+                    if (residue) {
+                        l.element = elements[residueSegment.start];
+                        residue(l);
+                    }
+
+                    if (!atom) continue;
+
+                    for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+                        l.element = elements[j];
+                        atom(l);
+                    }
+                }
+            }
+        }
+    }
+
     //
 
     export const DefaultSizeThresholds = {

src/mol-model/structure/structure/util/lookup3d.ts

@@ -94,6 +94,36 @@ export class StructureLookup3D {
         }
     }
 
+    findIntoBuilderIf(x: number, y: number, z: number, radius: number, builder: StructureUniqueSubsetBuilder, test: (l: StructureElement.Location) => boolean) {
+        const { units } = this.structure;
+        const closeUnits = this.unitLookup.find(x, y, z, radius);
+        if (closeUnits.count === 0) return;
+
+        const loc = StructureElement.Location.create(this.structure);
+
+        for (let t = 0, _t = closeUnits.count; t < _t; t++) {
+            const unit = units[closeUnits.indices[t]];
+            Vec3.set(this.pivot, x, y, z);
+            if (!unit.conformation.operator.isIdentity) {
+                Vec3.transformMat4(this.pivot, this.pivot, unit.conformation.operator.inverse);
+            }
+            const unitLookup = unit.lookup3d;
+            const groupResult = unitLookup.find(this.pivot[0], this.pivot[1], this.pivot[2], radius);
+            if (groupResult.count === 0) continue;
+
+            const elements = unit.elements;
+            loc.unit = unit;
+            builder.beginUnit(unit.id);
+            for (let j = 0, _j = groupResult.count; j < _j; j++) {
+                loc.element = elements[groupResult.indices[j]];
+                if (test(loc)) {
+                    builder.addElement(loc.element);
+                }
+            }
+            builder.commitUnit();
+        }
+    }
+
     findIntoBuilderWithRadius(x: number, y: number, z: number, pivotR: number, maxRadius: number, radius: number, eRadius: StructureElement.Property<number>, builder: StructureUniqueSubsetBuilder) {
         const { units } = this.structure;
         const closeUnits = this.unitLookup.find(x, y, z, radius);

src/mol-plugin-state/animation/built-in/state-interpolation.ts

@@ -6,12 +6,13 @@
 
 import { PluginCommands } from '../../../mol-plugin/commands';
 import { StateTransform } from '../../../mol-state';
+import { shallowEqual } from '../../../mol-util';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginStateAnimation } from '../model';
 
 export const AnimateStateInterpolation = PluginStateAnimation.create({
     name: 'built-in.animate-state-interpolation',
-    display: { name: 'Animate State Interpolation' },
+    display: { name: 'Animate State (experimental)' },
     params: () => ({
         transtionDurationInMs: PD.Numeric(2000, { min: 100, max: 30000, step: 10 })
     }),
@@ -42,15 +43,25 @@ export const AnimateStateInterpolation = PluginStateAnimation.create({
 
         for (const s of src) {
             for (const t of tar) {
+                // TODO: better than quadratic alg.
+                // TODO: support for adding/removing nodes
                 if (t.ref !== s.ref) continue;
                 if (t.version === s.version) continue;
 
                 const e = StateTransform.fromJSON(s), f = StateTransform.fromJSON(t);
 
+                const oldState = state.cells.get(s.ref);
+                if (!oldState) continue;
+
+                let newState;
                 if (!e.transformer.definition.interpolate) {
-                    update.to(s.ref).update(currentT <= 0.5 ? e.params : f.params);
+                    newState = currentT <= 0.5 ? e.params : f.params;
                 } else {
-                    update.to(s.ref).update(e.transformer.definition.interpolate(e.params, f.params, currentT, ctx.plugin));
+                    newState = e.transformer.definition.interpolate(e.params, f.params, currentT, ctx.plugin);
+                }
+
+                if (!shallowEqual(oldState, newState)) {
+                    update.to(s.ref).update(newState);
                 }
             }
         }

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

@@ -23,6 +23,7 @@ import { OperatorNameColorThemeProvider } from '../../../mol-theme/color/operato
 import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
 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';
 
 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; }
@@ -111,6 +112,8 @@ const auto = StructureRepresentationPresetProvider({
         const thresholds = plugin.config.get(PluginConfig.Structure.SizeThresholds) || Structure.DefaultSizeThresholds;
         const size = Structure.getSize(structure, thresholds);
 
+        const gapFraction = structure.polymerResidueCount / structure.polymerGapCount;
+
         switch (size) {
             case Structure.Size.Gigantic:
             case Structure.Size.Huge:
@@ -118,10 +121,14 @@ const auto = StructureRepresentationPresetProvider({
             case Structure.Size.Large:
                 return polymerCartoon.apply(ref, params, plugin);
             case Structure.Size.Medium:
-                return polymerAndLigand.apply(ref, params, plugin);
+                if (gapFraction > 3) {
+                    return polymerAndLigand.apply(ref, params, plugin);
+                } // else fall through
             case Structure.Size.Small:
-                // `showCarbohydrateSymbol: true` is nice e.g. for PDB 1aga
+                // `showCarbohydrateSymbol: true` is nice, e.g., for PDB 1aga
                 return atomicDetail.apply(ref, { ...params, showCarbohydrateSymbol: true }, plugin);
+            default:
+                assertUnreachable(size);
         }
     }
 });

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

@@ -123,14 +123,23 @@ export const GroProvider: TrajectoryFormatProvider = {
 };
 
 export const MolProvider: TrajectoryFormatProvider = {
-    label: 'MOL/SDF',
-    description: 'MOL/SDF',
+    label: 'MOL',
+    description: 'MOL',
     category: TrajectoryFormatCategory,
-    stringExtensions: ['mol', 'sdf', 'sd'],
+    stringExtensions: ['mol'],
     parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL),
     visuals: defaultVisuals
 };
 
+export const SdfProvider: TrajectoryFormatProvider = {
+    label: 'SDF',
+    description: 'SDF',
+    category: TrajectoryFormatCategory,
+    stringExtensions: ['sdf', 'sd'],
+    parse: directTrajectory(StateTransforms.Model.TrajectoryFromSDF),
+    visuals: defaultVisuals
+};
+
 export const Mol2Provider: TrajectoryFormatProvider = {
     label: 'MOL2',
     description: 'MOL2',
@@ -148,6 +157,7 @@ export const BuiltInTrajectoryFormats = [
     ['gro', GroProvider] as const,
     ['xyz', XyzProvider] as const,
     ['mol', MolProvider] as const,
+    ['sdf', SdfProvider] as const,
     ['mol2', Mol2Provider] as const,
 ] as const;
 

src/mol-plugin-state/helpers/structure-clipping.ts

@@ -21,7 +21,7 @@ export async function setStructureClipping(plugin: PluginContext, components: St
     await eachRepr(plugin, components, async (update, repr, clippingCell) => {
         if (types && types.length > 0 && !types.includes(repr.params!.values.type.name)) return;
 
-        const structure = repr.obj!.data.source.data;
+        const structure = repr.obj!.data.sourceData;
         // always use the root structure to get the loci so the clipping
         // stays applicable as long as the root structure does not change
         const loci = await lociGetter(structure.root);

src/mol-plugin-state/helpers/structure-overpaint.ts

@@ -22,7 +22,7 @@ export async function setStructureOverpaint(plugin: PluginContext, components: S
     await eachRepr(plugin, components, async (update, repr, overpaintCell) => {
         if (types && types.length > 0 && !types.includes(repr.params!.values.type.name)) return;
 
-        const structure = repr.obj!.data.source.data;
+        const structure = repr.obj!.data.sourceData;
         // always use the root structure to get the loci so the overpaint
         // stays applicable as long as the root structure does not change
         const loci = await lociGetter(structure.root);

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

@@ -425,6 +425,18 @@ const surroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of
     referencesCurrent: true
 });
 
+const surroundingLigands = StructureSelectionQuery('Surrounding Ligands (5 \u212B) of Selection', MS.struct.modifier.union([
+    MS.struct.modifier.surroundingLigands({
+        0: MS.internal.generator.current(),
+        radius: 5,
+        'include-water': true
+    })
+]), {
+    description: 'Select ligand components within 5 \u212B of the current selection.',
+    category: StructureSelectionCategory.Manipulate,
+    referencesCurrent: true
+});
+
 const complement = StructureSelectionQuery('Inverse / Complement of Selection', MS.struct.modifier.union([
     MS.struct.modifier.exceptBy({
         0: MS.struct.generator.all(),
@@ -645,6 +657,7 @@ export const StructureSelectionQueries = {
     ring,
     aromaticRing,
     surroundings,
+    surroundingLigands,
     complement,
     covalentlyBonded,
     covalentlyOrMetallicBonded,

src/mol-plugin-state/helpers/structure-transparency.ts

@@ -21,7 +21,7 @@ export async function setStructureTransparency(plugin: PluginContext, components
     await eachRepr(plugin, components, async (update, repr, transparencyCell) => {
         if (types && types.length > 0 && !types.includes(repr.params!.values.type.name)) return;
 
-        const structure = repr.obj!.data.source.data;
+        const structure = repr.obj!.data.sourceData;
         // always use the root structure to get the loci so the transparency
         // stays applicable as long as the root structure does not change
         const loci = await lociGetter(structure.root);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -12,7 +12,7 @@ import { StatefulPluginComponent } from '../component';
 import { PluginContext } from '../../mol-plugin/context';
 import { utf8ByteCount, utf8Write } from '../../mol-io/common/utf8';
 import { Asset } from '../../mol-util/assets';
-import { zip } from '../../mol-util/zip/zip';
+import { Zip } from '../../mol-util/zip/zip';
 import { readFromFile } from '../../mol-util/data-source';
 import { objectForEach } from '../../mol-util/object';
 import { PLUGIN_VERSION } from '../../mol-plugin/version';
@@ -217,7 +217,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
                 zipDataObj['assets.json'] = data;
             }
 
-            const zipFile = zip(zipDataObj);
+            const zipFile = await this.plugin.runTask(Zip(zipDataObj));
             return new Blob([zipFile], {type : 'application/zip'});
         }
     }

src/mol-plugin-state/objects.ts

@@ -41,8 +41,8 @@ export namespace PluginStateObject {
         return !!o && o.type.typeClass === 'Behavior';
     }
 
-    export interface Representation3DData<T extends Representation.Any, S extends StateObject = StateObject> { repr: T, source: S }
-    export function CreateRepresentation3D<T extends Representation.Any, S extends StateObject = StateObject>(type: { name: string }) {
+    export interface Representation3DData<T extends Representation.Any, S = any> { repr: T, sourceData: S }
+    export function CreateRepresentation3D<T extends Representation.Any, S = any>(type: { name: string }) {
         return Create<Representation3DData<T, S>>({ ...type, typeClass: 'Representation3D' });
     }
 
@@ -102,10 +102,10 @@ export namespace PluginStateObject {
         export class Structure extends Create<_Structure>({ name: 'Structure', typeClass: 'Object' }) { }
 
         export namespace Structure {
-            export class Representation3D extends CreateRepresentation3D<StructureRepresentation<any> | ShapeRepresentation<any, any, any>, Structure>({ name: 'Structure 3D' }) { }
+            export class Representation3D extends CreateRepresentation3D<StructureRepresentation<any>, _Structure>({ name: 'Structure 3D' }) { }
 
             export interface Representation3DStateData {
-                source: Representation3D,
+                repr: StructureRepresentation<any>,
                 /** used to restore state when the obj is removed */
                 initialState: Partial<StructureRepresentationState>,
                 state: Partial<StructureRepresentationState>,
@@ -120,12 +120,12 @@ export namespace PluginStateObject {
 
     export namespace Volume {
         export class Data extends Create<_Volume>({ name: 'Volume', typeClass: 'Object' }) { }
-        export class Representation3D extends CreateRepresentation3D<VolumeRepresentation<any>>({ name: 'Volume 3D' }) { }
+        export class Representation3D extends CreateRepresentation3D<VolumeRepresentation<any>, _Volume>({ name: 'Volume 3D' }) { }
     }
 
     export namespace Shape {
         export class Provider extends Create<ShapeProvider<any, any, any>>({ name: 'Shape Provider', typeClass: 'Object' }) { }
-        export class Representation3D extends CreateRepresentation3D<ShapeRepresentation<any, any, any>>({ name: 'Shape 3D' }) { }
+        export class Representation3D extends CreateRepresentation3D<ShapeRepresentation<any, any, any>, unknown>({ name: 'Shape 3D' }) { }
     }
 }
 

src/mol-plugin-state/transforms.ts

@@ -9,13 +9,15 @@ import * as Misc from './transforms/misc';
 import * as Model from './transforms/model';
 import * as Volume from './transforms/volume';
 import * as Representation from './transforms/representation';
+import * as Shape from './transforms/shape';
 
 export const StateTransforms = {
     Data,
     Misc,
     Model,
     Volume,
-    Representation
+    Representation,
+    Shape
 };
 
 export type StateTransforms = typeof StateTransforms

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

@@ -39,6 +39,7 @@ import { parseXtc } from '../../mol-io/reader/xtc/parser';
 import { coordinatesFromXtc } from '../../mol-model-formats/structure/xtc';
 import { parseXyz } from '../../mol-io/reader/xyz/parser';
 import { trajectoryFromXyz } from '../../mol-model-formats/structure/xyz';
+import { parseSdf } from '../../mol-io/reader/sdf/parser';
 
 export { CoordinatesFromDcd };
 export { CoordinatesFromXtc };
@@ -50,6 +51,7 @@ export { TrajectoryFromPDB };
 export { TrajectoryFromGRO };
 export { TrajectoryFromXYZ };
 export { TrajectoryFromMOL };
+export { TrajectoryFromSDF };
 export { TrajectoryFromMOL2 };
 export { TrajectoryFromCube };
 export { TrajectoryFromCifCore };
@@ -292,6 +294,36 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
     }
 });
 
+type TrajectoryFromSDF = typeof TrajectoryFromSDF
+const TrajectoryFromSDF = PluginStateTransform.BuiltIn({
+    name: 'trajectory-from-sdf',
+    display: { name: 'Parse SDF', description: 'Parse SDF string and create trajectory.' },
+    from: [SO.Data.String],
+    to: SO.Molecule.Trajectory
+})({
+    apply({ a }) {
+        return Task.create('Parse SDF', async ctx => {
+            const parsed = await parseSdf(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+
+            const models: Model[] = [];
+
+            for (const { molFile } of parsed.result.compounds) {
+                const traj = await trajectoryFromMol(molFile).runInContext(ctx);
+                for (let i = 0; i < traj.frameCount; i++) {
+                    models.push(await Task.resolveInContext(traj.getFrameAtIndex(i), ctx));
+                }
+            }
+
+            const traj = new ArrayTrajectory(models);
+
+            const props = trajectoryProps(traj);
+            return new SO.Molecule.Trajectory(traj, props);
+        });
+    }
+});
+
+
 type TrajectoryFromMOL2 = typeof TrajectoryFromMOL
 const TrajectoryFromMOL2 = PluginStateTransform.BuiltIn({
     name: 'trajectory-from-mol2',
@@ -382,6 +414,10 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
             return new SO.Molecule.Model(model, { label, description });
         });
     },
+    interpolate(a, b, t) {
+        const modelIndex = t >= 1 ? b.modelIndex : a.modelIndex + Math.floor((b.modelIndex - a.modelIndex + 1) * t);
+        return { modelIndex };
+    },
     dispose({ b }) {
         b?.data.customProperties.dispose();
     }

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

@@ -36,6 +36,10 @@ import { DihedralParams, DihedralRepresentation } from '../../mol-repr/shape/loc
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 import { Clipping } from '../../mol-theme/clipping';
 import { ObjectKeys } from '../../mol-util/type-helpers';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { getBoxMesh } from './shape';
+import { Shape } from '../../mol-model/shape';
+import { Box3D } from '../../mol-math/geometry';
 
 export { StructureRepresentation3D };
 export { ExplodeStructureRepresentation3D };
@@ -126,14 +130,15 @@ const StructureRepresentation3D = PluginStateTransform.BuiltIn({
         return Task.create('Structure Representation', async ctx => {
             const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
             const provider = plugin.representation.structure.registry.get(params.type.name);
-            if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
+            const data = provider.getData?.(a.data, params.type.params) || a.data;
+            if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, data);
             const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, provider.getParams);
-            await Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: a.data }, params);
-            repr.setTheme(Theme.create(plugin.representation.structure.themes, { structure: a.data }, params));
+            await Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: data }, params);
+            repr.setTheme(Theme.create(plugin.representation.structure.themes, { structure: data }, params));
 
             const props = params.type.params || {};
-            await repr.createOrUpdate(props, a.data).runInContext(ctx);
-            return new SO.Molecule.Structure.Representation3D({ repr, source: a }, { label: provider.label });
+            await repr.createOrUpdate(props, data).runInContext(ctx);
+            return new SO.Molecule.Structure.Representation3D({ repr, sourceData: a.data }, { label: provider.label });
         });
     },
     update({ a, b, oldParams, newParams, cache }, plugin: PluginContext) {
@@ -141,26 +146,28 @@ const StructureRepresentation3D = PluginStateTransform.BuiltIn({
             if (newParams.type.name !== oldParams.type.name) return StateTransformer.UpdateResult.Recreate;
 
             const provider = plugin.representation.structure.registry.get(newParams.type.name);
+            if (provider.mustRecreate?.(oldParams.type.params, newParams.type.params)) return StateTransformer.UpdateResult.Recreate;
+
+            const data = provider.getData?.(a.data, newParams.type.params) || a.data;
             const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
-            if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
+            if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, data);
 
             // TODO: if themes had a .needsUpdate method the following block could
             //       be optimized and only executed conditionally
-            // dispose isn't called on update so we need to handle it manually
-            Theme.releaseDependencies(plugin.representation.structure.themes, { structure: b.data.source.data }, oldParams);
-            await Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: a.data }, newParams);
-            b.data.repr.setTheme(Theme.create(plugin.representation.structure.themes, { structure: a.data }, newParams));
+            Theme.releaseDependencies(plugin.representation.structure.themes, { structure: b.data.sourceData }, oldParams);
+            await Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: data }, newParams);
+            b.data.repr.setTheme(Theme.create(plugin.representation.structure.themes, { structure: data }, newParams));
 
             const props = { ...b.data.repr.props, ...newParams.type.params };
-            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
-            b.data.source = a;
+            await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
+            b.data.sourceData = a.data;
             return StateTransformer.UpdateResult.Updated;
         });
     },
     dispose({ b, params }, plugin: PluginContext) {
         if (!b || !params) return;
 
-        const structure = b.data.source.data;
+        const structure = b.data.sourceData;
         const provider = plugin.representation.structure.registry.get(params.type.name);
         if (provider.ensureCustomProperties) provider.ensureCustomProperties.detach(structure);
         Theme.releaseDependencies(plugin.representation.structure.themes, { structure }, params);
@@ -191,26 +198,26 @@ const UnwindStructureAssemblyRepresentation3D = PluginStateTransform.BuiltIn({
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const unitTransforms = new StructureUnitTransforms(structure);
         unwindStructureAssembly(structure, unitTransforms, params.t);
         return new SO.Molecule.Structure.Representation3DState({
             state: { unitTransforms },
             initialState: { unitTransforms: new StructureUnitTransforms(structure) },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Unwind T = ${params.t.toFixed(2)}` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
-        if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.sourceData !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
         const unitTransforms = b.data.state.unitTransforms!;
         unwindStructureAssembly(structure, unitTransforms, newParams.t);
         b.label = `Unwind T = ${newParams.t.toFixed(2)}`;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         return StateTransformer.UpdateResult.Updated;
     }
 });
@@ -228,26 +235,26 @@ const ExplodeStructureRepresentation3D = PluginStateTransform.BuiltIn({
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const unitTransforms = new StructureUnitTransforms(structure.root);
         explodeStructure(structure, unitTransforms, params.t);
         return new SO.Molecule.Structure.Representation3DState({
             state: { unitTransforms },
             initialState: { unitTransforms: new StructureUnitTransforms(structure.root) },
             info: structure.root,
-            source: a
+            repr: a.data.repr
         }, { label: `Explode T = ${params.t.toFixed(2)}` });
     },
     update({ a, b, newParams, oldParams }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         if (b.data.info !== structure.root) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         if (oldParams.t === newParams.t) return StateTransformer.UpdateResult.Unchanged;
         const unitTransforms = b.data.state.unitTransforms!;
         explodeStructure(structure.root, unitTransforms, newParams.t);
         b.label = `Explode T = ${newParams.t.toFixed(2)}`;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         return StateTransformer.UpdateResult.Updated;
     }
 });
@@ -276,28 +283,28 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const overpaint = Overpaint.ofScript(params.layers, structure);
 
         return new SO.Molecule.Structure.Representation3DState({
             state: { overpaint },
             initialState: { overpaint: Overpaint.Empty },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Overpaint (${overpaint.layers.length} Layers)` });
     },
     update({ a, b, newParams, oldParams }) {
         const oldStructure = b.data.info as Structure;
-        const newStructure = a.data.source.data;
+        const newStructure = a.data.sourceData;
         if (newStructure !== oldStructure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         const oldOverpaint = b.data.state.overpaint!;
         const newOverpaint = Overpaint.ofScript(newParams.layers, newStructure);
         if (Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged;
 
         b.data.state.overpaint = newOverpaint;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         b.label = `Overpaint (${newOverpaint.layers.length} Layers)`;
         return StateTransformer.UpdateResult.Updated;
     }
@@ -328,28 +335,28 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const overpaint = Overpaint.ofBundle(params.layers, structure);
 
         return new SO.Molecule.Structure.Representation3DState({
             state: { overpaint },
             initialState: { overpaint: Overpaint.Empty },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Overpaint (${overpaint.layers.length} Layers)` });
     },
     update({ a, b, newParams, oldParams }) {
         const oldStructure = b.data.info as Structure;
-        const newStructure = a.data.source.data;
+        const newStructure = a.data.sourceData;
         if (newStructure !== oldStructure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         const oldOverpaint = b.data.state.overpaint!;
         const newOverpaint = Overpaint.ofBundle(newParams.layers, newStructure);
         if (Overpaint.areEqual(oldOverpaint, newOverpaint)) return StateTransformer.UpdateResult.Unchanged;
 
         b.data.state.overpaint = newOverpaint;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         b.label = `Overpaint (${newOverpaint.layers.length} Layers)`;
         return StateTransformer.UpdateResult.Updated;
     }
@@ -377,27 +384,27 @@ const TransparencyStructureRepresentation3DFromScript = PluginStateTransform.Bui
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const transparency = Transparency.ofScript(params.layers, structure);
 
         return new SO.Molecule.Structure.Representation3DState({
             state: { transparency },
             initialState: { transparency: Transparency.Empty },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Transparency (${transparency.layers.length} Layers)` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
-        if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.sourceData !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         const oldTransparency = b.data.state.transparency!;
         const newTransparency = Transparency.ofScript(newParams.layers, structure);
         if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged;
 
         b.data.state.transparency = newTransparency;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         b.label = `Transparency (${newTransparency.layers.length} Layers)`;
         return StateTransformer.UpdateResult.Updated;
     }
@@ -426,27 +433,27 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const transparency = Transparency.ofBundle(params.layers, structure);
 
         return new SO.Molecule.Structure.Representation3DState({
             state: { transparency },
             initialState: { transparency: Transparency.Empty },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Transparency (${transparency.layers.length} Layers)` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
-        if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.sourceData !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         const oldTransparency = b.data.state.transparency!;
         const newTransparency = Transparency.ofBundle(newParams.layers, structure);
         if (Transparency.areEqual(oldTransparency, newTransparency)) return StateTransformer.UpdateResult.Unchanged;
 
         b.data.state.transparency = newTransparency;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         b.label = `Transparency (${newTransparency.layers.length} Layers)`;
         return StateTransformer.UpdateResult.Updated;
     }
@@ -474,27 +481,27 @@ const ClippingStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const clipping = Clipping.ofScript(params.layers, structure);
 
         return new SO.Molecule.Structure.Representation3DState({
             state: { clipping },
             initialState: { clipping: Clipping.Empty },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Clipping (${clipping.layers.length} Layers)` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
-        if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.sourceData !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         const oldClipping = b.data.state.clipping!;
         const newClipping = Clipping.ofScript(newParams.layers, structure);
         if (Clipping.areEqual(oldClipping, newClipping)) return StateTransformer.UpdateResult.Unchanged;
 
         b.data.state.clipping = newClipping;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         b.label = `Clipping (${newClipping.layers.length} Layers)`;
         return StateTransformer.UpdateResult.Updated;
     }
@@ -523,27 +530,27 @@ const ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn
         return true;
     },
     apply({ a, params }) {
-        const structure = a.data.source.data;
+        const structure = a.data.sourceData;
         const clipping = Clipping.ofBundle(params.layers, structure);
 
         return new SO.Molecule.Structure.Representation3DState({
             state: { clipping },
             initialState: { clipping: Clipping.Empty },
             info: structure,
-            source: a
+            repr: a.data.repr
         }, { label: `Clipping (${clipping.layers.length} Layers)` });
     },
     update({ a, b, newParams, oldParams }) {
         const structure = b.data.info as Structure;
-        if (a.data.source.data !== structure) return StateTransformer.UpdateResult.Recreate;
-        if (a.data.repr !== b.data.source.data.repr) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.sourceData !== structure) return StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr) return StateTransformer.UpdateResult.Recreate;
 
         const oldClipping = b.data.state.clipping!;
         const newClipping = Clipping.ofBundle(newParams.layers, structure);
         if (Clipping.areEqual(oldClipping, newClipping)) return StateTransformer.UpdateResult.Unchanged;
 
         b.data.state.clipping = newClipping;
-        b.data.source = a;
+        b.data.repr = a.data.repr;
         b.label = `Clipping (${newClipping.layers.length} Layers)`;
         return StateTransformer.UpdateResult.Updated;
     }
@@ -646,7 +653,7 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
 
             const props = params.type.params || {};
             await repr.createOrUpdate(props, a.data).runInContext(ctx);
-            return new SO.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
+            return new SO.Volume.Representation3D({ repr, sourceData: a.data }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
@@ -659,6 +666,7 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams.type.params };
             b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            b.data.sourceData = a.data;
             b.description = VolumeRepresentation3DHelpers.getDescription(props);
             return StateTransformer.UpdateResult.Updated;
         });
@@ -686,13 +694,14 @@ const ShapeRepresentation3D = PluginStateTransform.BuiltIn({
             const props = { ...PD.getDefaultValues(a.data.params), ...params };
             const repr = ShapeRepresentation(a.data.getShape, a.data.geometryUtils);
             await repr.createOrUpdate(props, a.data.data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: a.data.label });
+            return new SO.Shape.Representation3D({ repr, sourceData: a.data }, { label: a.data.label });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
         return Task.create('Shape Representation', async ctx => {
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data.data).runInContext(ctx);
+            b.data.sourceData = a.data;
             return StateTransformer.UpdateResult.Updated;
         });
     }
@@ -720,7 +729,7 @@ const ModelUnitcell3D = PluginStateTransform.BuiltIn({
             const data = getUnitcellData(a.data, symmetry, params);
             const repr = UnitcellRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => UnitcellParams);
             await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Unit Cell`, description: symmetry.spacegroup.name });
+            return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Unit Cell`, description: symmetry.spacegroup.name });
         });
     },
     update({ a, b, newParams }) {
@@ -730,7 +739,42 @@ const ModelUnitcell3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams };
             const data = getUnitcellData(a.data, symmetry, props);
             await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.source = a;
+            b.data.sourceData = data;
+            return StateTransformer.UpdateResult.Updated;
+        });
+    }
+});
+
+export { StructureBoundingBox3D };
+type StructureBoundingBox3D = typeof StructureBoundingBox3D
+const StructureBoundingBox3D = PluginStateTransform.BuiltIn({
+    name: 'structure-bounding-box-3d',
+    display: 'Bounding Box',
+    from: SO.Molecule.Structure,
+    to: SO.Shape.Representation3D,
+    params: {
+        radius: PD.Numeric(0.05, { min: 0.01, max: 4, step: 0.01 }, { isEssential: true }),
+        color: PD.Color(ColorNames.red, { isEssential: true }),
+        ...Mesh.Params,
+    }
+})({
+    canAutoUpdate() {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Bounding Box', async ctx => {
+            const repr = ShapeRepresentation((_, data: { box: Box3D, radius: number, color: Color }, __, shape) => {
+                const mesh = getBoxMesh(data.box, data.radius, shape?.geometry);
+                return Shape.create('Bouding Box', data, mesh, () => data.color, () => 1, () => 'Bounding Box');
+            }, Mesh.Utils);
+            await repr.createOrUpdate(params, { box: a.data.boundary.box, radius: params.radius, color: params.color }).runInContext(ctx);
+            return new SO.Shape.Representation3D({ repr, sourceData: a.data }, { label: `Bounding Box` });
+        });
+    },
+    update({ a, b, oldParams, newParams }, plugin: PluginContext) {
+        return Task.create('Bounding Box', async ctx => {
+            await b.data.repr.createOrUpdate(newParams, { box: a.data.boundary.box, radius: newParams.radius, color: newParams.color }).runInContext(ctx);
+            b.data.sourceData = a.data;
             return StateTransformer.UpdateResult.Updated;
         });
     }
@@ -755,7 +799,7 @@ const StructureSelectionsDistance3D = PluginStateTransform.BuiltIn({
             const data = getDistanceDataFromStructureSelections(a.data);
             const repr = DistanceRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => DistanceParams);
             await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Distance` });
+            return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Distance` });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
@@ -763,7 +807,7 @@ const StructureSelectionsDistance3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams };
             const data = getDistanceDataFromStructureSelections(a.data);
             await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.source = a;
+            b.data.sourceData = data;
             return StateTransformer.UpdateResult.Updated;
         });
     },
@@ -788,7 +832,7 @@ const StructureSelectionsAngle3D = PluginStateTransform.BuiltIn({
             const data = getAngleDataFromStructureSelections(a.data);
             const repr = AngleRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => AngleParams);
             await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Angle` });
+            return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Angle` });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
@@ -796,7 +840,7 @@ const StructureSelectionsAngle3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams };
             const data = getAngleDataFromStructureSelections(a.data);
             await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.source = a;
+            b.data.sourceData = data;
             return StateTransformer.UpdateResult.Updated;
         });
     },
@@ -821,7 +865,7 @@ const StructureSelectionsDihedral3D = PluginStateTransform.BuiltIn({
             const data = getDihedralDataFromStructureSelections(a.data);
             const repr = DihedralRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => DihedralParams);
             await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Dihedral` });
+            return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Dihedral` });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
@@ -829,7 +873,7 @@ const StructureSelectionsDihedral3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams };
             const data = getDihedralDataFromStructureSelections(a.data);
             await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.source = a;
+            b.data.sourceData = data;
             return StateTransformer.UpdateResult.Updated;
         });
     },
@@ -854,7 +898,7 @@ const StructureSelectionsLabel3D = PluginStateTransform.BuiltIn({
             const data = getLabelDataFromStructureSelections(a.data);
             const repr = LabelRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => LabelParams);
             await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Label` });
+            return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Label` });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
@@ -862,7 +906,7 @@ const StructureSelectionsLabel3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams };
             const data = getLabelDataFromStructureSelections(a.data);
             await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.source = a;
+            b.data.sourceData = data;
             return StateTransformer.UpdateResult.Updated;
         });
     },
@@ -887,7 +931,7 @@ const StructureSelectionsOrientation3D = PluginStateTransform.BuiltIn({
             const data = getOrientationDataFromStructureSelections(a.data);
             const repr = OrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => OrientationParams);
             await repr.createOrUpdate(params, data).runInContext(ctx);
-            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Orientation` });
+            return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Orientation` });
         });
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
@@ -895,7 +939,7 @@ const StructureSelectionsOrientation3D = PluginStateTransform.BuiltIn({
             const props = { ...b.data.repr.props, ...newParams };
             const data = getOrientationDataFromStructureSelections(a.data);
             await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
-            b.data.source = a;
+            b.data.sourceData = data;
             return StateTransformer.UpdateResult.Updated;
         });
     },

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

@@ -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 { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+import { BoxCage } from '../../mol-geo/primitive/box';
+import { Box3D, Sphere3D } from '../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { Shape } from '../../mol-model/shape';
+import { Task } from '../../mol-task';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PluginStateObject as SO, PluginStateTransform } from '../objects';
+
+export { BoxShape3D };
+type BoxShape3D = typeof BoxShape3D
+const BoxShape3D = PluginStateTransform.BuiltIn({
+    name: 'box-shape-3d',
+    display: 'Box Shape',
+    from: SO.Root,
+    to: SO.Shape.Provider,
+    params: {
+        bottomLeft: PD.Vec3(Vec3()),
+        topRight: PD.Vec3(Vec3.create(1, 1, 1)),
+        radius: PD.Numeric(0.15, { min: 0.01, max: 4, step: 0.01 }),
+        color: PD.Color(ColorNames.red)
+    }
+})({
+    canAutoUpdate() {
+        return true;
+    },
+    apply({ params }) {
+        return Task.create('Shape Representation', async ctx => {
+            return new SO.Shape.Provider({
+                label: 'Box',
+                data: params,
+                params: Mesh.Params,
+                getShape: (_, data: typeof params) => {
+                    const mesh = getBoxMesh(Box3D.create(params.bottomLeft, params.topRight), params.radius);
+                    return Shape.create('Box', data, mesh, () => data.color, () => 1, () => 'Box');
+                },
+                geometryUtils: Mesh.Utils
+            }, { label: 'Box' });
+        });
+    }
+});
+
+export function getBoxMesh(box: Box3D, radius: number, oldMesh?: Mesh) {
+    const diag = Vec3.sub(Vec3(), box.max, box.min);
+    const translateUnit = Mat4.fromTranslation(Mat4(), Vec3.create(0.5, 0.5, 0.5));
+    const scale = Mat4.fromScaling(Mat4(), diag);
+    const translate = Mat4.fromTranslation(Mat4(), box.min);
+    const transform = Mat4.mul3(Mat4(), translate, scale, translateUnit);
+
+    // TODO: optimize?
+    const state = MeshBuilder.createState(256, 128, oldMesh);
+    state.currentGroup = 1;
+    MeshBuilder.addCage(state, transform, BoxCage(), radius, 2, 20);
+    const mesh = MeshBuilder.getMesh(state);
+
+    const center = Vec3.scaleAndAdd(Vec3(), box.min, diag, 0.5);
+    const sphereRadius = Vec3.distance(box.min, center);
+    mesh.setBoundingSphere(Sphere3D.create(center, sphereRadius));
+
+    return mesh;
+}

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

@@ -151,7 +151,7 @@ const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
             const densityServerCif = CIF.schema.densityServer(block);
             const volume = await volumeFromDensityServerData(densityServerCif, { entryId: params.entryId }).runInContext(ctx);
             const [x, y, z] = volume.grid.cells.space.dimensions;
-            const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `Volume ${x}\u00D7${y}\u00D7${z}` };
+            const props = { label: params.entryId ?? densityServerCif.volume_data_3d_info.name.value(0), description: `Volume ${x}\u00D7${y}\u00D7${z}` };
             return new SO.Volume.Data(volume, props);
         });
     },

src/mol-plugin-ui/controls/icons.tsx

@@ -41,6 +41,9 @@ export function MoleculeSvg() { return _Molecule; }
 const _CubeOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z" /></svg>;
 export function CubeOutlineSvg() { return _CubeOutline; }
 
+const _CubeSend = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M16,4L9,8.04V15.96L16,20L23,15.96V8.04M16,6.31L19.8,8.5L16,10.69L12.21,8.5M0,7V9H7V7M11,10.11L15,12.42V17.11L11,14.81M21,10.11V14.81L17,17.11V12.42M2,11V13H7V11M4,15V17H7V15" /></svg>;
+export function CubeSendSvg() { return _CubeSend; }
+
 const _CursorDefaultOutline = <svg width='24px' height='24px' viewBox='0 0 24 24'><path d='M10.07,14.27C10.57,14.03 11.16,14.25 11.4,14.75L13.7,19.74L15.5,18.89L13.19,13.91C12.95,13.41 13.17,12.81 13.67,12.58L13.95,12.5L16.25,12.05L8,5.12V15.9L9.82,14.43L10.07,14.27M13.64,21.97C13.14,22.21 12.54,22 12.31,21.5L10.13,16.76L7.62,18.78C7.45,18.92 7.24,19 7,19A1,1 0 0,1 6,18V3A1,1 0 0,1 7,2C7.24,2 7.47,2.09 7.64,2.23L7.65,2.22L19.14,11.86C19.57,12.22 19.62,12.85 19.27,13.27C19.12,13.45 18.91,13.57 18.7,13.61L15.54,14.23L17.74,18.96C18,19.46 17.76,20.05 17.26,20.28L13.64,21.97Z' /></svg>;
 export function CursorDefaultOutlineSvg() { return _CursorDefaultOutline; }
 

src/mol-plugin-ui/controls/parameters.tsx

@@ -240,8 +240,8 @@ function renderSimple(options: { props: ParamProps<any>, state: { showHelp: bool
     const help = props.param.help
         ? props.param.help(props.value)
         : { description: props.param.description, legend: props.param.legend };
-    const desc = props.param.description;
     const hasHelp = help.description || help.legend;
+    const desc = label + (hasHelp ? '. Click for help.' : '');
     return <>
         <ControlRow
             className={className}

src/mol-plugin-ui/custom/volume.tsx

@@ -6,7 +6,6 @@
 
 import { PluginUIComponent } from '../base';
 import { StateTransformParameters } from '../state/common';
-import * as React from 'react';
 import { VolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/behavior';
 import { ExpandableControlRow, IconButton } from '../controls/common';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';

src/mol-plugin-ui/sequence/polymer.ts

@@ -122,12 +122,11 @@ function applyMarkerAtomic(e: StructureElement.Loci.Element, action: MarkerActio
     const { index: residueIndex } = model.atomicHierarchy.residueAtomSegments;
     const { label_seq_id } = model.atomicHierarchy.residues;
 
-    let changed = false;
     OrderedSet.forEachSegment(e.indices, i => residueIndex[elements[i]], rI => {
         const seqId = label_seq_id.value(rI);
-        changed = applyMarkerActionAtPosition(markerArray, index(seqId), action) || changed;
+        applyMarkerActionAtPosition(markerArray, index(seqId), action);
     });
-    return changed;
+    return true;
 }
 
 function applyMarkerCoarse(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, index: (seqId: number) => number) {
@@ -135,12 +134,11 @@ function applyMarkerCoarse(e: StructureElement.Loci.Element, action: MarkerActio
     const begin = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_begin : model.coarseHierarchy.gaussians.seq_id_begin;
     const end = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_end : model.coarseHierarchy.gaussians.seq_id_end;
 
-    let changed = false;
     OrderedSet.forEach(e.indices, i => {
         const eI = elements[i];
         for (let s = index(begin.value(eI)), e = index(end.value(eI)); s <= e; s++) {
-            changed = applyMarkerActionAtPosition(markerArray, s, action) || changed;
+            applyMarkerActionAtPosition(markerArray, s, action);
         }
     });
-    return changed;
+    return true;
 }

src/mol-plugin-ui/spec.ts

@@ -5,13 +5,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { StateActions } from '../mol-plugin-state/actions';
-import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
-import { StateTransforms } from '../mol-plugin-state/transforms';
+
 import { StateTransformParameters } from '../mol-plugin-ui/state/common';
+import { CreateVolumeStreamingBehavior } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { DefaultPluginSpec, PluginSpec } from '../mol-plugin/spec';
 import { StateAction, StateTransformer } from '../mol-state';
-import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+import { VolumeStreamingCustomControls } from './custom/volume';
 
 export { PluginUISpec };
 
@@ -40,50 +39,7 @@ namespace PluginUISpec {
 
 export const DefaultPluginUISpec = (): PluginUISpec => ({
     ...DefaultPluginSpec(),
-    actions: [
-        PluginSpec.Action(StateActions.Structure.DownloadStructure),
-        PluginSpec.Action(StateActions.Structure.AddTrajectory),
-        PluginSpec.Action(StateActions.Volume.DownloadDensity),
-        PluginSpec.Action(StateActions.DataFormat.DownloadFile),
-        PluginSpec.Action(StateActions.DataFormat.OpenFiles),
-        PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
-        PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
-
-        // Volume streaming
-        PluginSpec.Action(InitVolumeStreaming),
-        PluginSpec.Action(BoxifyVolumeStreaming),
-        PluginSpec.Action(CreateVolumeStreamingBehavior),
-
-        PluginSpec.Action(StateTransforms.Data.Download),
-        PluginSpec.Action(StateTransforms.Data.ParseCif),
-        PluginSpec.Action(StateTransforms.Data.ParseCcp4),
-        PluginSpec.Action(StateTransforms.Data.ParseDsn6),
-
-        PluginSpec.Action(StateTransforms.Model.TrajectoryFromMmCif),
-        PluginSpec.Action(StateTransforms.Model.TrajectoryFromCifCore),
-        PluginSpec.Action(StateTransforms.Model.TrajectoryFromPDB),
-        PluginSpec.Action(StateTransforms.Model.TransformStructureConformation),
-        PluginSpec.Action(StateTransforms.Model.StructureFromModel),
-        PluginSpec.Action(StateTransforms.Model.StructureFromTrajectory),
-        PluginSpec.Action(StateTransforms.Model.ModelFromTrajectory),
-        PluginSpec.Action(StateTransforms.Model.StructureSelectionFromScript),
-        PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDistance3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsAngle3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDihedral3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsLabel3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsOrientation3D),
-        PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
-        PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
-        PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
-        PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
-        PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
-
-        PluginSpec.Action(AssignColorVolume),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromDsn6),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromCube),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromDx),
-        PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
-    ]
+    customParamEditors: [
+        [CreateVolumeStreamingBehavior, VolumeStreamingCustomControls]
+    ],
 });

src/mol-plugin-ui/state/actions.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as React from 'react';
 import { State } from '../../mol-state';
 import { PluginUIComponent } from '../base';
 import { Icon, CodeSvg } from '../controls/icons';

src/mol-plugin-ui/state/animation.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as React from 'react';
 import { PluginUIComponent } from '../base';
 import { ParameterControls, ParamOnChange } from '../controls/parameters';
 import { Button } from '../controls/common';

src/mol-plugin-ui/state/update-transform.tsx

@@ -8,7 +8,6 @@ import { State, StateTransform, StateTransformer } from '../../mol-state';
 import { memoizeLatest } from '../../mol-util/memoize';
 import { StateTransformParameters, TransformControlBase } from './common';
 import { Observable } from 'rxjs';
-import * as React from 'react';
 import { PluginUIComponent } from '../base';
 
 export { UpdateTransformControl, TransformUpdaterControl };

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

@@ -4,7 +4,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as React from 'react';
 import { OrderedSet, SortedArray } from '../../mol-data/int';
 import { Structure, StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
 import { UnitIndex } from '../../mol-model/structure/structure/element/element';

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

@@ -10,14 +10,17 @@ import { Loci } from '../../mol-model/loci';
 import { StructureElement } from '../../mol-model/structure';
 import { StructureMeasurementCell, StructureMeasurementOptions, StructureMeasurementParams } from '../../mol-plugin-state/manager/structure/measurement';
 import { StructureSelectionHistoryEntry } from '../../mol-plugin-state/manager/structure/selection';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { PluginCommands } from '../../mol-plugin/commands';
+import { AngleData } from '../../mol-repr/shape/loci/angle';
+import { DihedralData } from '../../mol-repr/shape/loci/dihedral';
+import { DistanceData } from '../../mol-repr/shape/loci/distance';
+import { LabelData } from '../../mol-repr/shape/loci/label';
 import { angleLabel, dihedralLabel, distanceLabel, lociLabel } from '../../mol-theme/label';
 import { FiniteArray } from '../../mol-util/type-helpers';
 import { CollapsableControls, PurePluginUIComponent } from '../base';
 import { ActionMenu } from '../controls/action-menu';
 import { Button, ExpandGroup, IconButton, ToggleButton } from '../controls/common';
-import { Icon, PencilRulerSvg, SetSvg, ArrowUpwardSvg, ArrowDownwardSvg, DeleteOutlinedSvg, HelpOutlineSvg, AddSvg, TuneSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg, MoreHorizSvg } from '../controls/icons';
+import { AddSvg, ArrowDownwardSvg, ArrowUpwardSvg, DeleteOutlinedSvg, HelpOutlineSvg, Icon, MoreHorizSvg, PencilRulerSvg, SetSvg, TuneSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg } from '../controls/icons';
 import { ParameterControls } from '../controls/parameters';
 import { UpdateTransformControl } from '../state/update-transform';
 import { ToggleSelectionModeButton } from './selection';
@@ -216,7 +219,7 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
     }
 
     get selections() {
-        return this.props.cell.obj?.data.source as PluginStateObject.Molecule.Structure.Selections | undefined;
+        return this.props.cell.obj?.data.sourceData as Partial<DistanceData & AngleData & DihedralData & LabelData> | undefined;
     }
 
     delete = () => {
@@ -234,8 +237,8 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
         if (!selections) return;
 
         this.plugin.managers.interactivity.lociHighlights.clearHighlights();
-        for (const d of selections.data) {
-            this.plugin.managers.interactivity.lociHighlights.highlight({ loci: d.loci }, false);
+        for (const loci of this.lociArray) {
+            this.plugin.managers.interactivity.lociHighlights.highlight({ loci }, false);
         }
         this.plugin.managers.interactivity.lociHighlights.highlight({ loci: this.props.cell.obj?.data.repr.getLoci()! }, false);
     }
@@ -250,21 +253,31 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
         const selections = this.selections;
         if (!selections) return;
 
-        const sphere = Loci.getBundleBoundingSphere(toLociBundle(selections.data));
+        const sphere = Loci.getBundleBoundingSphere({ loci: this.lociArray });
         if (sphere) {
             this.plugin.managers.camera.focusSphere(sphere);
         }
     }
 
+    private get lociArray(): FiniteArray<Loci> {
+        const selections = this.selections;
+        if (!selections) return [];
+        if (selections.infos) return [selections.infos[0].loci];
+        if (selections.pairs) return selections.pairs[0].loci;
+        if (selections.triples) return selections.triples[0].loci;
+        if (selections.quads) return selections.quads[0].loci;
+        return [];
+    }
+
     get label() {
         const selections = this.selections;
-        switch (selections?.data.length) {
-            case 1: return lociLabel(selections.data[0].loci, { condensed: true });
-            case 2: return distanceLabel(toLociBundle(selections.data), { condensed: true, unitLabel: this.plugin.managers.structure.measurement.state.options.distanceUnitLabel });
-            case 3: return angleLabel(toLociBundle(selections.data), { condensed: true });
-            case 4: return dihedralLabel(toLociBundle(selections.data), { condensed: true });
-            default: return '';
-        }
+
+        if (!selections) return '<empty>';
+        if (selections.infos) return lociLabel(selections.infos[0].loci, { condensed: true });
+        if (selections.pairs) return distanceLabel(selections.pairs[0], { condensed: true, unitLabel: this.plugin.managers.structure.measurement.state.options.distanceUnitLabel });
+        if (selections.triples) return angleLabel(selections.triples[0], { condensed: true });
+        if (selections.quads) return dihedralLabel(selections.quads[0], { condensed: true });
+        return '<empty>';
     }
 
     get actions(): ActionMenu.Items {
@@ -302,8 +315,4 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
             </>}
         </>;
     }
-}
-
-function toLociBundle(data: FiniteArray<{ loci: Loci }, any>): { loci: FiniteArray<Loci, any> } {
-    return { loci: (data.map(d => d.loci) as unknown as FiniteArray<Loci, any>) };
 }

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

@@ -5,7 +5,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as React from 'react';
 import { Model } from '../../mol-model/structure';
 import { ModelRef, StructureHierarchyRef, TrajectoryRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
@@ -195,12 +194,27 @@ export class StructureSourceControls extends CollapsableControls<{}, StructureSo
     get presetActions() {
         const actions: ActionMenu.Item[] = [];
         const { trajectories } = this.plugin.managers.structure.hierarchy.selection;
-        if (trajectories.length !== 1) return actions;
+        if (trajectories.length === 0) return actions;
+
+        let providers = this.plugin.builders.structure.hierarchy.getPresets(trajectories[0].cell.obj);
+
+        if (trajectories.length > 1) {
+            const providerSet = new Set(providers);
+            for (let i = 1; i < trajectories.length; i++) {
+                const providers = this.plugin.builders.structure.hierarchy.getPresets(trajectories[i].cell.obj);
+                const current = new Set(providers);
+
+                for (const p of providers) {
+                    if (!current.has(p)) providerSet.delete(p);
+                }
+            }
+            providers = providers.filter(p => providerSet.has(p));
+        }
 
-        const providers = this.plugin.builders.structure.hierarchy.getPresets(trajectories[0].cell.obj);
         for (const p of providers) {
             actions.push(ActionMenu.Item(p.display.name, p, { description: p.display.description }));
         }
+
         return actions;
     }
 

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

@@ -4,7 +4,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as React from 'react';
 import { CollapsableControls, PurePluginUIComponent } from '../base';
 import { Icon, ArrowUpwardSvg, ArrowDownwardSvg, DeleteOutlinedSvg, HelpOutlineSvg, TuneSvg, SuperposeAtomsSvg, SuperposeChainsSvg, SuperpositionSvg } from '../controls/icons';
 import { Button, ToggleButton, IconButton } from '../controls/common';

src/mol-plugin-ui/task.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as React from 'react';
 import { PluginUIComponent } from './base';
 import { OrderedMap } from 'immutable';
 import { TaskManager } from '../mol-plugin/util/task-manager';

src/mol-plugin-ui/toast.tsx

@@ -6,7 +6,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as React from 'react';
 import { PluginUIComponent } from './base';
 import { PluginToastManager } from '../mol-plugin/util/toast';
 import { IconButton } from './controls/common';

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

@@ -6,7 +6,6 @@
  */
 
 import { produce } from 'immer';
-import * as React from 'react';
 import { Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { StateTransform } from '../../mol-state';

src/mol-plugin/behavior/dynamic/camera.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,6 +11,8 @@ import { PluginBehavior } from '../behavior';
 import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
 import { Binding } from '../../../mol-util/binding';
 import { PluginCommands } from '../../commands';
+import { CameraHelperAxis, isCameraAxesLoci } from '../../../mol-canvas3d/helper/camera-helper';
+import { Vec3 } from '../../../mol-math/linear-algebra';
 
 const B = ButtonsType;
 const M = ModifiersKeys;
@@ -62,4 +64,67 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
     },
     params: () => FocusLociParams,
     display: { name: 'Camera Focus Loci on Canvas' }
+});
+
+export const CameraAxisHelper = PluginBehavior.create<{}>({
+    name: 'camera-axis-helper',
+    category: 'interaction',
+    ctor: class extends PluginBehavior.Handler<{}> {
+        register(): void {
+
+            let lastPlane = CameraHelperAxis.None;
+            let state = 0;
+
+            this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current }) => {
+                if (!this.ctx.canvas3d || !isCameraAxesLoci(current.loci)) return;
+
+                const axis = current.loci.elements[0].groupId;
+                if (axis === CameraHelperAxis.None) {
+                    lastPlane = CameraHelperAxis.None;
+                    state = 0;
+                    return;
+                }
+
+                const { camera } = this.ctx.canvas3d;
+                let dir: Vec3, up: Vec3;
+
+                if (axis >= CameraHelperAxis.X && axis <= CameraHelperAxis.Z) {
+                    lastPlane = CameraHelperAxis.None;
+                    state = 0;
+
+                    const d = Vec3.sub(Vec3(), camera.target, camera.position);
+                    const c = Vec3.cross(Vec3(), d, camera.up);
+
+                    up = Vec3();
+                    up[axis - 1] = 1;
+                    dir = Vec3.cross(Vec3(), up, c);
+                    if (Vec3.magnitude(dir) === 0) dir = d;
+                } else {
+                    if (lastPlane === axis) {
+                        state = (state + 1) % 2;
+                    } else {
+                        lastPlane = axis;
+                        state = 0;
+                    }
+
+                    if (axis === CameraHelperAxis.XY) {
+                        up = state ? Vec3.unitX : Vec3.unitY;
+                        dir = Vec3.negUnitZ;
+                    } else if (axis === CameraHelperAxis.XZ) {
+                        up = state ? Vec3.unitX : Vec3.unitZ;
+                        dir = Vec3.negUnitY;
+                    } else {
+                        up = state ? Vec3.unitY : Vec3.unitZ;
+                        dir = Vec3.negUnitX;
+                    }
+                }
+
+                this.ctx.canvas3d.requestCameraReset({
+                    snapshot: (scene, camera) => camera.getInvariantFocus(scene.boundingSphereVisible.center, scene.boundingSphereVisible.radius, up, dir)
+                });
+            });
+        }
+    },
+    params: () => ({}),
+    display: { name: 'Camera Axis Helper' }
 });

src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts

@@ -267,7 +267,7 @@ const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
         const transform = structure?.models.length === 0 ? void 0 : GlobalModelTransformInfo.get(structure?.models[0]!);
         await repr.createOrUpdate(props, channel.data).runInContext(ctx);
         if (transform) repr.setState({ transform });
-        return new SO.Volume.Representation3D({ repr, source: a }, { label: `${Math.round(channel.isoValue.relativeValue * 100) / 100} σ [${srcParams.channel}]` });
+        return new SO.Volume.Representation3D({ repr, sourceData: channel.data }, { label: `${Math.round(channel.isoValue.relativeValue * 100) / 100} σ [${srcParams.channel}]` });
     }),
     update: ({ a, b, newParams, spine }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
         // TODO : check if params/underlying data/etc have changed; maybe will need to export "data" or some other "tag" in the Representation for this to work
@@ -280,6 +280,7 @@ const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
         const props = { ...b.data.repr.props, ...params.type.params };
         b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
         await b.data.repr.createOrUpdate(props, channel.data).runInContext(ctx);
+        b.data.sourceData = channel.data;
 
         // TODO: set the transform here as well in case the structure moves?
         //       doing this here now breaks the code for some reason...

src/mol-plugin/behavior/static/representation.ts

@@ -54,20 +54,20 @@ export function SyncStructureRepresentation3DState(ctx: PluginContext) {
     events.object.created.subscribe(e => {
         if (!SO.Molecule.Structure.Representation3DState.is(e.obj)) return;
         const data = e.obj.data as SO.Molecule.Structure.Representation3DStateData;
-        data.source.data.repr.setState(data.state);
-        ctx.canvas3d?.update(data.source.data.repr);
+        data.repr.setState(data.state);
+        ctx.canvas3d?.update(data.repr);
     });
     events.object.updated.subscribe(e => {
         if (!SO.Molecule.Structure.Representation3DState.is(e.obj)) return;
         const data = e.obj.data as SO.Molecule.Structure.Representation3DStateData;
-        data.source.data.repr.setState(data.state);
-        ctx.canvas3d?.update(data.source.data.repr);
+        data.repr.setState(data.state);
+        ctx.canvas3d?.update(data.repr);
     });
     events.object.removed.subscribe(e => {
         if (!SO.Molecule.Structure.Representation3DState.is(e.obj)) return;
         const data = e.obj.data as SO.Molecule.Structure.Representation3DStateData;
-        data.source.data.repr.setState(data.initialState);
-        ctx.canvas3d?.update(data.source.data.repr);
+        data.repr.setState(data.initialState);
+        ctx.canvas3d?.update(data.repr);
     });
 }
 

src/mol-plugin/spec.ts

@@ -17,6 +17,11 @@ import { PluginBehaviors } from './behavior';
 import { StructureFocusRepresentation } from './behavior/dynamic/selection/structure-focus-representation';
 import { PluginConfigItem } from './config';
 import { PluginLayoutStateProps } from './layout';
+import { StateActions } from '../mol-plugin-state/actions';
+import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
+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';
 
 export { PluginSpec };
 
@@ -55,12 +60,60 @@ namespace PluginSpec {
 }
 
 export const DefaultPluginSpec = (): PluginSpec => ({
+    actions: [
+        PluginSpec.Action(StateActions.Structure.DownloadStructure),
+        PluginSpec.Action(StateActions.Structure.AddTrajectory),
+        PluginSpec.Action(StateActions.Volume.DownloadDensity),
+        PluginSpec.Action(StateActions.DataFormat.DownloadFile),
+        PluginSpec.Action(StateActions.DataFormat.OpenFiles),
+        PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
+        PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
+
+        // Volume streaming
+        PluginSpec.Action(InitVolumeStreaming),
+        PluginSpec.Action(BoxifyVolumeStreaming),
+        PluginSpec.Action(CreateVolumeStreamingBehavior),
+
+        PluginSpec.Action(StateTransforms.Data.Download),
+        PluginSpec.Action(StateTransforms.Data.ParseCif),
+        PluginSpec.Action(StateTransforms.Data.ParseCcp4),
+        PluginSpec.Action(StateTransforms.Data.ParseDsn6),
+
+        PluginSpec.Action(StateTransforms.Model.TrajectoryFromMmCif),
+        PluginSpec.Action(StateTransforms.Model.TrajectoryFromCifCore),
+        PluginSpec.Action(StateTransforms.Model.TrajectoryFromPDB),
+        PluginSpec.Action(StateTransforms.Model.TransformStructureConformation),
+        PluginSpec.Action(StateTransforms.Model.StructureFromModel),
+        PluginSpec.Action(StateTransforms.Model.StructureFromTrajectory),
+        PluginSpec.Action(StateTransforms.Model.ModelFromTrajectory),
+        PluginSpec.Action(StateTransforms.Model.StructureSelectionFromScript),
+        PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDistance3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsAngle3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDihedral3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsLabel3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsOrientation3D),
+        PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureBoundingBox3D),
+        PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
+        PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
+        PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
+        PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
+
+        PluginSpec.Action(AssignColorVolume),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromDsn6),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromCube),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromDx),
+        PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
+    ],
     behaviors: [
         PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
         PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
         PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
         PluginSpec.Behavior(PluginBehaviors.Representation.FocusLoci),
         PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
+        PluginSpec.Behavior(PluginBehaviors.Camera.CameraAxisHelper),
         PluginSpec.Behavior(StructureFocusRepresentation),
 
         PluginSpec.Behavior(PluginBehaviors.CustomProps.StructureInfo),
@@ -74,6 +127,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
         AnimateModelIndex,
         AnimateCameraSpin,
         AnimateStateSnapshots,
-        AnimateAssemblyUnwind
+        AnimateAssemblyUnwind,
+        AnimateStateInterpolation
     ]
 });

src/mol-repr/representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -24,9 +24,6 @@ import { Visual } from './visual';
 import { CustomProperty } from '../mol-model-props/common/custom-property';
 import { Clipping } from '../mol-theme/clipping';
 
-// export interface RepresentationProps {
-//     visuals?: string[]
-// }
 export type RepresentationProps = { [k: string]: any }
 
 export interface RepresentationContext {
@@ -54,6 +51,8 @@ export interface RepresentationProvider<D = any, P extends PD.Params = any, S ex
         attach: (ctx: CustomProperty.Context, data: D) => Promise<void>,
         detach: (data: D) => void
     }
+    readonly getData?: (data: D, props: PD.Values<P>) => D
+    readonly mustRecreate?: (oldProps: PD.Values<P>, newProps: PD.Values<P>) => boolean
 }
 
 export namespace RepresentationProvider {
@@ -66,7 +65,7 @@ export namespace RepresentationProvider {
 
 export type AnyRepresentationProvider = RepresentationProvider<any, {}, Representation.State>
 
-export const EmptyRepresentationProvider = {
+const EmptyRepresentationProvider = {
     label: '',
     description: '',
     factory: () => Representation.Empty,

src/mol-repr/structure/complex-representation.ts

@@ -66,7 +66,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
     }
 
     function getLoci(pickingId?: PickingId) {
-        if (pickingId === undefined) return Structure.Loci(_structure);
+        if (pickingId === undefined) return Structure.Loci(_structure.target);
         return visual ? visual.getLoci(pickingId) : EmptyLoci;
     }