2.0.0-dev.9

Move part of PluginContext to mol-plugin-ui

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.5",
+  "version": "2.0.0-dev.9",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/apps/docking-viewer/index.ts

@@ -5,31 +5,32 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import '../../mol-util/polyfill';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import './index.html';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { PluginConfig } from '../../mol-plugin/config';
-import { ObjectKeys } from '../../mol-util/type-helpers';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { Structure } from '../../mol-model/structure';
-import { PluginStateTransform, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Task } from '../../mol-task';
-import { StateObject } from '../../mol-state';
-import { ViewportComponent, StructurePreset, ShowButtons } from './viewport';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
+import { createPlugin } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginBehaviors } from '../../mol-plugin/behavior';
-import { ColorNames } from '../../mol-util/color/names';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { StateObject } from '../../mol-state';
+import { Task } from '../../mol-task';
 import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import './index.html';
+import { ShowButtons, StructurePreset, ViewportComponent } from './viewport';
 
 require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { Viewer as DockingViewer };
 
 const DefaultViewerOptions = {
     extensions: ObjectKeys({}),
@@ -53,7 +54,7 @@ const DefaultViewerOptions = {
 };
 
 class Viewer {
-    plugin: PluginContext
+    plugin: PluginUIContext
 
     constructor(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
         const o = { ...DefaultViewerOptions, ...{
@@ -70,10 +71,10 @@ class Viewer {
             viewportShowSelectionMode: false,
             viewportShowAnimation: false,
         } };
-        const defaultSpec = DefaultPluginSpec();
+        const defaultSpec = DefaultPluginUISpec();
 
-        const spec: PluginSpec = {
-            actions: [...defaultSpec.actions],
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
             behaviors: [
                 PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
                 PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
@@ -83,7 +84,7 @@ class Viewer {
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
             ],
-            animations: [...defaultSpec.animations || []],
+            animations: defaultSpec.animations,
             customParamEditors: defaultSpec.customParamEditors,
             layout: {
                 initial: {
@@ -91,15 +92,15 @@ class Viewer {
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
                 },
-                controls: {
-                    ...defaultSpec.layout && defaultSpec.layout.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                }
             },
             components: {
                 ...defaultSpec.components,
+                controls: {
+                    ...defaultSpec.components?.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                },
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
                 viewport: {
                     view: ViewportComponent
@@ -210,4 +211,3 @@ const MergeStructures = PluginStateTransform.BuiltIn({
 });
 
 (window as any).DockingViewer = Viewer;
-export { Viewer as DockingViewer };

src/apps/viewer/index.html

@@ -48,18 +48,14 @@
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
             if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
-            var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
-            var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
             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', {
-                disableAntialiasing: disableAntialiasing,
-                pixelScale: pixelScale,
-                enableWboit: !disableWboit,
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
                 pdbProvider: pdbProvider || 'pdbe',
                 emdbProvider: emdbProvider || 'pdbe',
             });

src/apps/viewer/index.ts

@@ -5,43 +5,43 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import '../../mol-util/polyfill';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
-import './index.html';
-import './embedded.html';
-import './favicon.ico';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
-import { PluginConfig } from '../../mol-plugin/config';
-import { CellPack } from '../../extensions/cellpack';
-import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
-import { PDBeStructureQualityReport } from '../../extensions/pdbe';
-import { Asset } from '../../mol-util/assets';
-import { ObjectKeys } from '../../mol-util/type-helpers';
-import { PluginState } from '../../mol-plugin/state';
-import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { CellPack } from '../../extensions/cellpack';
 import { DnatcoConfalPyramids } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
-import { Color } from '../../mol-util/color';
-import { StateObjectSelector } from '../../mol-state';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
-import { Mp4Export } from '../../extensions/mp4-export';
-import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { createPlugin } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectSelector } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import './embedded.html';
+import './favicon.ico';
+import './index.html';
 
 require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 
 const CustomFormats = [
     ['g3d', G3dProvider] as const
@@ -68,6 +68,7 @@ const DefaultViewerOptions = {
     layoutShowSequence: true,
     layoutShowLog: true,
     layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
     disableAntialiasing: false,
     pixelScale: 1,
     enableWboit: true,
@@ -86,14 +87,14 @@ const DefaultViewerOptions = {
 type ViewerOptions = typeof DefaultViewerOptions;
 
 export class Viewer {
-    plugin: PluginContext
+    plugin: PluginUIContext
 
     constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
         const o = { ...DefaultViewerOptions, ...options };
-        const defaultSpec = DefaultPluginSpec();
+        const defaultSpec = DefaultPluginUISpec();
 
-        const spec: PluginSpec = {
-            actions: [...defaultSpec.actions],
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
             behaviors: [
                 ...defaultSpec.behaviors,
                 ...o.extensions.map(e => Extensions[e]),
@@ -106,16 +107,22 @@ export class Viewer {
                     isExpanded: o.layoutIsExpanded,
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: 'full',
+                        top: 'full',
+                    }
                 },
-                controls: {
-                    ...defaultSpec.layout && defaultSpec.layout.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                }
             },
             components: {
                 ...defaultSpec.components,
+                controls: {
+                    ...defaultSpec.components?.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                },
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
             },
             config: [

src/cli/state-docs/index.ts

@@ -18,7 +18,6 @@ _.StateTransforms.Data.Download.id;
 
 // Empty plugin context
 const ctx = new PluginContext({
-    actions: [],
     behaviors: []
 });
 

src/examples/alpha-orbitals/index.ts

@@ -4,25 +4,25 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
+import { BehaviorSubject } from 'rxjs';
+import { debounceTime, skip } from 'rxjs/operators';
+import { AlphaOrbital, Basis } from '../../extensions/alpha-orbitals/data-model';
 import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
 import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
-import { createPluginAsync } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { createPluginAsync } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginConfig } from '../../mol-plugin/config';
-import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector, StateTransformer } from '../../mol-state';
 import { Color } from '../../mol-util/color';
 import { ColorNames } from '../../mol-util/color/names';
 import { ParamDefinition } from '../../mol-util/param-definition';
 import { mountControls } from './controls';
 import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
-import { BehaviorSubject } from 'rxjs';
-import { debounceTime, skip } from 'rxjs/operators';
 import './index.html';
-import { Basis, AlphaOrbital } from '../../extensions/alpha-orbitals/data-model';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
 require('mol-plugin-ui/skin/light.scss');
 
 interface DemoInput {
@@ -50,10 +50,10 @@ type Selectors = {
 }
 
 export class AlphaOrbitalsExample {
-    plugin: PluginContext;
+    plugin: PluginUIContext;
 
     async init(target: string | HTMLElement) {
-        const defaultSpec = DefaultPluginSpec();
+        const defaultSpec = DefaultPluginUISpec();
         this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
             ...defaultSpec,
             layout: {
@@ -61,15 +61,13 @@ export class AlphaOrbitalsExample {
                     isExpanded: false,
                     showControls: false
                 },
-                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
             },
             components: {
-                viewport: {
-                    canvas3d: {
-                        camera: {
-                            helper: { axes: { name: 'off', params: { } } }
-                        }
-                    }
+                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
+            },
+            canvas3d: {
+                camera: {
+                    helper: { axes: { name: 'off', params: { } } }
                 }
             },
             config: [

src/examples/basic-wrapper/index.ts

@@ -4,39 +4,36 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { EmptyLoci } from '../../mol-model/loci';
 import { StructureSelection } from '../../mol-model/structure';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { createPlugin } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
 import { Script } from '../../mol-script/script';
+import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import { StripedResidues } from './coloring';
 import { CustomToastMessage } from './controls';
 import './index.html';
 import { buildStaticSuperposition, dynamicSuperpositionTest, StaticSuperpositionTestData } from './superposition';
-import { PDBeStructureQualityReport } from '../../extensions/pdbe';
-import { Asset } from '../../mol-util/assets';
 require('mol-plugin-ui/skin/light.scss');
 
 type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
 
 class BasicWrapper {
-    plugin: PluginContext;
+    plugin: PluginUIContext;
 
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec(),
+            ...DefaultPluginUISpec(),
             layout: {
                 initial: {
                     isExpanded: false,
                     showControls: false
-                },
-                controls: {
-                    // left: 'none'
                 }
             },
             components: {

src/examples/lighting/index.ts

@@ -5,13 +5,13 @@
  */
 
 import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { createPlugin } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
-import './index.html';
 import { Asset } from '../../mol-util/assets';
+import './index.html';
 require('mol-plugin-ui/skin/light.scss');
 
 type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
@@ -62,7 +62,7 @@ const Canvas3DPresets = {
 type Canvas3DPreset = keyof typeof Canvas3DPresets
 
 class LightingDemo {
-    plugin: PluginContext;
+    plugin: PluginUIContext;
 
     private radius = 5;
     private bias = 1.1;
@@ -70,12 +70,14 @@ class LightingDemo {
 
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec(),
+            ...DefaultPluginUISpec(),
             layout: {
                 initial: {
                     isExpanded: false,
                     showControls: false
                 },
+            },
+            components: {
                 controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
             }
         });

src/examples/proteopedia-wrapper/index.ts

@@ -6,15 +6,15 @@
 
 import * as ReactDOM from 'react-dom';
 import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
-import { createPlugin } from '../../mol-plugin';
-import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { createPlugin } from '../../mol-plugin-ui';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
 import { PluginState } from '../../mol-plugin/state';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
@@ -41,13 +41,13 @@ class MolStarProteopediaWrapper {
         modelInfo: this._ev<ModelInfo>()
     };
 
-    plugin: PluginContext;
+    plugin: PluginUIContext;
 
     init(target: string | HTMLElement, options?: {
         customColorList?: number[]
     }) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec(),
+            ...DefaultPluginUISpec(),
             animations: [
                 AnimateModelIndex
             ],

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

@@ -6,12 +6,12 @@
 
 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';
 import { TransformUpdaterControl } from '../../../mol-plugin-ui/state/update-transform';
-import { PluginContext } from '../../../mol-plugin/context';
 import { StateElements } from '../helpers';
 
-export function volumeStreamingControls(plugin: PluginContext, parent: Element) {
+export function volumeStreamingControls(plugin: PluginUIContext, parent: Element) {
     ReactDOM.render(<PluginContextContainer plugin={plugin}>
         <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} />
     </PluginContextContainer>, parent);

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

@@ -192,6 +192,15 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
 
 //
 
+/**
+ * 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, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     // console.time('calcActiveVoxels');
     const activeVoxelsTex = calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);

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

@@ -74,7 +74,7 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
         let cI = 0;
         let seqId = 0;
         for (let i = 0, il = seqIds.length; i < il; ++i) {
-            if (residueOffsets[i] > chainOffsets[cI + 1]) {
+            if (residueOffsets[i] >= chainOffsets[cI + 1]) {
                 cI += 1;
                 seqId = 0;
             }

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

@@ -84,7 +84,7 @@ function getModels(mol: XyzFile, ctx: RuntimeContext) {
         atom_site
     });
 
-    return createModels(basics, MolFormat.create(mol), ctx);
+    return createModels(basics, XyzFormat.create(mol), ctx);
 }
 
 //
@@ -93,9 +93,9 @@ export { XyzFormat };
 
 type XyzFormat = ModelFormat<XyzFile>
 
-namespace MolFormat {
+namespace XyzFormat {
     export function is(x?: ModelFormat): x is XyzFormat {
-        return x?.kind === 'mol';
+        return x?.kind === 'xyz';
     }
 
     export function create(mol: XyzFile): XyzFormat {

src/mol-model-props/computed/secondary-structure.ts

@@ -69,7 +69,7 @@ async function computeDssp(structure: Structure, props: DSSPComputationProps): P
     const map = new Map<number, SecondaryStructure>();
     for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
         const u = structure.unitSymmetryGroups[i].units[0];
-        if (Unit.isAtomic(u)) {
+        if (Unit.isAtomic(u) && !Model.isCoarseGrained(u.model)) {
             const secondaryStructure = await computeUnitDSSP(u, props);
             map.set(u.invariantId, secondaryStructure);
         }

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

@@ -227,7 +227,7 @@ export namespace Model {
 
     const CoarseGrainedProp = '__CoarseGrained__';
     /**
-     * Has typical coarse grained atom names (BB, SC1) or less than twice as many
+     * Has typical coarse grained atom names (BB, SC1) or less than three times as many
      * atoms as polymer residues (C-alpha only models).
      */
     export function isCoarseGrained(model: Model): boolean {
@@ -251,7 +251,7 @@ export namespace Model {
 
         const coarseGrained = (hasBB && hasSC1) || (
             polymerResidueCount && atomCount
-                ? atomCount / polymerResidueCount < 2
+                ? atomCount / polymerResidueCount < 3
                 : false
         );
         model._staticPropertyData[CoarseGrainedProp] = coarseGrained;

src/mol-model/structure/query/utils/structure-distance.ts

@@ -23,7 +23,7 @@ export function checkStructureMaxRadiusDistance(ctx: QueryContext, a: Structure,
 }
 
 namespace MinMaxDist {
-    const enum Result {
+    export const enum Result {
         BelowMin,
         WithinMax,
         Miss

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

@@ -164,7 +164,10 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
 
         plugin.state.data.events.object.updated.subscribe(({ oldData, obj, action }) => {
             if (!PluginStateObject.Molecule.Structure.is(obj)) return;
+            // structure NOT changed, keep everything as is; fixes #123
+            if (oldData === obj.data) return;
 
+            // structure changed (e.g. coordinates), try to remap and re-focus
             if (action === 'in-place') {
                 const current = this.state.current;
                 const structure = obj.data as Structure;

src/mol-plugin-ui/base.tsx

@@ -7,15 +7,15 @@
 
 import * as React from 'react';
 import { Observable, Subscription } from 'rxjs';
-import { PluginContext } from '../mol-plugin/context';
+import { PluginUIContext } from './context';
 import { Button, ColorAccent } from './controls/common';
 import { Icon, ArrowRightSvg, ArrowDropDownSvg } from './controls/icons';
 
-export const PluginReactContext = React.createContext(void 0 as any as PluginContext);
+export const PluginReactContext = React.createContext(void 0 as any as PluginUIContext);
 
 export abstract class PluginUIComponent<P = {}, S = {}, SS = {}> extends React.Component<P, S, SS> {
     static contextType = PluginReactContext;
-    readonly plugin: PluginContext;
+    readonly plugin: PluginUIContext;
 
     private subs: Subscription[] | undefined = void 0;
 
@@ -33,7 +33,7 @@ export abstract class PluginUIComponent<P = {}, S = {}, SS = {}> extends React.C
     protected init?(): void;
 
     constructor(props: P, context?: any) {
-        super(props, context);
+        super(props);
         this.plugin = context;
         if (this.init) this.init();
     }
@@ -41,7 +41,7 @@ export abstract class PluginUIComponent<P = {}, S = {}, SS = {}> extends React.C
 
 export abstract class PurePluginUIComponent<P = {}, S = {}, SS = {}> extends React.PureComponent<P, S, SS> {
     static contextType = PluginReactContext;
-    readonly plugin: PluginContext;
+    readonly plugin: PluginUIContext;
 
     private subs: Subscription[] | undefined = void 0;
 

src/mol-plugin-ui/context.ts

@@ -0,0 +1,33 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+
+import { PluginContext } from '../mol-plugin/context';
+import { PluginUISpec } from './spec';
+import { StateTransformParameters } from './state/common';
+
+export class PluginUIContext extends PluginContext {
+    readonly customParamEditors = new Map<string, StateTransformParameters.Class>();
+
+    private initCustomParamEditors() {
+        if (!this.spec.customParamEditors) return;
+
+        for (const [t, e] of this.spec.customParamEditors) {
+            this.customParamEditors.set(t.id, e);
+        }
+    }
+
+    dispose(options?: { doNotForceWebGLContextLoss?: boolean }) {
+        super.dispose(options);
+        this.layout.dispose();
+    }
+
+    constructor(public spec: PluginUISpec) {
+        super(spec);
+
+        this.initCustomParamEditors();
+    }
+}

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

@@ -7,7 +7,6 @@
 
 import * as React from 'react';
 import { Mat4, Vec2, Vec3 } from '../../mol-math/linear-algebra';
-import { PluginContext } from '../../mol-plugin/context';
 import { Color } from '../../mol-util/color';
 import { ColorListName, ColorListOptions, ColorListOptionsScale, ColorListOptionsSet, getColorListFromName } from '../../mol-util/color/lists';
 import { Legend as LegendData } from '../../mol-util/legend';
@@ -26,6 +25,7 @@ import { LineGraphComponent } from './line-graph/line-graph-component';
 import { Slider, Slider2 } from './slider';
 import { Asset } from '../../mol-util/assets';
 import { ColorListEntry } from '../../mol-util/color/color';
+import { PluginUIContext } from '../context';
 
 export type ParameterControlsCategoryFilter = string | null | (string | null)[]
 
@@ -104,7 +104,7 @@ export class ParameterControls<P extends PD.Params> extends React.PureComponent<
     }
 }
 
-export class ParameterMappingControl<S, T> extends PluginUIComponent<{ mapping: ParamMapping<S, T, PluginContext> }> {
+export class ParameterMappingControl<S, T> extends PluginUIComponent<{ mapping: ParamMapping<S, T, PluginUIContext> }> {
     setSettings = (p: { param: PD.Base<any>, name: string, value: any }, old: any) => {
         const values = { ...old, [p.name]: p.value };
         const t = this.props.mapping.update(values, this.plugin);

src/mol-plugin-ui/index.ts

@@ -7,20 +7,20 @@
 
 import * as React from 'react';
 import * as ReactDOM from 'react-dom';
-import { Plugin } from '../mol-plugin-ui/plugin';
-import { PluginContext } from './context';
-import { DefaultPluginSpec, PluginSpec } from './spec';
+import { Plugin } from './plugin';
+import { PluginUIContext } from './context';
+import { DefaultPluginUISpec, PluginUISpec } from './spec';
 
-export function createPlugin(target: HTMLElement, spec?: PluginSpec): PluginContext {
-    const ctx = new PluginContext(spec || DefaultPluginSpec());
+export function createPlugin(target: HTMLElement, spec?: PluginUISpec): PluginUIContext {
+    const ctx = new PluginUIContext(spec || DefaultPluginUISpec());
     ctx.init();
     ReactDOM.render(React.createElement(Plugin, { plugin: ctx }), target);
     return ctx;
 }
 
 /** Returns the instance of the plugin after all behaviors have been initialized */
-export async function createPluginAsync(target: HTMLElement, spec?: PluginSpec) {
-    const ctx = new PluginContext(spec || DefaultPluginSpec());
+export async function createPluginAsync(target: HTMLElement, spec?: PluginUISpec) {
+    const ctx = new PluginUIContext(spec || DefaultPluginUISpec());
     const init = ctx.init();
     ReactDOM.render(React.createElement(Plugin, { plugin: ctx }), target);
     await init;

src/mol-plugin-ui/plugin.tsx

@@ -7,7 +7,6 @@
 
 import { List } from 'immutable';
 import * as React from 'react';
-import { PluginContext } from '../mol-plugin/context';
 import { formatTime } from '../mol-util';
 import { LogEntry } from '../mol-util/log-entry';
 import { PluginReactContext, PluginUIComponent } from './base';
@@ -18,8 +17,9 @@ import { BackgroundTaskProgress, OverlayTaskProgress } from './task';
 import { Toasts } from './toast';
 import { Viewport, ViewportControls } from './viewport';
 import { PluginCommands } from '../mol-plugin/commands';
+import { PluginUIContext } from './context';
 
-export class Plugin extends React.Component<{ plugin: PluginContext }, {}> {
+export class Plugin extends React.Component<{ plugin: PluginUIContext }, {}> {
     region(kind: 'left' | 'right' | 'bottom' | 'main', element: JSX.Element) {
         return <div className={`msp-layout-region msp-layout-${kind}`}>
             <div className='msp-layout-static'>
@@ -35,7 +35,7 @@ export class Plugin extends React.Component<{ plugin: PluginContext }, {}> {
     }
 }
 
-export class PluginContextContainer extends React.Component<{ plugin: PluginContext }> {
+export class PluginContextContainer extends React.Component<{ plugin: PluginUIContext }> {
     render() {
         return <PluginReactContext.Provider value={this.props.plugin}>
             <div className='msp-plugin'>
@@ -62,7 +62,7 @@ class Layout extends PluginUIComponent {
 
     get layoutVisibilityClassName() {
         const layout = this.plugin.layout.state;
-        const controls = (this.plugin.spec.layout && this.plugin.spec.layout.controls) || {};
+        const controls = this.plugin.spec.components?.controls ?? {};
 
         const classList: string[] = [];
         if (controls.top === 'none' || !layout.showControls || layout.regionState.top === 'hidden') {
@@ -127,7 +127,7 @@ class Layout extends PluginUIComponent {
 
     render() {
         const layout = this.plugin.layout.state;
-        const controls = this.plugin.spec.layout?.controls || {};
+        const controls = this.plugin.spec.components?.controls || {};
         const viewport = this.plugin.spec.components?.viewport?.view || DefaultViewport;
 
         return <div className='msp-plugin' onDrop={this.onDrop} onDragOver={this.onDragOver}>
@@ -149,7 +149,6 @@ export class ControlsWrapper extends PluginUIComponent {
     render() {
         const StructureTools = this.plugin.spec.components?.structureTools || DefaultStructureTools;
         return <div className='msp-scrollable-container'>
-            {/* <CurrentObject /> */}
             <StructureTools />
         </div>;
     }

src/mol-plugin-ui/spec.ts

@@ -0,0 +1,40 @@
+/**
+ * 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>
+ */
+
+
+import { StateTransformParameters } from '../mol-plugin-ui/state/common';
+import { DefaultPluginSpec, PluginSpec } from '../mol-plugin/spec';
+import { StateAction, StateTransformer } from '../mol-state';
+
+export { PluginUISpec };
+
+interface PluginUISpec extends PluginSpec {
+    customParamEditors?: [StateAction | StateTransformer, StateTransformParameters.Class][],
+    components?: {
+        controls?: PluginUISpec.LayoutControls
+        remoteState?: 'none' | 'default',
+        structureTools?: React.ComponentClass,
+        viewport?: {
+            view?: React.ComponentClass,
+            controls?: React.ComponentClass
+        },
+        hideTaskOverlay?: boolean
+    },
+}
+
+namespace PluginUISpec {
+    export interface LayoutControls {
+        top?: React.ComponentClass | 'none',
+        left?: React.ComponentClass | 'none',
+        right?: React.ComponentClass | 'none',
+        bottom?: React.ComponentClass | 'none'
+    }
+}
+
+export const DefaultPluginUISpec = (): PluginUISpec => ({
+    ...DefaultPluginSpec(),
+});

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

@@ -9,13 +9,13 @@ import { produce } from 'immer';
 import * as React from 'react';
 import { Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
 import { StateTransform } from '../../mol-state';
 import { Color } from '../../mol-util/color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ParamMapping } from '../../mol-util/param-mapping';
 import { Mutable } from '../../mol-util/type-helpers';
 import { PluginUIComponent } from '../base';
+import { PluginUIContext } from '../context';
 import { ParameterMappingControl } from '../controls/parameters';
 import { ViewportHelpContent } from './help';
 
@@ -71,9 +71,9 @@ const SimpleSettingsParams = {
 
 type SimpleSettingsParams = typeof SimpleSettingsParams
 const SimpleSettingsMapping = ParamMapping({
-    params: (ctx: PluginContext) => {
+    params: (ctx: PluginUIContext) => {
         const params = PD.clone(SimpleSettingsParams);
-        const controls = ctx.spec.layout?.controls;
+        const controls = ctx.spec.components?.controls;
         if (controls) {
             const options: [LayoutOptions, string][] = [];
             if (controls.top !== 'none') options.push(['sequence', LayoutOptions.sequence]);
@@ -83,8 +83,8 @@ const SimpleSettingsMapping = ParamMapping({
         }
         return params;
     },
-    target(ctx: PluginContext) {
-        const c = ctx.spec.layout?.controls;
+    target(ctx: PluginUIContext) {
+        const c = ctx.spec.components?.controls;
         const r = ctx.layout.state.regionState;
         const layout: SimpleSettingsParams['layout']['defaultValue'] = [];
         if (r.top !== 'hidden' && (!c || c.top !== 'none')) layout.push('sequence');

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

@@ -64,8 +64,8 @@ export namespace VolumeStreaming {
         };
     }
 
-    export type EntryParamDefinition = typeof createEntryParams extends (...args: any[]) => (infer T) ? T : never
-    export type EntryParams = EntryParamDefinition extends PD.Params ? PD.Values<EntryParamDefinition> : {}
+    export type EntryParamDefinition = ReturnType<typeof createEntryParams>
+    export type EntryParams = PD.Values<EntryParamDefinition>
 
     export function createEntryParams(options: { entryData?: VolumeServerInfo.EntryData, defaultView?: ViewTypes, structure?: Structure, channelParams?: DefaultChannelParams }) {
         const { entryData, defaultView, structure, channelParams = { } } = options;
@@ -86,7 +86,7 @@ export namespace VolumeStreaming {
                     bottomLeft: PD.Vec3(Vec3.create(0, 0, 0), {}, { isHidden: true }),
                     topRight: PD.Vec3(Vec3.create(0, 0, 0), {}, { isHidden: true }),
                 }, { description: 'Box around focused element.', isFlat: true }),
-                'cell': PD.Group({}),
+                'cell': PD.Group<{}>({}),
                 // Show selection-box if available and cell otherwise.
                 'auto': PD.Group({
                     radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }, { description: 'Radius in \u212B within which the volume is shown.' }),
@@ -115,8 +115,8 @@ export namespace VolumeStreaming {
 
     export type ViewTypes = 'off' | 'box' | 'selection-box' | 'cell' | 'auto'
 
-    export type ParamDefinition = typeof createParams extends (...args: any[]) => (infer T) ? T : never
-    export type Params = ParamDefinition extends PD.Params ? PD.Values<ParamDefinition> : {}
+    export type ParamDefinition = ReturnType<typeof createParams>
+    export type Params = PD.Values<ParamDefinition>
 
     type ChannelsInfo = { [name in ChannelType]?: { isoValue: Volume.IsoValue, color: Color, wireframe: boolean, opacity: number } }
     type ChannelsData = { [name in 'EM' | '2FO-FC' | 'FO-FC']?: Volume }

src/mol-plugin/context.ts

@@ -8,44 +8,51 @@
 import produce, { setAutoFreeze } from 'immer';
 import { List } from 'immutable';
 import { merge, Subscription } from 'rxjs';
+import { filter, take } from 'rxjs/operators';
 import { Canvas3D, Canvas3DContext, DefaultCanvas3DParams } from '../mol-canvas3d/canvas3d';
+import { resizeCanvas } from '../mol-canvas3d/util';
+import { Vec2 } from '../mol-math/linear-algebra';
 import { CustomProperty } from '../mol-model-props/common/custom-property';
 import { Model, Structure } from '../mol-model/structure';
 import { DataBuilder } from '../mol-plugin-state/builder/data';
 import { StructureBuilder } from '../mol-plugin-state/builder/structure';
 import { DataFormatRegistry } from '../mol-plugin-state/formats/registry';
 import { StructureSelectionQueryRegistry } from '../mol-plugin-state/helpers/structure-selection-query';
+import { PluginAnimationManager } from '../mol-plugin-state/manager/animation';
 import { CameraManager } from '../mol-plugin-state/manager/camera';
 import { InteractivityManager } from '../mol-plugin-state/manager/interactivity';
 import { LociLabel, LociLabelManager } from '../mol-plugin-state/manager/loci-label';
+import { PluginStateSnapshotManager } from '../mol-plugin-state/manager/snapshots';
 import { StructureComponentManager } from '../mol-plugin-state/manager/structure/component';
 import { StructureFocusManager } from '../mol-plugin-state/manager/structure/focus';
 import { StructureHierarchyManager } from '../mol-plugin-state/manager/structure/hierarchy';
 import { StructureHierarchyRef } from '../mol-plugin-state/manager/structure/hierarchy-state';
 import { StructureMeasurementManager } from '../mol-plugin-state/manager/structure/measurement';
 import { StructureSelectionManager } from '../mol-plugin-state/manager/structure/selection';
-import { PluginUIComponent } from '../mol-plugin-ui/base';
-import { StateTransformParameters } from '../mol-plugin-ui/state/common';
+import { VolumeHierarchyManager } from '../mol-plugin-state/manager/volume/hierarchy';
+import { LeftPanelTabName, PluginLayout } from './layout';
 import { Representation } from '../mol-repr/representation';
 import { StructureRepresentationRegistry } from '../mol-repr/structure/registry';
 import { VolumeRepresentationRegistry } from '../mol-repr/volume/registry';
 import { StateTransform } from '../mol-state';
-import { Task, RuntimeContext } from '../mol-task';
+import { RuntimeContext, Task } from '../mol-task';
 import { ColorTheme } from '../mol-theme/color';
 import { SizeTheme } from '../mol-theme/size';
 import { ThemeRegistryContext } from '../mol-theme/theme';
+import { AssetManager } from '../mol-util/assets';
 import { Color } from '../mol-util/color';
 import { ajaxGet } from '../mol-util/data-source';
 import { isDebugMode, isProductionMode } from '../mol-util/debug';
 import { ModifiersKeys } from '../mol-util/input/input-observer';
 import { LogEntry } from '../mol-util/log-entry';
+import { objectForEach } from '../mol-util/object';
 import { RxEventHelper } from '../mol-util/rx-event-helper';
+import { PluginAnimationLoop } from './animation-loop';
 import { BuiltInPluginBehaviors } from './behavior';
 import { PluginBehavior } from './behavior/behavior';
 import { PluginCommandManager } from './command';
 import { PluginCommands } from './commands';
 import { PluginConfig, PluginConfigManager } from './config';
-import { LeftPanelTabName, PluginLayout } from './layout';
 import { PluginSpec } from './spec';
 import { PluginState } from './state';
 import { SubstructureParentHelper } from './util/substructure-parent-helper';
@@ -53,15 +60,6 @@ import { TaskManager } from './util/task-manager';
 import { PluginToastManager } from './util/toast';
 import { ViewportScreenshotHelper } from './util/viewport-screenshot';
 import { PLUGIN_VERSION, PLUGIN_VERSION_DATE } from './version';
-import { AssetManager } from '../mol-util/assets';
-import { PluginStateSnapshotManager } from '../mol-plugin-state/manager/snapshots';
-import { PluginAnimationManager } from '../mol-plugin-state/manager/animation';
-import { objectForEach } from '../mol-util/object';
-import { VolumeHierarchyManager } from '../mol-plugin-state/manager/volume/hierarchy';
-import { filter, take } from 'rxjs/operators';
-import { Vec2 } from '../mol-math/linear-algebra';
-import { PluginAnimationLoop } from './animation-loop';
-import { resizeCanvas } from '../mol-canvas3d/util';
 
 export class PluginContext {
     runTask = <T>(task: Task<T>, params?: { useOverlay?: boolean }) => this.managers.task.run(task, params);
@@ -71,7 +69,7 @@ export class PluginContext {
         return object;
     }
 
-    private subs: Subscription[] = [];
+    protected subs: Subscription[] = [];
 
     private disposed = false;
     private ev = RxEventHelper.create();
@@ -109,8 +107,8 @@ export class PluginContext {
 
     readonly canvas3dContext: Canvas3DContext | undefined;
     readonly canvas3d: Canvas3D | undefined;
-    readonly animationLoop = new PluginAnimationLoop(this);
     readonly layout = new PluginLayout(this);
+    readonly animationLoop = new PluginAnimationLoop(this);
 
     readonly representation = {
         structure: {
@@ -176,9 +174,8 @@ export class PluginContext {
 
     readonly customModelProperties = new CustomProperty.Registry<Model>();
     readonly customStructureProperties = new CustomProperty.Registry<Structure>();
-    readonly customParamEditors = new Map<string, StateTransformParameters.Class>();
 
-    readonly customStructureControls = new Map<string, { new(): PluginUIComponent<any, any, any> }>();
+    readonly customStructureControls = new Map<string, { new(): any /* constructible react components with <action.customControl /> */ }>();
     readonly genericRepresentationControls = new Map<string, (selection: StructureHierarchyManager['selection']) => [StructureHierarchyRef[], string]>();
 
     /**
@@ -200,7 +197,7 @@ export class PluginContext {
             (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, { antialias, preserveDrawingBuffer, pixelScale, pickScale, enableWboit });
             (this.canvas3d as Canvas3D) = Canvas3D.create(this.canvas3dContext!);
             this.canvas3dInit.next(true);
-            let props = this.spec.components?.viewport?.canvas3d;
+            let props = this.spec.canvas3d;
 
             const backgroundColor = Color(0xFCFBF9);
             if (!props) {
@@ -294,7 +291,6 @@ export class PluginContext {
         this.ev.dispose();
         this.state.dispose();
         this.managers.task.dispose();
-        this.layout.dispose();
         this.helpers.substructureParent.dispose();
 
         objectForEach(this.managers, m => (m as any)?.dispose?.());
@@ -385,12 +381,6 @@ export class PluginContext {
         }
     }
 
-    private initDataActions() {
-        for (const a of this.spec.actions) {
-            this.state.data.actions.add(a.action);
-        }
-    }
-
     private initAnimations() {
         if (!this.spec.animations) return;
         for (const anim of this.spec.animations) {
@@ -398,11 +388,10 @@ export class PluginContext {
         }
     }
 
-    private initCustomParamEditors() {
-        if (!this.spec.customParamEditors) return;
-
-        for (const [t, e] of this.spec.customParamEditors) {
-            this.customParamEditors.set(t.id, e);
+    private initDataActions() {
+        if (!this.spec.actions) return;
+        for (const a of this.spec.actions) {
+            this.state.data.actions.add(a.action);
         }
     }
 
@@ -417,9 +406,8 @@ export class PluginContext {
         (this.managers.lociLabels as LociLabelManager) = new LociLabelManager(this);
         (this.builders.structure as StructureBuilder) = new StructureBuilder(this);
 
-        this.initDataActions();
         this.initAnimations();
-        this.initCustomParamEditors();
+        this.initDataActions();
 
         await this.initBehaviors();
 

src/mol-plugin/layout.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 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>
@@ -7,8 +7,8 @@
 
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { StatefulPluginComponent } from '../mol-plugin-state/component';
-import { PluginContext } from './context';
 import { PluginCommands } from './commands';
+import { PluginContext } from './context';
 
 const regionStateOptions = [
     ['full', 'Full'],

src/mol-plugin/spec.ts

@@ -1,50 +1,37 @@
 /**
- * Copyright (c) 2018-2019 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>
  */
 
-import { StateTransformer, StateAction } from '../mol-state';
-import { StateTransformParameters } from '../mol-plugin-ui/state/common';
-import { PluginLayoutStateProps } from './layout';
-import { PluginStateAnimation } from '../mol-plugin-state/animation/model';
-import { PluginConfigItem } from './config';
 import { PartialCanvas3DProps } from '../mol-canvas3d/canvas3d';
-import { DataFormatProvider } from '../mol-plugin-state/formats/provider';
-import { StateActions } from '../mol-plugin-state/actions';
-import { StateTransforms } from '../mol-plugin-state/transforms';
-import { VolumeStreamingCustomControls } from '../mol-plugin-ui/custom/volume';
-import { PluginBehaviors } from './behavior';
-import { StructureFocusRepresentation } from './behavior/dynamic/selection/structure-focus-representation';
-import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from './behavior/dynamic/volume-streaming/transformers';
-import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
-import { AnimateModelIndex } from '../mol-plugin-state/animation/built-in/model-index';
 import { AnimateAssemblyUnwind } from '../mol-plugin-state/animation/built-in/assembly-unwind';
 import { AnimateCameraSpin } from '../mol-plugin-state/animation/built-in/camera-spin';
+import { AnimateModelIndex } from '../mol-plugin-state/animation/built-in/model-index';
 import { AnimateStateSnapshots } from '../mol-plugin-state/animation/built-in/state-snapshots';
+import { PluginStateAnimation } from '../mol-plugin-state/animation/model';
+import { DataFormatProvider } from '../mol-plugin-state/formats/provider';
+import { StateAction, StateTransformer } from '../mol-state';
+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';
 
 export { PluginSpec };
 
 interface PluginSpec {
-    actions: PluginSpec.Action[],
+    actions?: PluginSpec.Action[],
     behaviors: PluginSpec.Behavior[],
     animations?: PluginStateAnimation[],
-    customParamEditors?: [StateAction | StateTransformer, StateTransformParameters.Class][],
-    customFormats?: [string, DataFormatProvider][]
+    customFormats?: [string, DataFormatProvider][],
+    canvas3d?: PartialCanvas3DProps,
     layout?: {
         initial?: Partial<PluginLayoutStateProps>,
-        controls?: PluginSpec.LayoutControls
-    },
-    components?: {
-        remoteState?: 'none' | 'default',
-        structureTools?: React.ComponentClass,
-        viewport?: {
-            view?: React.ComponentClass,
-            controls?: React.ComponentClass,
-            canvas3d?: PartialCanvas3DProps
-        },
-        hideTaskOverlay?: boolean
     },
     config?: [PluginConfigItem, unknown][]
 }
@@ -52,11 +39,12 @@ interface PluginSpec {
 namespace PluginSpec {
     export interface Action {
         action: StateAction | StateTransformer,
-        customControl?: StateTransformParameters.Class,
+        /* constructible react component with <action.customControl /> */
+        customControl?: any,
         autoUpdate?: boolean
     }
 
-    export function Action(action: StateAction | StateTransformer, params?: { customControl?: StateTransformParameters.Class, autoUpdate?: boolean }): Action {
+    export function Action(action: StateAction | StateTransformer, params?: { customControl?: any /* constructible react component with <action.customControl /> */, autoUpdate?: boolean }): Action {
         return { action, customControl: params && params.customControl, autoUpdate: params && params.autoUpdate };
     }
 
@@ -68,13 +56,6 @@ namespace PluginSpec {
     export function Behavior<T extends StateTransformer>(transformer: T, defaultParams: Partial<StateTransformer.Params<T>> = {}): Behavior {
         return { transformer, defaultParams };
     }
-
-    export interface LayoutControls {
-        top?: React.ComponentClass | 'none',
-        left?: React.ComponentClass | 'none',
-        right?: React.ComponentClass | 'none',
-        bottom?: React.ComponentClass | 'none'
-    }
 }
 
 export const DefaultPluginSpec = (): PluginSpec => ({
@@ -139,9 +120,6 @@ export const DefaultPluginSpec = (): PluginSpec => ({
         PluginSpec.Behavior(PluginBehaviors.CustomProps.ValenceModel),
         PluginSpec.Behavior(PluginBehaviors.CustomProps.CrossLinkRestraint),
     ],
-    customParamEditors: [
-        [CreateVolumeStreamingBehavior, VolumeStreamingCustomControls]
-    ],
     animations: [
         AnimateModelIndex,
         AnimateCameraSpin,

src/mol-plugin/util/toast.ts

@@ -14,9 +14,9 @@ import { PluginCommands } from '../commands';
 export interface PluginToast {
     title: string,
     /**
-     * The message can be either a string, html string, or an arbitrary React component.
+     * The message can be either a string, html string, or an arbitrary React (Function) component.
      */
-    message: string | React.ComponentClass,
+    message: string | Function,
     /**
      * Only one message with a given key can be shown.
      */
@@ -103,7 +103,7 @@ export namespace PluginToastManager {
         serialNumber: number,
         key?: string,
         title: string,
-        message: string | React.ComponentClass,
+        message: string | Function,
         hide: () => void,
         timeout?: number
     }