added mol-plugin-state, refactored PluginCommand

README.md

@@ -31,6 +31,7 @@ The core of Mol* currently consists of these modules (see under `src/`):
 - `mol-state` State representation tree with state saving and automatic updates.
 - `mol-app` Components for builduing 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 to 3rd party solutions.
 - `mol-util` Useful things that do not fit elsewhere.
 

src/apps/basic-wrapper/helpers.ts

@@ -6,9 +6,9 @@
 
 import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { StructureRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { StateBuilder } from '../../mol-state';
 import Expression from '../../mol-script/language/expression';

src/apps/basic-wrapper/index.ts

@@ -7,12 +7,12 @@
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import './index.html'
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/command';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { StructureRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
 import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin/state/objects';
-import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
+import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin-state/objects';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
 import { StateBuilder, StateTransform } from '../../mol-state';
 import { StripedResidues } from './coloring';
 import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
@@ -103,7 +103,7 @@ class BasicWrapper {
 
         let tree: StateBuilder.Root;
         if (loadType === 'full') {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
+            await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref });
             tree = state.build();
             this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
         } else {
@@ -118,14 +118,14 @@ class BasicWrapper {
             tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
         }
 
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.dataState, tree });
         this.loadedParams = { url, format, assemblyId };
-        PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+        PluginCommands.Camera.Reset(this.plugin, { });
     }
 
     setBackground(color: number) {
         const renderer = this.plugin.canvas3d!.props.renderer;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
     }
 
     toggleSpin() {
@@ -133,8 +133,8 @@ class BasicWrapper {
 
         const trackball = this.plugin.canvas3d.props.trackball;
         const spinning = trackball.spin;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
-        if (!spinning) PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
+        if (!spinning) PluginCommands.Camera.Reset(this.plugin, { });
     }
 
     animate = {
@@ -160,7 +160,7 @@ class BasicWrapper {
                 tree.to(v).update(old => ({ ...old, colorTheme }));
             }
 
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+            await PluginCommands.State.Update(this.plugin, { state, tree });
         }
     }
 
@@ -184,34 +184,34 @@ class BasicWrapper {
         staticSuperposition: async () => {
             const state = this.plugin.state.dataState;
             const tree = buildStaticSuperposition(this.plugin, StaticSuperpositionTestData);
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: StateTransform.RootRef });
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+            await PluginCommands.State.RemoveObject(this.plugin, { state, ref: StateTransform.RootRef });
+            await PluginCommands.State.Update(this.plugin, { state, tree });
         },
         dynamicSuperposition: async () => {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
+            await PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
             await dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
         },
         toggleValidationTooltip: async () => {
             const state = this.plugin.state.behaviorState;
             const tree = state.build().to(PDBeStructureQualityReport.id).update(PDBeStructureQualityReport, p => ({ ...p, showTooltip: !p.showTooltip }));
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+            await PluginCommands.State.Update(this.plugin, { state, tree });
         },
         showToasts: () => {
-            PluginCommands.Toast.Show.dispatch(this.plugin, {
+            PluginCommands.Toast.Show(this.plugin, {
                 title: 'Toast 1',
                 message: 'This is an example text, timeout 3s',
                 key: 'toast-1',
                 timeoutMs: 3000
             });
-            PluginCommands.Toast.Show.dispatch(this.plugin, {
+            PluginCommands.Toast.Show(this.plugin, {
                 title: 'Toast 2',
                 message: CustomToastMessage,
                 key: 'toast-2'
             });
         },
         hideToasts: () => {
-            PluginCommands.Toast.Hide.dispatch(this.plugin, { key: 'toast-1' });
-            PluginCommands.Toast.Hide.dispatch(this.plugin, { key: 'toast-2' });
+            PluginCommands.Toast.Hide(this.plugin, { key: 'toast-1' });
+            PluginCommands.Toast.Hide(this.plugin, { key: 'toast-2' });
         }
     }
 }

src/apps/basic-wrapper/superposition.ts

@@ -9,9 +9,9 @@
 import { PluginContext } from '../../mol-plugin/context';
 import { Mat4 } from '../../mol-math/linear-algebra';
 import { StateHelper } from './helpers';
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { StateSelection, StateBuilder } from '../../mol-state';
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { StructureSelection, QueryContext } from '../../mol-model/structure';
@@ -71,7 +71,7 @@ export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[]
             StateHelper.getModel(StateHelper.download(structures, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`), 'cif'));
     }
 
-    await PluginCommands.State.Update.dispatch(ctx, { state, tree: structures });
+    await PluginCommands.State.Update(ctx, { state, tree: structures });
 
     const pivot = MS.struct.filter.first([
         MS.struct.generator.atomGroups({
@@ -99,7 +99,7 @@ export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[]
             pivot, rest);
     }
 
-    await PluginCommands.State.Update.dispatch(ctx, { state, tree: visuals });
+    await PluginCommands.State.Update(ctx, { state, tree: visuals });
 }
 
 function siteVisual(ctx: PluginContext, b: StateBuilder.To<PSO.Molecule.Structure>, pivot: Expression, rest: Expression) {

src/apps/demos/lighting/index.ts

@@ -7,10 +7,10 @@
 import { createPlugin, DefaultPluginSpec } from '../../../mol-plugin';
 import './index.html'
 import { PluginContext } from '../../../mol-plugin/context';
-import { PluginCommands } from '../../../mol-plugin/command';
-import { StateTransforms } from '../../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../../mol-plugin/state/transforms/representation';
-import { PluginStateObject as PSO } from '../../../mol-plugin/state/objects';
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { StructureRepresentation3DHelpers } from '../../../mol-plugin-state/transforms/representation';
+import { PluginStateObject as PSO } from '../../../mol-plugin-state/objects';
 import { StateBuilder } from '../../../mol-state';
 import { Canvas3DProps } from '../../../mol-canvas3d/canvas3d';
 require('mol-plugin-ui/skin/light.scss')
@@ -94,7 +94,7 @@ class LightingDemo {
 
     setPreset(preset: Canvas3DPreset) {
         const props = getPreset(preset)
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
             ...props,
             multiSample: {
                 ...this.plugin.canvas3d!.props.multiSample,
@@ -155,7 +155,7 @@ class LightingDemo {
 
         let tree: StateBuilder.Root;
         if (loadType === 'full') {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
+            await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref });
             tree = state.build();
             this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
         } else {
@@ -169,9 +169,9 @@ class LightingDemo {
             tree.to('asm').update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));
         }
 
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.dataState, tree });
         this.loadedParams = { url, format, assemblyId };
-        PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+        PluginCommands.Camera.Reset(this.plugin, { });
     }
 }
 

src/apps/state-docs/index.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as _ from '../../mol-plugin/state/transforms'
+import * as _ from '../../mol-plugin-state/transforms'
 import { StateTransformer, StateObject } from '../../mol-state';
 import { StringBuilder } from '../../mol-util';
 import * as fs from 'fs';

src/apps/viewer/extensions/cellpack/model.ts

@@ -6,7 +6,7 @@
 
 import { StateAction } from '../../../../mol-state';
 import { PluginContext } from '../../../../mol-plugin/context';
-import { PluginStateObject as PSO } from '../../../../mol-plugin/state/objects';
+import { PluginStateObject as PSO } from '../../../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Ingredient, CellPacking, Cell } from './data';
 import { getFromPdb, getFromCellPackDB } from './util';
@@ -16,8 +16,8 @@ import { trajectoryFromPDB } from '../../../../mol-model-formats/structure/pdb';
 import { Mat4, Vec3, Quat } from '../../../../mol-math/linear-algebra';
 import { SymmetryOperator } from '../../../../mol-math/geometry';
 import { Task } from '../../../../mol-task';
-import { StructureRepresentation3DHelpers } from '../../../../mol-plugin/state/transforms/representation';
-import { StateTransforms } from '../../../../mol-plugin/state/transforms';
+import { StructureRepresentation3DHelpers } from '../../../../mol-plugin-state/transforms/representation';
+import { StateTransforms } from '../../../../mol-plugin-state/transforms';
 import { distinctColors } from '../../../../mol-util/color/distinct';
 import { ModelIndexColorThemeProvider } from '../../../../mol-theme/color/model-index';
 import { Hcl } from '../../../../mol-util/color/spaces/hcl';

src/apps/viewer/extensions/cellpack/state.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin/state/objects';
+import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Task } from '../../../../mol-task';
 import { CellPack as _CellPack, Cell, CellPacking } from './data';

src/apps/viewer/index.ts

@@ -10,11 +10,11 @@ import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import './index.html'
 import './favicon.ico'
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginSpec } from '../../mol-plugin/spec';
 import { LoadCellPackModel } from './extensions/cellpack/model';
 import { StructureFromCellpack } from './extensions/cellpack/state';
-import { DownloadStructure } from '../../mol-plugin/state/actions/structure';
+import { DownloadStructure } from '../../mol-plugin-state/actions/structure';
 require('mol-plugin-ui/skin/light.scss')
 
 function getParam(name: string, regex: string): string {
@@ -60,7 +60,7 @@ async function trySetSnapshot(ctx: PluginContext) {
         const url = snapshotId
             ? `https://webchem.ncbr.muni.cz/molstar-state/get/${snapshotId}`
             : snapshotUrl;
-        await PluginCommands.State.Snapshots.Fetch.dispatch(ctx, { url })
+        await PluginCommands.State.Snapshots.Fetch(ctx, { url })
     } catch (e) {
         ctx.log.error('Failed to load snapshot.');
         console.warn('Failed to load snapshot', e);

src/examples/proteopedia-wrapper/index.ts

@@ -8,12 +8,12 @@ import * as ReactDOM from 'react-dom';
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import './index.html'
 import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/command';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { StructureRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
 import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin/state/objects';
-import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
+import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin-state/objects';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
 import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
 import { EvolutionaryConservation } from './annotation';
 import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo, StateElements } from './helpers';
@@ -192,7 +192,7 @@ class MolStarProteopediaWrapper {
     }
 
     private applyState(tree: StateBuilder) {
-        return PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        return PluginCommands.State.Update(this.plugin, { state: this.plugin.state.dataState, tree });
     }
 
     private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
@@ -208,7 +208,7 @@ class MolStarProteopediaWrapper {
         }
 
         if (loadType === 'full') {
-            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
+            await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref });
             const modelTree = this.model(this.download(state.build().toRoot(), url), format);
             await this.applyState(modelTree);
             const info = await this.doInfo(true);
@@ -232,32 +232,32 @@ class MolStarProteopediaWrapper {
         await this.updateStyle(representationStyle);
 
         this.loadedParams = { url, format, assemblyId };
-        Scheduler.setImmediate(() => PluginCommands.Camera.Reset.dispatch(this.plugin, { }));
+        Scheduler.setImmediate(() => PluginCommands.Camera.Reset(this.plugin, { }));
     }
 
     async updateStyle(style?: RepresentationStyle, partial?: boolean) {
         const tree = this.visual(style, partial);
         if (!tree) return;
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.dataState, tree });
     }
 
     setBackground(color: number) {
         if (!this.plugin.canvas3d) return;
         const renderer = this.plugin.canvas3d.props.renderer;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
     }
 
     toggleSpin() {
         if (!this.plugin.canvas3d) return;
         const trackball = this.plugin.canvas3d.props.trackball;
         const spinning = trackball.spin;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
-        if (!spinning) PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
+        if (!spinning) PluginCommands.Camera.Reset(this.plugin, { });
     }
 
     viewport = {
         setSettings: (settings?: Canvas3DProps) => {
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
+            PluginCommands.Canvas3D.SetSettings(this.plugin, {
                 settings: settings || DefaultCanvas3DParams
             });
         }
@@ -265,10 +265,10 @@ class MolStarProteopediaWrapper {
 
     camera = {
         toggleSpin: () => this.toggleSpin(),
-        resetPosition: () => PluginCommands.Camera.Reset.dispatch(this.plugin, { }),
+        resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { }),
         // setClip: (options?: { distance?: number, near?: number, far?: number }) => {
         //     if (!options) {
-        //         PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
+        //         PluginCommands.Canvas3D.SetSettings(this.plugin, {
         //             settings: {
         //                 cameraClipDistance: DefaultCanvas3DParams.cameraClipDistance,
         //                 clip: DefaultCanvas3DParams.clip
@@ -281,7 +281,7 @@ class MolStarProteopediaWrapper {
         //     const props = this.plugin.canvas3d.props;
         //     const clipNear = typeof options.near === 'undefined' ? props.clip[0] : options.near;
         //     const clipFar = typeof options.far === 'undefined' ? props.clip[1] : options.far;
-        //     PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, {
+        //     PluginCommands.Canvas3D.SetSettings(this.plugin, {
         //         settings: { cameraClipDistance: options.distance, clip: [clipNear, clipFar] }
         //     });
         // }
@@ -320,7 +320,7 @@ class MolStarProteopediaWrapper {
                 tree.to(StateElements.HetVisual).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
             }
 
-            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+            await PluginCommands.State.Update(this.plugin, { state, tree });
         }
     }
 
@@ -340,7 +340,7 @@ class MolStarProteopediaWrapper {
         remove: () => {
             const r = this.state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0];
             if (!r) return;
-            PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.state, ref: r.transform.ref });
+            PluginCommands.State.RemoveObject(this.plugin, { state: this.state, ref: r.transform.ref });
             if (this.experimentalDataElement) {
                 ReactDOM.unmountComponentAtNode(this.experimentalDataElement);
                 this.experimentalDataElement = void 0;
@@ -351,12 +351,12 @@ class MolStarProteopediaWrapper {
     hetGroups = {
         reset: () => {
             const update = this.state.build().delete(StateElements.HetGroupFocusGroup);
-            PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
-            PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+            PluginCommands.State.Update(this.plugin, { state: this.state, tree: update });
+            PluginCommands.Camera.Reset(this.plugin, { });
         },
         focusFirst: async (compId: string) => {
             if (!this.state.transforms.has(StateElements.Assembly)) return;
-            await PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+            await PluginCommands.Camera.Reset(this.plugin, { });
 
             // const asm = (this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure).data;
 
@@ -389,7 +389,7 @@ class MolStarProteopediaWrapper {
             //     }
             // });
 
-            await PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
+            await PluginCommands.State.Update(this.plugin, { state: this.state, tree: update });
 
             const focus = (this.state.select(StateElements.HetGroupFocus)[0].obj as PluginStateObject.Molecule.Structure).data;
             const sphere = focus.boundary.sphere;
@@ -399,7 +399,7 @@ class MolStarProteopediaWrapper {
             // Vec3.scaleAndAdd(position, sphere.center, position, sphere.radius);
             const radius = Math.max(sphere.radius, 5)
             const snapshot = this.plugin.canvas3d!.camera.getFocus(sphere.center, radius, radius);
-            PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, { snapshot, durationMs: 250 });
+            PluginCommands.Camera.SetSnapshot(this.plugin, { snapshot, durationMs: 250 });
         }
     }
 

src/mol-plugin/state/actions/data-format.ts → src/mol-plugin-state/actions/data-format.ts

@@ -4,16 +4,16 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginContext } from '../../../mol-plugin/context';
-import { State, StateBuilder, StateAction } from '../../../mol-state';
-import { Task } from '../../../mol-task';
-import { FileInfo, getFileInfo } from '../../../mol-util/file-info';
+import { PluginContext } from '../../mol-plugin/context';
+import { State, StateBuilder, StateAction } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { FileInfo, getFileInfo } from '../../mol-util/file-info';
 import { PluginStateObject } from '../objects';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Ccp4Provider, Dsn6Provider, DscifProvider } from './volume';
 import { StateTransforms } from '../transforms';
 import { MmcifProvider, PdbProvider, GroProvider, Provider3dg, DcdProvider, PsfProvider } from './structure';
-import msgpackDecode from '../../../mol-io/common/msgpack/decode'
+import msgpackDecode from '../../mol-io/common/msgpack/decode'
 import { PlyProvider } from './shape';
 
 export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> {

src/mol-plugin/state/actions/shape.ts → src/mol-plugin-state/actions/shape.ts

@@ -4,10 +4,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginContext } from '../../../mol-plugin/context';
-import { State, StateBuilder } from '../../../mol-state';
-import { Task } from '../../../mol-task';
-import { FileInfo } from '../../../mol-util/file-info';
+import { PluginContext } from '../../mol-plugin/context';
+import { State, StateBuilder } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { FileInfo } from '../../mol-util/file-info';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
 import { DataFormatProvider, DataFormatBuilderOptions } from './data-format';

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

@@ -5,18 +5,18 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginContext } from '../../../mol-plugin/context';
-import { StateAction, StateBuilder, StateSelection, StateTransformer, State } from '../../../mol-state';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateAction, StateBuilder, StateSelection, StateTransformer, State } from '../../mol-state';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
 import { Download, ParsePsf } from '../transforms/data';
 import { CustomModelProperties, StructureSelectionFromExpression, CustomStructureProperties, CoordinatesFromDcd, TrajectoryFromModelAndCoordinates, TopologyFromPsf } from '../transforms/model';
 import { DataFormatProvider, guessCifVariant, DataFormatBuilderOptions } from './data-format';
-import { FileInfo } from '../../../mol-util/file-info';
-import { Task } from '../../../mol-task';
-import { StructureElement } from '../../../mol-model/structure';
-import { createDefaultStructureComplex } from '../../util/structure-complex-helper';
+import { FileInfo } from '../../mol-util/file-info';
+import { Task } from '../../mol-task';
+import { StructureElement } from '../../mol-model/structure';
+import { createDefaultStructureComplex } from '../../mol-plugin/util/structure-complex-helper';
 import { ModelStructureRepresentation } from '../representation/model';
 
 export const MmcifProvider: DataFormatProvider<any> = {

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

@@ -5,13 +5,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeIsoValue } from '../../../mol-model/volume';
-import { PluginContext } from '../../../mol-plugin/context';
-import { State, StateAction, StateBuilder, StateTransformer } from '../../../mol-state';
-import { Task } from '../../../mol-task';
-import { ColorNames } from '../../../mol-util/color/names';
-import { FileInfo, getFileInfo } from '../../../mol-util/file-info';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { VolumeIsoValue } from '../../mol-model/volume';
+import { PluginContext } from '../../mol-plugin/context';
+import { State, StateAction, StateBuilder, StateTransformer } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { ColorNames } from '../../mol-util/color/names';
+import { FileInfo, getFileInfo } from '../../mol-util/file-info';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
 import { Download } from '../transforms/data';

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

@@ -7,10 +7,10 @@
 import { PluginStateAnimation } from './model';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
-import { StateSelection, StateTransform } from '../../../mol-state';
-import { PluginCommands } from '../../../mol-plugin/command';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { PluginContext } from '../../../mol-plugin/context';
+import { StateSelection, StateTransform } from '../../mol-state';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PluginContext } from '../../mol-plugin/context';
 
 export const AnimateModelIndex = PluginStateAnimation.create({
     name: 'built-in.animate-model-index',
@@ -79,7 +79,7 @@ export const AnimateModelIndex = PluginStateAnimation.create({
             });
         }
 
-        await PluginCommands.State.Update.dispatch(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
 
         if (allSingles || (params.mode.name === 'once' && isEnd)) return { kind: 'finished' };
         if (params.mode.name === 'palindrome') return { kind: 'next', state: { palindromeDirections } };
@@ -159,7 +159,7 @@ export const AnimateAssemblyUnwind = PluginStateAnimation.create({
             update.to(m).update({ t: newTime });
         }
 
-        await PluginCommands.State.Update.dispatch(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
 
         if (finished) return { kind: 'finished' };
         return { kind: 'next', state: { t: newTime } };
@@ -219,7 +219,7 @@ export const AnimateUnitsExplode = PluginStateAnimation.create({
             update.to(m).update({ t: newTime });
         }
 
-        await PluginCommands.State.Update.dispatch(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
 
         return { kind: 'next', state: { t: newTime } };
     }
@@ -269,7 +269,7 @@ export const AnimateStateInterpolation = PluginStateAnimation.create({
             }
         }
 
-        await PluginCommands.State.Update.dispatch(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
 
         return { kind: 'next', state: { } };
     }

src/mol-plugin/state/animation/helpers.ts → src/mol-plugin-state/animation/helpers.ts

@@ -4,10 +4,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { SymmetryOperator } from '../../../mol-math/geometry';
-import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
-import { Structure } from '../../../mol-model/structure';
-import { StructureUnitTransforms } from '../../../mol-model/structure/structure/util/unit-transforms';
+import { SymmetryOperator } from '../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { Structure } from '../../mol-model/structure';
+import { StructureUnitTransforms } from '../../mol-model/structure/structure/util/unit-transforms';
 
 const _unwindMatrix = Mat4.zero();
 export function unwindStructureAssembly(structure: Structure, unitTransforms: StructureUnitTransforms, t: number) {

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

@@ -4,10 +4,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginComponent } from '../../../mol-plugin/component';
-import { PluginContext } from '../../../mol-plugin/context';
+import { PluginComponent } from '../../mol-plugin/component';
+import { PluginContext } from '../../mol-plugin/context';
 import { PluginStateAnimation } from './model';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 
 export { PluginAnimationManager }
 

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

@@ -4,8 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { PluginContext } from '../../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PluginContext } from '../../mol-plugin/context';
 
 export { PluginStateAnimation }
 

src/mol-plugin/state/camera.ts → src/mol-plugin-state/camera.ts

@@ -4,10 +4,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Camera } from '../../mol-canvas3d/camera';
+import { Camera } from '../mol-canvas3d/camera';
 import { OrderedMap } from 'immutable';
-import { UUID } from '../../mol-util';
-import { PluginComponent } from '../../mol-plugin/component';
+import { UUID } from '../mol-util';
+import { PluginComponent } from '../mol-plugin/component';
 
 export { CameraSnapshotManager }
 

src/mol-plugin/state/manager/base.ts → src/mol-plugin-state/manager/base.ts

@@ -6,9 +6,9 @@
 
 // TODO: primites
 
-import { StateObject, State, StateObjectCell, StateBuilder, StateTransformer, StateTransform } from '../../../mol-state';
-import { RuntimeContext } from '../../../mol-task';
-import { PluginContext } from '../../context';
+import { StateObject, State, StateObjectCell, StateBuilder, StateTransformer, StateTransform } from '../../mol-state';
+import { RuntimeContext } from '../../mol-task';
+import { PluginContext } from '../../mol-plugin/context';
 
 export { StateAction, BuilderAction }
 

src/mol-plugin/state/manager/data.ts → src/mol-plugin-state/manager/data.ts

@@ -4,13 +4,13 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { StateTransformer, StateTransform, StateObjectSelector, StateObjectCell } from '../../../mol-state';
-import { PluginContext } from '../../context';
+import { StateTransformer, StateTransform, StateObjectSelector, StateObjectCell } from '../../mol-state';
+import { PluginContext } from '../../mol-plugin/context';
 import { Download, ReadFile } from '../transforms/data';
-import { getFileInfo } from '../../../mol-util/file-info';
+import { getFileInfo } from '../../mol-util/file-info';
 import { DataFormatProvider } from './data/provider';
 import { BuiltInDataFormats } from './data/formats';
-import { objectForEach } from '../../../mol-util/object';
+import { objectForEach } from '../../mol-util/object';
 
 export class DataManager {
     readonly formats: DataFormatProvider[] = [];

src/mol-plugin/state/manager/data/actions.ts → src/mol-plugin-state/manager/data/actions.ts

@@ -5,7 +5,7 @@
  */
 
 import { BuilderAction } from '../base';
-import { StateTransformer } from '../../../../mol-state';
+import { StateTransformer } from '../../../mol-state';
 import { Download as DownloadData, ReadFile } from '../../transforms/data';
 
 export const Download = BuilderAction((builder, params: StateTransformer.Params<DownloadData>, { options }) => {

src/mol-plugin/state/manager/data/formats.ts → src/mol-plugin-state/manager/data/formats.ts

@@ -5,8 +5,8 @@
  */
 
 import { DataFormatProvider } from './provider';
-import { PluginContext } from '../../../context';
-import { FileInfo } from '../../../../mol-util/file-info';
+import { PluginContext } from '../../../mol-plugin/context';
+import { FileInfo } from '../../../mol-util/file-info';
 import { StateTransforms } from '../../transforms';
 
 export const MmcifFormatProvider = DataFormatProvider({

src/mol-plugin/state/manager/data/provider.ts → src/mol-plugin-state/manager/data/provider.ts

@@ -4,11 +4,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginContext } from '../../../context';
-import { State, StateObjectCell } from '../../../../mol-state';
-import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { PluginContext } from '../../../mol-plugin/context';
+import { State, StateObjectCell } from '../../../mol-state';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginStateObject } from '../../objects';
-import { FileInfo } from '../../../../mol-util/file-info';
+import { FileInfo } from '../../../mol-util/file-info';
 
 export { DataFormatProvider }
 

src/mol-plugin/state/objects.ts → src/mol-plugin-state/objects.ts

@@ -5,25 +5,25 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CifFile } from '../../mol-io/reader/cif';
-import { PlyFile } from '../../mol-io/reader/ply/schema';
-import { Coordinates as _Coordinates } from '../../mol-model/structure';
-import { Topology as _Topology } from '../../mol-model/structure';
-import { Model as _Model, Structure as _Structure, StructureElement } from '../../mol-model/structure';
-import { VolumeData } from '../../mol-model/volume';
-import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-import { Representation } from '../../mol-repr/representation';
-import { StructureRepresentation, StructureRepresentationState } from '../../mol-repr/structure/representation';
-import { VolumeRepresentation } from '../../mol-repr/volume/representation';
-import { StateObject, StateTransformer } from '../../mol-state';
-import { Ccp4File } from '../../mol-io/reader/ccp4/schema';
-import { Dsn6File } from '../../mol-io/reader/dsn6/schema';
-import { ShapeRepresentation } from '../../mol-repr/shape/representation';
-import { Shape as _Shape } from '../../mol-model/shape';
-import { ShapeProvider } from '../../mol-model/shape/provider';
-import { File3DG } from '../../mol-io/reader/3dg/parser';
-import { DcdFile } from '../../mol-io/reader/dcd/parser';
-import { PsfFile } from '../../mol-io/reader/psf/parser';
+import { CifFile } from '../mol-io/reader/cif';
+import { PlyFile } from '../mol-io/reader/ply/schema';
+import { Coordinates as _Coordinates } from '../mol-model/structure';
+import { Topology as _Topology } from '../mol-model/structure';
+import { Model as _Model, Structure as _Structure, StructureElement } from '../mol-model/structure';
+import { VolumeData } from '../mol-model/volume';
+import { PluginBehavior } from '../mol-plugin/behavior/behavior';
+import { Representation } from '../mol-repr/representation';
+import { StructureRepresentation, StructureRepresentationState } from '../mol-repr/structure/representation';
+import { VolumeRepresentation } from '../mol-repr/volume/representation';
+import { StateObject, StateTransformer } from '../mol-state';
+import { Ccp4File } from '../mol-io/reader/ccp4/schema';
+import { Dsn6File } from '../mol-io/reader/dsn6/schema';
+import { ShapeRepresentation } from '../mol-repr/shape/representation';
+import { Shape as _Shape } from '../mol-model/shape';
+import { ShapeProvider } from '../mol-model/shape/provider';
+import { File3DG } from '../mol-io/reader/3dg/parser';
+import { DcdFile } from '../mol-io/reader/dcd/parser';
+import { PsfFile } from '../mol-io/reader/psf/parser';
 
 export type TypeClass = 'root' | 'data' | 'prop'
 

src/mol-plugin/state/representation/model.ts → src/mol-plugin-state/representation/model.ts

@@ -5,16 +5,16 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Model, Structure, StructureSymmetry } from '../../../mol-model/structure';
-import { stringToWords } from '../../../mol-util/string';
-import { SpacegroupCell, Spacegroup } from '../../../mol-math/geometry';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { RuntimeContext } from '../../../mol-task';
-import { PluginContext } from '../../context';
-import { Assembly, Symmetry } from '../../../mol-model/structure/model/properties/symmetry';
+import { Model, Structure, StructureSymmetry } from '../../mol-model/structure';
+import { stringToWords } from '../../mol-util/string';
+import { SpacegroupCell, Spacegroup } from '../../mol-math/geometry';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../mol-task';
+import { PluginContext } from '../../mol-plugin/context';
+import { Assembly, Symmetry } from '../../mol-model/structure/model/properties/symmetry';
 import { PluginStateObject as SO } from '../objects';
-import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 
 export namespace ModelStructureRepresentation {
     export function getParams(model?: Model, defaultValue?: 'deposited' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly') {

src/mol-plugin/state/representation/structure.ts → src/mol-plugin-state/representation/structure.ts

@@ -4,17 +4,17 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { arrayFind } from '../../../mol-data/util';
-import { Structure } from '../../../mol-model/structure';
-import { StateTransform, StateTree, StateSelection } from '../../../mol-state';
-import { Task } from '../../../mol-task';
-import { isProductionMode } from '../../../mol-util/debug';
-import { objectForEach } from '../../../mol-util/object';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { PluginContext } from '../../context';
+import { arrayFind } from '../../mol-data/util';
+import { Structure } from '../../mol-model/structure';
+import { StateTransform, StateTree, StateSelection } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { isProductionMode } from '../../mol-util/debug';
+import { objectForEach } from '../../mol-util/object';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PluginContext } from '../../mol-plugin/context';
 import { PresetStructureReprentations } from './structure/preset';
 import { StructureRepresentationProvider, RepresentationProviderTags } from './structure/provider';
-import { UniqueArray } from '../../../mol-data/generic';
+import { UniqueArray } from '../../mol-data/generic';
 
 // TODO: support quality
 // TODO: support ignore hydrogens

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

@@ -7,10 +7,10 @@
 import { StateTransforms } from '../../transforms';
 import { StructureComplexElementTypes } from '../../transforms/model';
 import { StructureRepresentation3DHelpers } from '../../transforms/representation';
-import { StructureSelectionQueries as Q } from '../../../util/structure-selection-helper';
-import { BuiltInStructureRepresentations } from '../../../../mol-repr/structure/registry';
+import { StructureSelectionQueries as Q } from '../../../mol-plugin/util/structure-selection-helper';
+import { BuiltInStructureRepresentations } from '../../../mol-repr/structure/registry';
 import { StructureRepresentationProvider, RepresentationProviderTags } from './provider';
-import { StateBuilder } from '../../../../mol-state';
+import { StateBuilder } from '../../../mol-state';
 import { PluginStateObject } from '../../objects';
 
 const auto = StructureRepresentationProvider({

src/mol-plugin/state/representation/structure/provider.ts → src/mol-plugin-state/representation/structure/provider.ts

@@ -4,11 +4,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginContext } from '../../../context';
-import { State, StateObjectCell } from '../../../../mol-state';
-import { RuntimeContext } from '../../../../mol-task';
-import { Structure } from '../../../../mol-model/structure';
-import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { PluginContext } from '../../../mol-plugin/context';
+import { State, StateObjectCell } from '../../../mol-state';
+import { RuntimeContext } from '../../../mol-task';
+import { Structure } from '../../../mol-model/structure';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginStateObject } from '../../objects';
 
 export interface StructureRepresentationProvider<P = any, S = {}> {

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

@@ -5,10 +5,10 @@
  */
 
 import { List } from 'immutable';
-import { UUID } from '../../mol-util';
-import { PluginState } from '../state';
-import { PluginComponent } from '../../mol-plugin/component';
-import { PluginContext } from '../../mol-plugin/context';
+import { UUID } from '../mol-util';
+import { PluginState } from '../mol-plugin/state';
+import { PluginComponent } from '../mol-plugin/component';
+import { PluginContext } from '../mol-plugin/context';
 
 export { PluginStateSnapshotManager }
 

src/mol-plugin/state/transforms/data.ts → src/mol-plugin-state/transforms/data.ts

@@ -7,16 +7,16 @@
 
 import { PluginStateTransform } from '../objects';
 import { PluginStateObject as SO } from '../objects';
-import { Task } from '../../../mol-task';
-import { CIF } from '../../../mol-io/reader/cif'
-import { PluginContext } from '../../../mol-plugin/context';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { StateTransformer } from '../../../mol-state';
-import { readFromFile, ajaxGetMany } from '../../../mol-util/data-source';
-import * as CCP4 from '../../../mol-io/reader/ccp4/parser'
-import * as DSN6 from '../../../mol-io/reader/dsn6/parser'
-import * as PLY from '../../../mol-io/reader/ply/parser'
-import { parsePsf } from '../../../mol-io/reader/psf/parser';
+import { Task } from '../../mol-task';
+import { CIF } from '../../mol-io/reader/cif'
+import { PluginContext } from '../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { StateTransformer } from '../../mol-state';
+import { readFromFile, ajaxGetMany } from '../../mol-util/data-source';
+import * as CCP4 from '../../mol-io/reader/ccp4/parser'
+import * as DSN6 from '../../mol-io/reader/dsn6/parser'
+import * as PLY from '../../mol-io/reader/ply/parser'
+import { parsePsf } from '../../mol-io/reader/psf/parser';
 
 export { Download }
 type Download = typeof Download

src/mol-plugin/state/transforms/helpers.ts → src/mol-plugin-state/transforms/helpers.ts

@@ -5,11 +5,11 @@
  */
 
 import { PluginStateObject } from '../objects';
-import { DistanceData } from '../../../mol-repr/shape/loci/distance';
-import { LabelData } from '../../../mol-repr/shape/loci/label';
-import { OrientationData } from '../../../mol-repr/shape/loci/orientation';
-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 { OrientationData } from '../../mol-repr/shape/loci/orientation';
+import { AngleData } from '../../mol-repr/shape/loci/angle';
+import { DihedralData } from '../../mol-repr/shape/loci/dihedral';
 
 export function getDistanceDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): DistanceData {
     const lociA = s[0].loci

src/mol-plugin/state/transforms/misc.ts → src/mol-plugin-state/transforms/misc.ts

@@ -4,9 +4,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { StateTransformer } from '../../../mol-state';
-import { shallowEqualObjects } from '../../../mol-util';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { StateTransformer } from '../../mol-state';
+import { shallowEqualObjects } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 
 export { CreateGroup };

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

@@ -5,32 +5,32 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { parsePDB } from '../../../mol-io/reader/pdb/parser';
-import { Vec3, Mat4, Quat } from '../../../mol-math/linear-algebra';
-import { trajectoryFromMmCIF } from '../../../mol-model-formats/structure/mmcif';
-import { trajectoryFromPDB } from '../../../mol-model-formats/structure/pdb';
-import { Model, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureElement, Coordinates, Topology } from '../../../mol-model/structure';
-import { PluginContext } from '../../../mol-plugin/context';
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-import Expression from '../../../mol-script/language/expression';
-import { StateObject, StateTransformer } from '../../../mol-state';
-import { RuntimeContext, Task } from '../../../mol-task';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { parsePDB } from '../../mol-io/reader/pdb/parser';
+import { Vec3, Mat4, Quat } from '../../mol-math/linear-algebra';
+import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
+import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
+import { Model, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureElement, Coordinates, Topology } from '../../mol-model/structure';
+import { PluginContext } from '../../mol-plugin/context';
+import { MolScriptBuilder } from '../../mol-script/language/builder';
+import Expression from '../../mol-script/language/expression';
+import { StateObject, StateTransformer } from '../../mol-state';
+import { RuntimeContext, Task } from '../../mol-task';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
-import { trajectoryFromGRO } from '../../../mol-model-formats/structure/gro';
-import { parseGRO } from '../../../mol-io/reader/gro/parser';
-import { shapeFromPly } from '../../../mol-model-formats/shape/ply';
-import { SymmetryOperator } from '../../../mol-math/geometry';
-import { Script } from '../../../mol-script/script';
-import { parse3DG } from '../../../mol-io/reader/3dg/parser';
-import { trajectoryFrom3DG } from '../../../mol-model-formats/structure/3dg';
-import { StructureSelectionQueries } from '../../util/structure-selection-helper';
-import { StructureQueryHelper } from '../../util/structure-query';
+import { trajectoryFromGRO } from '../../mol-model-formats/structure/gro';
+import { parseGRO } from '../../mol-io/reader/gro/parser';
+import { shapeFromPly } from '../../mol-model-formats/shape/ply';
+import { SymmetryOperator } from '../../mol-math/geometry';
+import { Script } from '../../mol-script/script';
+import { parse3DG } from '../../mol-io/reader/3dg/parser';
+import { trajectoryFrom3DG } from '../../mol-model-formats/structure/3dg';
+import { StructureSelectionQueries } from '../../mol-plugin/util/structure-selection-helper';
+import { StructureQueryHelper } from '../../mol-plugin/util/structure-query';
 import { ModelStructureRepresentation } from '../representation/model';
-import { parseDcd } from '../../../mol-io/reader/dcd/parser';
-import { coordinatesFromDcd } from '../../../mol-model-formats/structure/dcd';
-import { topologyFromPsf } from '../../../mol-model-formats/structure/psf';
-import { deepEqual } from '../../../mol-util';
+import { parseDcd } from '../../mol-io/reader/dcd/parser';
+import { coordinatesFromDcd } from '../../mol-model-formats/structure/dcd';
+import { topologyFromPsf } from '../../mol-model-formats/structure/psf';
+import { deepEqual } from '../../mol-util';
 
 export { CoordinatesFromDcd };
 export { TopologyFromPsf };

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

@@ -5,38 +5,38 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Structure, StructureElement } from '../../../mol-model/structure';
-import { VolumeData, VolumeIsoValue } from '../../../mol-model/volume';
-import { PluginContext } from '../../../mol-plugin/context';
-import { RepresentationProvider } from '../../../mol-repr/representation';
-import { BuiltInStructureRepresentationsName } from '../../../mol-repr/structure/registry';
-import { StructureParams } from '../../../mol-repr/structure/representation';
-import { BuiltInVolumeRepresentationsName } from '../../../mol-repr/volume/registry';
-import { VolumeParams } from '../../../mol-repr/volume/representation';
-import { StateTransformer, StateObject } from '../../../mol-state';
-import { Task } from '../../../mol-task';
-import { BuiltInColorThemeName, ColorTheme, BuiltInColorThemes } from '../../../mol-theme/color';
-import { BuiltInSizeThemeName, SizeTheme } from '../../../mol-theme/size';
-import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Structure, StructureElement } from '../../mol-model/structure';
+import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { PluginContext } from '../../mol-plugin/context';
+import { RepresentationProvider } from '../../mol-repr/representation';
+import { BuiltInStructureRepresentationsName } from '../../mol-repr/structure/registry';
+import { StructureParams } from '../../mol-repr/structure/representation';
+import { BuiltInVolumeRepresentationsName } from '../../mol-repr/volume/registry';
+import { VolumeParams } from '../../mol-repr/volume/representation';
+import { StateTransformer, StateObject } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { BuiltInColorThemeName, ColorTheme, BuiltInColorThemes } from '../../mol-theme/color';
+import { BuiltInSizeThemeName, SizeTheme } from '../../mol-theme/size';
+import { Theme, ThemeRegistryContext } from '../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
-import { ColorNames } from '../../../mol-util/color/names';
-import { ShapeRepresentation } from '../../../mol-repr/shape/representation';
-import { StructureUnitTransforms } from '../../../mol-model/structure/structure/util/unit-transforms';
+import { ColorNames } from '../../mol-util/color/names';
+import { ShapeRepresentation } from '../../mol-repr/shape/representation';
+import { StructureUnitTransforms } from '../../mol-model/structure/structure/util/unit-transforms';
 import { unwindStructureAssembly, explodeStructure } from '../animation/helpers';
-import { Color } from '../../../mol-util/color';
-import { Overpaint } from '../../../mol-theme/overpaint';
-import { Transparency } from '../../../mol-theme/transparency';
-import { BaseGeometry } from '../../../mol-geo/geometry/base';
-import { Script } from '../../../mol-script/script';
-import { getUnitcellRepresentation, UnitcellParams } from '../../util/model-unitcell';
-import { DistanceParams, DistanceRepresentation } from '../../../mol-repr/shape/loci/distance';
+import { Color } from '../../mol-util/color';
+import { Overpaint } from '../../mol-theme/overpaint';
+import { Transparency } from '../../mol-theme/transparency';
+import { BaseGeometry } from '../../mol-geo/geometry/base';
+import { Script } from '../../mol-script/script';
+import { getUnitcellRepresentation, UnitcellParams } from '../../mol-plugin/util/model-unitcell';
+import { DistanceParams, DistanceRepresentation } from '../../mol-repr/shape/loci/distance';
 import { getDistanceDataFromStructureSelections, getLabelDataFromStructureSelections, getOrientationDataFromStructureSelections, getAngleDataFromStructureSelections, getDihedralDataFromStructureSelections } from './helpers';
-import { LabelParams, LabelRepresentation } from '../../../mol-repr/shape/loci/label';
-import { OrientationRepresentation, OrientationParams } from '../../../mol-repr/shape/loci/orientation';
-import { AngleParams, AngleRepresentation } from '../../../mol-repr/shape/loci/angle';
-import { DihedralParams, DihedralRepresentation } from '../../../mol-repr/shape/loci/dihedral';
-import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { LabelParams, LabelRepresentation } from '../../mol-repr/shape/loci/label';
+import { OrientationRepresentation, OrientationParams } from '../../mol-repr/shape/loci/orientation';
+import { AngleParams, AngleRepresentation } from '../../mol-repr/shape/loci/angle';
+import { DihedralParams, DihedralRepresentation } from '../../mol-repr/shape/loci/dihedral';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 
 export { StructureRepresentation3D }
 export { StructureRepresentation3DHelpers }

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

@@ -5,13 +5,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CIF } from '../../../mol-io/reader/cif';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { volumeFromCcp4 } from '../../../mol-model-formats/volume/ccp4';
-import { volumeFromDensityServerData } from '../../../mol-model-formats/volume/density-server';
-import { volumeFromDsn6 } from '../../../mol-model-formats/volume/dsn6';
-import { Task } from '../../../mol-task';
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { CIF } from '../../mol-io/reader/cif';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { volumeFromCcp4 } from '../../mol-model-formats/volume/ccp4';
+import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
+import { volumeFromDsn6 } from '../../mol-model-formats/volume/dsn6';
+import { Task } from '../../mol-task';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 
 export { VolumeFromCcp4 };

src/mol-plugin-ui/camera.tsx

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginCommands } from '../mol-plugin/command';
+import { PluginCommands } from '../mol-plugin/commands';
 import * as React from 'react';
 import { PluginUIComponent } from './base';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
@@ -29,12 +29,12 @@ class CameraSnapshotControls extends PluginUIComponent<{ }, { name: string, desc
     state = PD.getDefaultValues(CameraSnapshotControls.Params);
 
     add = () => {
-        PluginCommands.Camera.Snapshots.Add.dispatch(this.plugin, this.state);
+        PluginCommands.Camera.Snapshots.Add(this.plugin, this.state);
         this.setState({ name: '', description: '' })
     }
 
     clear = () => {
-        PluginCommands.Camera.Snapshots.Clear.dispatch(this.plugin, {});
+        PluginCommands.Camera.Snapshots.Clear(this.plugin, {});
     }
 
     render() {
@@ -55,12 +55,12 @@ class CameraSnapshotList extends PluginUIComponent<{ }, { }> {
     }
 
     apply(id: string) {
-        return () => PluginCommands.Camera.Snapshots.Apply.dispatch(this.plugin, { id });
+        return () => PluginCommands.Camera.Snapshots.Apply(this.plugin, { id });
     }
 
     remove(id: string) {
         return () => {
-            PluginCommands.Camera.Snapshots.Remove.dispatch(this.plugin, { id });
+            PluginCommands.Camera.Snapshots.Remove(this.plugin, { id });
         }
     }
 

src/mol-plugin-ui/controls.tsx

@@ -6,15 +6,15 @@
  */
 
 import * as React from 'react';
-import { PluginCommands } from '../mol-plugin/command';
-import { UpdateTrajectory } from '../mol-plugin/state/actions/structure';
+import { PluginCommands } from '../mol-plugin/commands';
+import { UpdateTrajectory } from '../mol-plugin-state/actions/structure';
 import { PluginUIComponent } from './base';
 import { LociLabelEntry } from '../mol-plugin/util/loci-label-manager';
 import { IconButton, Icon } from './controls/common';
-import { PluginStateObject } from '../mol-plugin/state/objects';
-import { StateTransforms } from '../mol-plugin/state/transforms';
+import { PluginStateObject } from '../mol-plugin-state/objects';
+import { StateTransforms } from '../mol-plugin-state/transforms';
 import { StateTransformer } from '../mol-state';
-import { ModelFromTrajectory } from '../mol-plugin/state/transforms/model';
+import { ModelFromTrajectory } from '../mol-plugin-state/transforms/model';
 import { AnimationControls } from './state/animation';
 import { StructureRepresentationControls } from './structure/representation';
 import { StructureSelectionControls } from './structure/selection';
@@ -62,17 +62,17 @@ export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: bo
         this.subscribe(this.plugin.behaviors.state.isAnimating, this.update);
     }
 
-    reset = () => PluginCommands.State.ApplyAction.dispatch(this.plugin, {
+    reset = () => PluginCommands.State.ApplyAction(this.plugin, {
         state: this.plugin.state.dataState,
         action: UpdateTrajectory.create({ action: 'reset' })
     });
 
-    prev = () => PluginCommands.State.ApplyAction.dispatch(this.plugin, {
+    prev = () => PluginCommands.State.ApplyAction(this.plugin, {
         state: this.plugin.state.dataState,
         action: UpdateTrajectory.create({ action: 'advance', by: -1 })
     });
 
-    next = () => PluginCommands.State.ApplyAction.dispatch(this.plugin, {
+    next = () => PluginCommands.State.ApplyAction(this.plugin, {
         state: this.plugin.state.dataState,
         action: UpdateTrajectory.create({ action: 'advance', by: 1 })
     });
@@ -146,7 +146,7 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
 
     async update(id: string) {
         this.setState({ isBusy: true });
-        await PluginCommands.State.Snapshots.Apply.dispatch(this.plugin, { id });
+        await PluginCommands.State.Snapshots.Apply(this.plugin, { id });
         this.setState({ isBusy: false });
     }
 

src/mol-plugin-ui/left-panel.tsx

@@ -10,7 +10,7 @@ import { StateTree } from './state/tree';
 import { IconButton, SectionHeader } from './controls/common';
 import { StateObjectActions } from './state/actions';
 import { StateTransform } from '../mol-state';
-import { PluginCommands } from '../mol-plugin/command';
+import { PluginCommands } from '../mol-plugin/commands';
 import { ParameterControls } from './controls/parameters';
 import { Canvas3DParams } from '../mol-canvas3d/canvas3d';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
@@ -35,7 +35,7 @@ export class LeftPanelControls extends PluginUIComponent<{}, { tab: LeftPanelTab
     set = (tab: LeftPanelTabName) => {
         if (this.state.tab === tab) {
             this.setState({ tab: 'none' }, () => this.plugin.behaviors.layout.leftPanelTabName.next('none'));
-            PluginCommands.Layout.Update.dispatch(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'collapsed' } } });
+            PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'collapsed' } } });
             return;
         }
 
@@ -46,7 +46,7 @@ export class LeftPanelControls extends PluginUIComponent<{}, { tab: LeftPanelTab
 
         this.setState({ tab }, () => this.plugin.behaviors.layout.leftPanelTabName.next(tab));
         if (this.plugin.layout.state.regionState.left !== 'full') {
-            PluginCommands.Layout.Update.dispatch(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'full' } } });
+            PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'full' } } });
         }
     }
 
@@ -121,7 +121,7 @@ class DataIcon extends PluginUIComponent<{ set: (tab: LeftPanelTabName) => void
 
 class FullSettings extends PluginUIComponent {
     private setSettings = (p: { param: PD.Base<any>, name: string, value: any }) => {
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { [p.name]: p.value } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { [p.name]: p.value } });
     }
 
     componentDidMount() {
@@ -159,7 +159,7 @@ export class RemoveAllButton extends PluginUIComponent<{ }> {
 
     remove = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
-        PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
+        PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
     }
 
     render() {

src/mol-plugin-ui/sequence.tsx

@@ -7,7 +7,7 @@
 
 import * as React from 'react'
 import { PluginUIComponent } from './base';
-import { PluginStateObject as PSO } from '../mol-plugin/state/objects';
+import { PluginStateObject as PSO } from '../mol-plugin-state/objects';
 import { Sequence } from './sequence/sequence';
 import { Structure, StructureElement, StructureProperties as SP, Unit } from '../mol-model/structure';
 import { SequenceWrapper } from './sequence/wrapper';

src/mol-plugin-ui/state/apply-action.tsx

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
 import { State, StateTransform, StateAction } from '../../mol-state';
 import { memoizeLatest } from '../../mol-util/memoize';
@@ -35,7 +35,7 @@ namespace ApplyActionControl {
 
 class ApplyActionControl extends TransformControlBase<ApplyActionControl.Props, ApplyActionControl.ComponentState> {
     applyAction() {
-        return PluginCommands.State.ApplyAction.dispatch(this.plugin, {
+        return PluginCommands.State.ApplyAction(this.plugin, {
             state: this.props.state,
             action: this.props.action.create(this.state.params),
             ref: this.props.nodeRef

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

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import * as React from 'react';
 import { PluginUIComponent, PurePluginUIComponent } from '../base';
 import { shallowEqualObjects } from '../../mol-util';
@@ -19,13 +19,13 @@ import { PluginConfig } from '../../mol-plugin/config';
 
 export class StateSnapshots extends PluginUIComponent<{ }> {
     downloadToFile = () => {
-        PluginCommands.State.Snapshots.DownloadToFile.dispatch(this.plugin, { });
+        PluginCommands.State.Snapshots.DownloadToFile(this.plugin, { });
     }
 
     open = (e: React.ChangeEvent<HTMLInputElement>) => {
         if (!e.target.files || !e.target.files![0]) return;
 
-        PluginCommands.State.Snapshots.OpenFile.dispatch(this.plugin, { file: e.target.files![0] });
+        PluginCommands.State.Snapshots.OpenFile(this.plugin, { file: e.target.files![0] });
     }
 
     render() {
@@ -60,7 +60,7 @@ class LocalStateSnapshots extends PluginUIComponent<
     };
 
     add = () => {
-        PluginCommands.State.Snapshots.Add.dispatch(this.plugin, {
+        PluginCommands.State.Snapshots.Add(this.plugin, {
             name: this.state.params.name,
             description: this.state.params.options.description,
             params: this.state.params.options
@@ -77,7 +77,7 @@ class LocalStateSnapshots extends PluginUIComponent<
     }
 
     clear = () => {
-        PluginCommands.State.Snapshots.Clear.dispatch(this.plugin, {});
+        PluginCommands.State.Snapshots.Clear(this.plugin, {});
     }
 
     shouldComponentUpdate(nextProps: any, nextState: any) {
@@ -111,31 +111,31 @@ class LocalStateSnapshotList extends PluginUIComponent<{ }, { }> {
     apply = (e: React.MouseEvent<HTMLElement>) => {
         const id = e.currentTarget.getAttribute('data-id');
         if (!id) return;
-        PluginCommands.State.Snapshots.Apply.dispatch(this.plugin, { id });
+        PluginCommands.State.Snapshots.Apply(this.plugin, { id });
     }
 
     remove = (e: React.MouseEvent<HTMLElement>) => {
         const id = e.currentTarget.getAttribute('data-id');
         if (!id) return;
-        PluginCommands.State.Snapshots.Remove.dispatch(this.plugin, { id });
+        PluginCommands.State.Snapshots.Remove(this.plugin, { id });
     }
 
     moveUp = (e: React.MouseEvent<HTMLElement>) => {
         const id = e.currentTarget.getAttribute('data-id');
         if (!id) return;
-        PluginCommands.State.Snapshots.Move.dispatch(this.plugin, { id, dir: -1 });
+        PluginCommands.State.Snapshots.Move(this.plugin, { id, dir: -1 });
     }
 
     moveDown = (e: React.MouseEvent<HTMLElement>) => {
         const id = e.currentTarget.getAttribute('data-id');
         if (!id) return;
-        PluginCommands.State.Snapshots.Move.dispatch(this.plugin, { id, dir: 1 });
+        PluginCommands.State.Snapshots.Move(this.plugin, { id, dir: 1 });
     }
 
     replace = (e: React.MouseEvent<HTMLElement>) => {
         const id = e.currentTarget.getAttribute('data-id');
         if (!id) return;
-        PluginCommands.State.Snapshots.Replace.dispatch(this.plugin, { id, params: this.plugin.state.snapshots.currentGetSnapshotParams });
+        PluginCommands.State.Snapshots.Replace(this.plugin, { id, params: this.plugin.state.snapshots.currentGetSnapshotParams });
     }
 
     render() {
@@ -224,14 +224,14 @@ export class RemoteStateSnapshots extends PluginUIComponent<
         this.plugin.config.set(PluginConfig.State.CurrentServer, this.state.params.options.serverUrl);
 
         if (this.plugin.state.snapshots.state.entries.size === 0) {
-            await PluginCommands.State.Snapshots.Add.dispatch(this.plugin, {
+            await PluginCommands.State.Snapshots.Add(this.plugin, {
                 name: this.state.params.name,
                 description: this.state.params.options.description,
                 params: this.plugin.state.snapshots.currentGetSnapshotParams
             });
         }
 
-        await PluginCommands.State.Snapshots.Upload.dispatch(this.plugin, {
+        await PluginCommands.State.Snapshots.Upload(this.plugin, {
             name: this.state.params.name,
             description: this.state.params.options.description,
             playOnLoad: this.state.params.options.playOnLoad,
@@ -250,7 +250,7 @@ export class RemoteStateSnapshots extends PluginUIComponent<
 
         this.setState({ isBusy: true });
         try {
-            await PluginCommands.State.Snapshots.Fetch.dispatch(this.plugin, { url: entry.url });
+            await PluginCommands.State.Snapshots.Fetch(this.plugin, { url: entry.url });
         } finally {
             this.setState({ isBusy: false });
         }

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

@@ -5,9 +5,9 @@
  */
 
 import * as React from 'react';
-import { PluginStateObject } from '../../mol-plugin/state/objects';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { State, StateObject, StateTransform, StateObjectCell } from '../../mol-state'
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginUIComponent, _Props, _State } from '../base';
 import { Icon } from '../controls/common';
 
@@ -165,41 +165,41 @@ class StateTreeNodeLabel extends PluginUIComponent<
     setCurrent = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
         e.currentTarget.blur();
-        PluginCommands.State.SetCurrentObject.dispatch(this.plugin, { state: this.props.cell.parent, ref: this.ref });
+        PluginCommands.State.SetCurrentObject(this.plugin, { state: this.props.cell.parent, ref: this.ref });
     }
 
     setCurrentRoot = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
         e.currentTarget.blur();
-        PluginCommands.State.SetCurrentObject.dispatch(this.plugin, { state: this.props.cell.parent, ref: StateTransform.RootRef });
+        PluginCommands.State.SetCurrentObject(this.plugin, { state: this.props.cell.parent, ref: StateTransform.RootRef });
     }
 
     remove = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
-        PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.props.cell.parent, ref: this.ref, removeParentGhosts: true });
+        PluginCommands.State.RemoveObject(this.plugin, { state: this.props.cell.parent, ref: this.ref, removeParentGhosts: true });
     }
 
     toggleVisible = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
-        PluginCommands.State.ToggleVisibility.dispatch(this.plugin, { state: this.props.cell.parent, ref: this.ref });
+        PluginCommands.State.ToggleVisibility(this.plugin, { state: this.props.cell.parent, ref: this.ref });
         e.currentTarget.blur();
     }
 
     toggleExpanded = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
-        PluginCommands.State.ToggleExpanded.dispatch(this.plugin, { state: this.props.cell.parent, ref: this.ref });
+        PluginCommands.State.ToggleExpanded(this.plugin, { state: this.props.cell.parent, ref: this.ref });
         e.currentTarget.blur();
     }
 
     highlight = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
-        PluginCommands.State.Highlight.dispatch(this.plugin, { state: this.props.cell.parent, ref: this.ref });
+        PluginCommands.State.Highlight(this.plugin, { state: this.props.cell.parent, ref: this.ref });
         e.currentTarget.blur();
     }
 
     clearHighlight = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
-        PluginCommands.State.ClearHighlight.dispatch(this.plugin, { state: this.props.cell.parent, ref: this.ref });
+        PluginCommands.State.ClearHighlight(this.plugin, { state: this.props.cell.parent, ref: this.ref });
         e.currentTarget.blur();
     }
 

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

@@ -15,7 +15,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { VisualQuality, VisualQualityOptions } from '../../mol-geo/geometry/base';
 import { CollapsableControls } from '../base';
 import { StateSelection, StateObject } from '../../mol-state';
-import { PluginStateObject } from '../../mol-plugin/state/objects';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { ColorOptions } from '../controls/color';
 
 interface BaseStructureRepresentationControlsState {

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

@@ -8,7 +8,7 @@
 import * as React from 'react';
 import { CollapsableControls, CollapsableState } from '../base';
 import { StructureSelectionQuery, SelectionModifier, StructureSelectionQueryList } from '../../mol-plugin/util/structure-selection-helper';
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Interactivity } from '../../mol-plugin/util/interactivity';
 import { ParameterControls } from '../controls/parameters';
@@ -107,7 +107,7 @@ export class StructureSelectionControls<P, S extends StructureSelectionControlsS
 
     setProps = (p: { param: PD.Base<any>, name: string, value: any }) => {
         if (p.name === 'granularity') {
-            PluginCommands.Interactivity.SetProps.dispatch(this.plugin, { props: { granularity: p.value } });
+            PluginCommands.Interactivity.SetProps(this.plugin, { props: { granularity: p.value } });
         }
     }
 

src/mol-plugin-ui/toast.tsx

@@ -8,7 +8,7 @@
 
 import * as React from 'react';
 import { PluginUIComponent } from './base';
-import { PluginToastManager } from '../mol-plugin/state/toast';
+import { PluginToastManager } from '../mol-plugin/util/toast';
 import { IconButton } from './controls/common';
 
 class ToastEntry extends PluginUIComponent<{ entry: PluginToastManager.Entry }> {

src/mol-plugin-ui/viewport.tsx

@@ -7,7 +7,7 @@
 
 import * as React from 'react';
 import { resizeCanvas } from '../mol-canvas3d/util';
-import { PluginCommands } from '../mol-plugin/command';
+import { PluginCommands } from '../mol-plugin/commands';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { PluginUIComponent } from './base';
 import { ControlGroup, IconButton } from './controls/common';
@@ -31,7 +31,7 @@ export class ViewportControls extends PluginUIComponent<ViewportControlsProps, V
     state = { ...this.allCollapsedState } as ViewportControlsState;
 
     resetCamera = () => {
-        PluginCommands.Camera.Reset.dispatch(this.plugin, {});
+        PluginCommands.Camera.Reset(this.plugin, {});
     }
 
     private toggle(panel: keyof ViewportControlsState) {
@@ -45,23 +45,23 @@ export class ViewportControls extends PluginUIComponent<ViewportControlsProps, V
     toggleScreenshotExpanded = this.toggle('isScreenshotExpanded');
 
     toggleControls = () => {
-        PluginCommands.Layout.Update.dispatch(this.plugin, { state: { showControls: !this.plugin.layout.state.showControls } });
+        PluginCommands.Layout.Update(this.plugin, { state: { showControls: !this.plugin.layout.state.showControls } });
     }
 
     toggleExpanded = () => {
-        PluginCommands.Layout.Update.dispatch(this.plugin, { state: { isExpanded: !this.plugin.layout.state.isExpanded } });
+        PluginCommands.Layout.Update(this.plugin, { state: { isExpanded: !this.plugin.layout.state.isExpanded } });
     }
 
     setSettings = (p: { param: PD.Base<any>, name: string, value: any }) => {
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { [p.name]: p.value } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { [p.name]: p.value } });
     }
 
     setLayout = (p: { param: PD.Base<any>, name: string, value: any }) => {
-        PluginCommands.Layout.Update.dispatch(this.plugin, { state: { [p.name]: p.value } });
+        PluginCommands.Layout.Update(this.plugin, { state: { [p.name]: p.value } });
     }
 
     setInteractivityProps = (p: { param: PD.Base<any>, name: string, value: any }) => {
-        PluginCommands.Interactivity.SetProps.dispatch(this.plugin, { props: { [p.name]: p.value } });
+        PluginCommands.Interactivity.SetProps(this.plugin, { props: { [p.name]: p.value } });
     }
 
     screenshot = () => {

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

@@ -7,7 +7,7 @@
 
 import * as React from 'react';
 import { Canvas3DParams } from '../../mol-canvas3d/canvas3d';
-import { PluginCommands } from '../../mol-plugin/command';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { ColorNames } from '../../mol-util/color/names';
 import { ParameterMappingControl } from '../controls/parameters';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -97,6 +97,6 @@ const SimpleSettingsMapping = ParamMapping({
         t.cameraClipFar = s.clipFar;
     },
     apply(settings, ctx) {
-        return PluginCommands.Canvas3D.SetSettings.dispatch(ctx, { settings });
+        return PluginCommands.Canvas3D.SetSettings(ctx, { settings });
     }
 })

src/mol-plugin/behavior/behavior.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginStateTransform, PluginStateObject } from '../state/objects';
+import { PluginStateTransform, PluginStateObject } from '../../mol-plugin-state/objects';
 import { StateTransformer, StateTransform } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { PluginContext } from '../../mol-plugin/context';

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

@@ -10,7 +10,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../behavior';
 import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
 import { Binding } from '../../../mol-util/binding';
-import { PluginCommands } from '../../command';
+import { PluginCommands } from '../../commands';
 
 const B = ButtonsType
 const M = ModifiersKeys
@@ -42,7 +42,7 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
                 if (Binding.match(this.params.bindings.clickCenterFocus, button, modifiers)) {
                     const loci = Loci.normalize(current.loci, this.ctx.interactivity.props.granularity)
                     if (Loci.isEmpty(loci)) {
-                        PluginCommands.Camera.Reset.dispatch(this.ctx, { })
+                        PluginCommands.Camera.Reset(this.ctx, { })
                     } else {
                         const sphere = Loci.getBoundingSphere(loci);
                         if (sphere) {

src/mol-plugin/behavior/dynamic/custom-props/computed/interactions.ts

@@ -9,7 +9,7 @@ import { ParamDefinition as PD } from '../../../../../mol-util/param-definition'
 import { InteractionsProvider } from '../../../../../mol-model-props/computed/interactions';
 import { Structure } from '../../../../../mol-model/structure';
 import { StateSelection } from '../../../../../mol-state';
-import { PluginStateObject } from '../../../../state/objects';
+import { PluginStateObject } from '../../../../../mol-plugin-state/objects';
 import StructureElement from '../../../../../mol-model/structure/structure/element';
 import { OrderedSet } from '../../../../../mol-data/int';
 import { featureGroupLabel, featureTypeLabel } from '../../../../../mol-model-props/computed/interactions/common';

src/mol-plugin/behavior/dynamic/custom-props/computed/valence-model.ts

@@ -8,7 +8,7 @@ import { PluginBehavior } from '../../../behavior';
 import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
 import { ValenceModelProvider } from '../../../../../mol-model-props/computed/valence-model';
 import { Loci } from '../../../../../mol-model/loci';
-import { PluginStateObject } from '../../../../state/objects';
+import { PluginStateObject } from '../../../../../mol-plugin-state/objects';
 import { StateSelection } from '../../../../../mol-state';
 import { Structure, StructureElement } from '../../../../../mol-model/structure';
 import { OrderedSet } from '../../../../../mol-data/int';

src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts

@@ -9,7 +9,7 @@ import { AssemblySymmetryProvider, AssemblySymmetry, getSymmetrySelectParam } fr
 import { PluginBehavior } from '../../../behavior';
 import { AssemblySymmetryParams, AssemblySymmetryRepresentation } from '../../../../../mol-model-props/rcsb/representations/assembly-symmetry';
 import { AssemblySymmetryClusterColorThemeProvider } from '../../../../../mol-model-props/rcsb/themes/assembly-symmetry-cluster';
-import { PluginStateTransform, PluginStateObject } from '../../../../state/objects';
+import { PluginStateTransform, PluginStateObject } from '../../../../../mol-plugin-state/objects';
 import { Task } from '../../../../../mol-task';
 import { PluginContext } from '../../../../context';
 import { StateTransformer, StateAction, StateObject } from '../../../../../mol-state';

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

@@ -7,7 +7,7 @@
 
 import { MarkerAction } from '../../../mol-util/marker-action';
 import { PluginContext } from '../../../mol-plugin/context';
-import { PluginStateObject as SO } from '../../state/objects';
+import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
 import { lociLabel } from '../../../mol-theme/label';
 import { PluginBehavior } from '../behavior';
 import { Interactivity } from '../../util/interactivity';

src/mol-plugin/behavior/dynamic/selection/structure-representation-interaction.ts

@@ -7,10 +7,10 @@
 
 import { Structure, StructureElement, Bond } from '../../../../mol-model/structure';
 import { PluginBehavior } from '../../../../mol-plugin/behavior';
-import { PluginCommands } from '../../../../mol-plugin/command';
-import { PluginStateObject } from '../../../../mol-plugin/state/objects';
-import { StateTransforms } from '../../../../mol-plugin/state/transforms';
-import { StructureRepresentation3DHelpers } from '../../../../mol-plugin/state/transforms/representation';
+import { PluginCommands } from '../../../commands';
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
+import { StateTransforms } from '../../../../mol-plugin-state/transforms';
+import { StructureRepresentation3DHelpers } from '../../../../mol-plugin-state/transforms/representation';
 import { BuiltInStructureRepresentations } from '../../../../mol-repr/structure/registry';
 import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
 import { StateObjectCell, StateSelection, StateTransform } from '../../../../mol-state';
@@ -129,7 +129,7 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
             if (surr) update.to(surr).update(StateTransforms.Model.StructureSelectionFromExpression, old => ({ ...old, expression }));
         }
 
-        PluginCommands.State.Update.dispatch(this.plugin, { state, tree: update, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
+        PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
     }
 
     register(ref: string): void {
@@ -197,7 +197,7 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
                 builder.to(refs[Tags.ResidueSel]!).update(StateTransforms.Model.StructureSelectionFromBundle, old => ({ ...old, bundle: residueBundle }));
                 builder.to(refs[Tags.SurrSel]!).update(StateTransforms.Model.StructureSelectionFromExpression, old => ({ ...old, expression: surroundings }));
 
-                PluginCommands.State.Update.dispatch(this.plugin, { state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
+                PluginCommands.State.Update(this.plugin, { state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
             }
         });
     }

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

@@ -6,7 +6,7 @@
  */
 
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { PluginStateObject } from '../../../state/objects';
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
 import { VolumeIsoValue, VolumeData } from '../../../../mol-model/volume';
 import { createIsoValueParam } from '../../../../mol-repr/volume/isosurface';
 import { VolumeServerHeader, VolumeServerInfo } from './model';
@@ -18,7 +18,7 @@ import { LRUCache } from '../../../../mol-util/lru-cache';
 import { urlCombine } from '../../../../mol-util/url';
 import { CIF } from '../../../../mol-io/reader/cif';
 import { volumeFromDensityServerData } from '../../../../mol-model-formats/volume/density-server';
-import { PluginCommands } from '../../../command';
+import { PluginCommands } from '../../../commands';
 import { StateSelection } from '../../../../mol-state';
 import { Representation } from '../../../../mol-repr/representation';
 import { ButtonsType, ModifiersKeys } from '../../../../mol-util/input/input-observer';
@@ -222,7 +222,7 @@ export namespace VolumeStreaming {
             };
             const update = state.build().to(this.ref).update(newParams);
 
-            PluginCommands.State.Update.dispatch(this.plugin, { state, tree: update, options: { doNotUpdateCurrent: true } });
+            PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotUpdateCurrent: true } });
         }
 
         private getStructureRoot() {

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginStateObject } from '../../../state/objects';
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
 import { VolumeIsoValue } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginStateObject as SO, PluginStateTransform } from '../../../state/objects';
+import { PluginStateObject as SO, PluginStateTransform } from '../../../../mol-plugin-state/objects';
 import { VolumeServerInfo, VolumeServerHeader } from './model';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Task } from '../../../../mol-task';
@@ -16,7 +16,7 @@ import { VolumeIsoValue } from '../../../../mol-model/volume';
 import { StateAction, StateObject, StateTransformer } from '../../../../mol-state';
 import { getStreamingMethod, getIds, getContourLevel, getEmdbIds } from './util';
 import { VolumeStreaming } from './behavior';
-import { VolumeRepresentation3DHelpers } from '../../../../mol-plugin/state/transforms/representation';
+import { VolumeRepresentation3DHelpers } from '../../../../mol-plugin-state/transforms/representation';
 import { BuiltInVolumeRepresentations } from '../../../../mol-repr/volume/registry';
 import { Theme } from '../../../../mol-theme/theme';
 import { Box3D } from '../../../../mol-math/geometry';

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

@@ -5,8 +5,8 @@
  */
 
 import { PluginContext } from '../../../mol-plugin/context';
-import { PluginCommands } from '../../../mol-plugin/command';
-import { CameraSnapshotManager } from '../../../mol-plugin/state/camera';
+import { PluginCommands } from '../../commands';
+import { CameraSnapshotManager } from '../../../mol-plugin-state/camera';
 
 export function registerDefault(ctx: PluginContext) {
     Reset(ctx);
@@ -42,6 +42,6 @@ export function Snapshots(ctx: PluginContext) {
 
     PluginCommands.Camera.Snapshots.Apply.subscribe(ctx, ({ id }) => {
         const e = ctx.state.cameraSnapshots.getEntry(id);
-        return PluginCommands.Camera.SetSnapshot.dispatch(ctx, { snapshot: e.snapshot, durationMs: 200 });
+        return PluginCommands.Camera.SetSnapshot(ctx, { snapshot: e.snapshot, durationMs: 200 });
     });
 }

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

@@ -6,7 +6,7 @@
  */
 
 import { PluginContext } from '../../../mol-plugin/context';
-import { PluginCommands } from '../../../mol-plugin/command';
+import { PluginCommands } from '../../commands';
 
 export function registerDefault(ctx: PluginContext) {
     Canvas3DSetSettings(ctx);

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

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { PluginStateObject as SO } from '../../state/objects';
+import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
 import { PluginContext } from '../../../mol-plugin/context';
 import { Representation } from '../../../mol-repr/representation';
 import { StateObjectCell } from '../../../mol-state';

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

@@ -5,11 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginCommands } from '../../command';
+import { PluginCommands } from '../../commands';
 import { PluginContext } from '../../context';
 import { StateTree, StateTransform, State } from '../../../mol-state';
-import { PluginStateSnapshotManager } from '../../../mol-plugin/state/snapshots';
-import { PluginStateObject as SO } from '../../state/objects';
+import { PluginStateSnapshotManager } from '../../../mol-plugin-state/snapshots';
+import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
 import { getFormattedTime } from '../../../mol-util/date';
 import { readFromFile } from '../../../mol-util/data-source';
 import { download } from '../../../mol-util/download';

src/mol-plugin/command.ts

@@ -4,71 +4,100 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Camera } from '../mol-canvas3d/camera';
-import { PluginCommand } from './command/base';
-import { StateTransform, State, StateAction } from '../mol-state';
-import { Canvas3DProps } from '../mol-canvas3d/canvas3d';
-import { PluginLayoutStateProps } from './layout';
-import { StructureElement } from '../mol-model/structure';
-import { PluginState } from './state';
-import { Interactivity } from './util/interactivity';
-import { PluginToast } from './state/toast';
-
-export * from './command/base';
-
-export const PluginCommands = {
-    State: {
-        SetCurrentObject: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
-        ApplyAction: PluginCommand<{ state: State, action: StateAction.Instance, ref?: StateTransform.Ref }>(),
-        Update: PluginCommand<{ state: State, tree: State.Tree | State.Builder, options?: Partial<State.UpdateOptions> }>(),
-
-        RemoveObject: PluginCommand<{ state: State, ref: StateTransform.Ref, removeParentGhosts?: boolean }>(),
-
-        ToggleExpanded: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
-        ToggleVisibility: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
-        Highlight: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
-        ClearHighlight: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
-
-        Snapshots: {
-            Add: PluginCommand<{ name?: string, description?: string, params?: PluginState.GetSnapshotParams }>(),
-            Replace: PluginCommand<{ id: string, params?: PluginState.GetSnapshotParams }>(),
-            Move: PluginCommand<{ id: string, dir: -1 | 1 }>(),
-            Remove: PluginCommand<{ id: string }>(),
-            Apply: PluginCommand<{ id: string }>(),
-            Clear: PluginCommand<{}>(),
-
-            Upload: PluginCommand<{ name?: string, description?: string, playOnLoad?: boolean, serverUrl: string }>(),
-            Fetch: PluginCommand<{ url: string }>(),
-
-            DownloadToFile: PluginCommand<{ name?: string }>(),
-            OpenFile: PluginCommand<{ file: File }>(),
+import { PluginContext } from './context';
+import { UUID } from '../mol-util';
+
+export { PluginCommand, PluginCommandManager }
+
+interface PluginCommand<T = unknown> {
+    (ctx: PluginContext, params?: T): Promise<void>,
+    readonly id: UUID,
+    subscribe(ctx: PluginContext, action: PluginCommand.Action<T>): PluginCommand.Subscription
+}
+
+function PluginCommand<T>(): PluginCommand<T> {
+    const ret: PluginCommand<T> = ((ctx, params) => ctx.commands.dispatch(ret, params || {} as any)) as PluginCommand<T>;
+    ret.subscribe = (ctx, action) => ctx.commands.subscribe(ret, action);
+    (ret.id as UUID) = UUID.create22();
+
+    return ret;
+}
+
+namespace PluginCommand {
+    export type Id = string & { '@type': 'plugin-command-id' }
+
+    export interface Subscription {
+        unsubscribe(): void
+    }
+
+    export type Action<T> = (params: T) => unknown | Promise<unknown>
+}
+
+type Instance = { cmd: PluginCommand<any>, params: any, resolve: () => void, reject: (e: any) => void }
+class PluginCommandManager {
+    private subs = new Map<string, PluginCommand.Action<any>[]>();
+    private disposing = false;
+
+    subscribe<T>(cmd: PluginCommand<T>, action: PluginCommand.Action<T>): PluginCommand.Subscription {
+        let actions = this.subs.get(cmd.id);
+        if (!actions) {
+            actions = [];
+            this.subs.set(cmd.id, actions);
+        }
+        actions.push(action);
+
+        return {
+            unsubscribe: () => {
+                const actions = this.subs.get(cmd.id);
+                if (!actions) return;
+                const idx = actions.indexOf(action);
+                if (idx < 0) return;
+                for (let i = idx + 1; i < actions.length; i++) {
+                    actions[i - 1] = actions[i];
+                }
+                actions.pop();
+            }
         }
-    },
-    Interactivity: {
-        SetProps: PluginCommand<{ props: Partial<Interactivity.Props> }>(),
-        Structure: {
-            Highlight: PluginCommand<{ loci: StructureElement.Loci, isOff?: boolean }>(),
-            Select: PluginCommand<{ loci: StructureElement.Loci, isOff?: boolean }>()
+    }
+
+
+    /** Resolves after all actions have completed */
+    dispatch<T>(cmd: PluginCommand<T>, params: T) {
+        return new Promise<void>((resolve, reject) => {
+            if (this.disposing) {
+                reject('disposed');
+                return;
+            }
+
+            const actions = this.subs.get(cmd.id);
+            if (!actions) {
+                resolve();
+                return;
+            }
+
+            this.resolve({ cmd, params, resolve, reject });
+        });
+    }
+
+    dispose() {
+        this.subs.clear();
+    }
+
+    private async resolve(instance: Instance) {
+        const actions = this.subs.get(instance.cmd.id);
+        if (!actions) {
+            instance.resolve();
+            return;
         }
-    },
-    Layout: {
-        Update: PluginCommand<{ state: Partial<PluginLayoutStateProps> }>()
-    },
-    Toast: {
-        Show: PluginCommand<PluginToast>(),
-        Hide: PluginCommand<{ key: string }>()
-    },
-    Camera: {
-        Reset: PluginCommand<{ durationMs?: number, snapshot?: Partial<Camera.Snapshot> }>(),
-        SetSnapshot: PluginCommand<{ snapshot: Partial<Camera.Snapshot>, durationMs?: number }>(),
-        Snapshots: {
-            Add: PluginCommand<{ name?: string, description?: string }>(),
-            Remove: PluginCommand<{ id: string }>(),
-            Apply: PluginCommand<{ id: string }>(),
-            Clear: PluginCommand<{}>(),
+
+        try {
+            // TODO: should actions be called "asynchronously" ("setImmediate") instead?
+            for (const a of actions) {
+                await a(instance.params);
+            }
+            instance.resolve();
+        } catch (e) {
+            instance.reject(e);
         }
-    },
-    Canvas3D: {
-        SetSettings: PluginCommand<{ settings: Partial<Canvas3DProps> }>()
     }
 }

src/mol-plugin/command/base.ts

@@ -1,112 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { PluginContext } from '../context';
-import { UUID } from '../../mol-util';
-
-export { PluginCommand }
-
-interface PluginCommand<T = unknown> {
-    readonly id: UUID,
-    dispatch(ctx: PluginContext, params: T): Promise<void>,
-    subscribe(ctx: PluginContext, action: PluginCommand.Action<T>): PluginCommand.Subscription
-}
-
-/** namespace.id must a globally unique identifier */
-function PluginCommand<T>(): PluginCommand<T> {
-    return new Impl();
-}
-
-class Impl<T> implements PluginCommand<T> {
-    dispatch(ctx: PluginContext, params: T): Promise<void> {
-        return ctx.commands.dispatch(this, params);
-    }
-    subscribe(ctx: PluginContext, action: PluginCommand.Action<T>): PluginCommand.Subscription {
-        return ctx.commands.subscribe(this, action);
-    }
-    id = UUID.create22();
-    constructor() {
-    }
-}
-
-namespace PluginCommand {
-    export type Id = string & { '@type': 'plugin-command-id' }
-
-    export interface Subscription {
-        unsubscribe(): void
-    }
-
-    export type Action<T> = (params: T) => unknown | Promise<unknown>
-    type Instance = { cmd: PluginCommand<any>, params: any, resolve: () => void, reject: (e: any) => void }
-
-    export class Manager {
-        private subs = new Map<string, Action<any>[]>();
-        private disposing = false;
-
-        subscribe<T>(cmd: PluginCommand<T>, action: Action<T>): Subscription {
-            let actions = this.subs.get(cmd.id);
-            if (!actions) {
-                actions = [];
-                this.subs.set(cmd.id, actions);
-            }
-            actions.push(action);
-
-            return {
-                unsubscribe: () => {
-                    const actions = this.subs.get(cmd.id);
-                    if (!actions) return;
-                    const idx = actions.indexOf(action);
-                    if (idx < 0) return;
-                    for (let i = idx + 1; i < actions.length; i++) {
-                        actions[i - 1] = actions[i];
-                    }
-                    actions.pop();
-                }
-            }
-        }
-
-
-        /** Resolves after all actions have completed */
-        dispatch<T>(cmd: PluginCommand<T>, params: T) {
-            return new Promise<void>((resolve, reject) => {
-                if (this.disposing) {
-                    reject('disposed');
-                    return;
-                }
-
-                const actions = this.subs.get(cmd.id);
-                if (!actions) {
-                    resolve();
-                    return;
-                }
-
-                this.resolve({ cmd, params, resolve, reject });
-            });
-        }
-
-        dispose() {
-            this.subs.clear();
-        }
-
-        private async resolve(instance: Instance) {
-            const actions = this.subs.get(instance.cmd.id);
-            if (!actions) {
-                instance.resolve();
-                return;
-            }
-
-            try {
-                // TODO: should actions be called "asynchronously" ("setImmediate") instead?
-                for (const a of actions) {
-                    await a(instance.params);
-                }
-                instance.resolve();
-            } catch (e) {
-                instance.reject(e);
-            }
-        }
-    }
-}

src/mol-plugin/commands.ts

@@ -0,0 +1,72 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Camera } from '../mol-canvas3d/camera';
+import { PluginCommand } from './command';
+import { StateTransform, State, StateAction } from '../mol-state';
+import { Canvas3DProps } from '../mol-canvas3d/canvas3d';
+import { PluginLayoutStateProps } from './layout';
+import { StructureElement } from '../mol-model/structure';
+import { PluginState } from './state';
+import { Interactivity } from './util/interactivity';
+import { PluginToast } from './util/toast';
+
+export const PluginCommands = {
+    State: {
+        SetCurrentObject: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
+        ApplyAction: PluginCommand<{ state: State, action: StateAction.Instance, ref?: StateTransform.Ref }>(),
+        Update: PluginCommand<{ state: State, tree: State.Tree | State.Builder, options?: Partial<State.UpdateOptions> }>(),
+
+        RemoveObject: PluginCommand<{ state: State, ref: StateTransform.Ref, removeParentGhosts?: boolean }>(),
+
+        ToggleExpanded: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
+        ToggleVisibility: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
+        Highlight: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
+        ClearHighlight: PluginCommand<{ state: State, ref: StateTransform.Ref }>(),
+
+        Snapshots: {
+            Add: PluginCommand<{ name?: string, description?: string, params?: PluginState.GetSnapshotParams }>(),
+            Replace: PluginCommand<{ id: string, params?: PluginState.GetSnapshotParams }>(),
+            Move: PluginCommand<{ id: string, dir: -1 | 1 }>(),
+            Remove: PluginCommand<{ id: string }>(),
+            Apply: PluginCommand<{ id: string }>(),
+            Clear: PluginCommand<{}>(),
+
+            Upload: PluginCommand<{ name?: string, description?: string, playOnLoad?: boolean, serverUrl: string }>(),
+            Fetch: PluginCommand<{ url: string }>(),
+
+            DownloadToFile: PluginCommand<{ name?: string }>(),
+            OpenFile: PluginCommand<{ file: File }>(),
+        }
+    },
+    Interactivity: {
+        SetProps: PluginCommand<{ props: Partial<Interactivity.Props> }>(),
+        Structure: {
+            Highlight: PluginCommand<{ loci: StructureElement.Loci, isOff?: boolean }>(),
+            Select: PluginCommand<{ loci: StructureElement.Loci, isOff?: boolean }>()
+        }
+    },
+    Layout: {
+        Update: PluginCommand<{ state: Partial<PluginLayoutStateProps> }>()
+    },
+    Toast: {
+        Show: PluginCommand<PluginToast>(),
+        Hide: PluginCommand<{ key: string }>()
+    },
+    Camera: {
+        Reset: PluginCommand<{ durationMs?: number, snapshot?: Partial<Camera.Snapshot> }>(),
+        SetSnapshot: PluginCommand<{ snapshot: Partial<Camera.Snapshot>, durationMs?: number }>(),
+        Snapshots: {
+            Add: PluginCommand<{ name?: string, description?: string }>(),
+            Remove: PluginCommand<{ id: string }>(),
+            Apply: PluginCommand<{ id: string }>(),
+            Clear: PluginCommand<{}>(),
+        }
+    },
+    Canvas3D: {
+        SetSettings: PluginCommand<{ settings: Partial<Canvas3DProps> }>()
+    }
+}

src/mol-plugin/context.ts

@@ -21,11 +21,12 @@ import { RxEventHelper } from '../mol-util/rx-event-helper';
 import { merge } from 'rxjs';
 import { BuiltInPluginBehaviors } from './behavior';
 import { PluginBehavior } from './behavior/behavior';
-import { PluginCommand, PluginCommands } from './command';
+import { PluginCommands } from './commands';
+import { PluginCommandManager } from './command';
 import { PluginLayout, LeftPanelTabName } from './layout';
 import { PluginSpec } from './spec';
 import { PluginState } from './state';
-import { DataFormatRegistry } from './state/actions/data-format';
+import { DataFormatRegistry } from '../mol-plugin-state/actions/data-format';
 import { StateTransformParameters } from '../mol-plugin-ui/state/common';
 import { LociLabelEntry, LociLabelManager } from './util/loci-label-manager';
 import { TaskManager } from './util/task-manager';
@@ -39,30 +40,20 @@ import { Interactivity } from './util/interactivity';
 import { StructureRepresentationHelper } from './util/structure-representation-helper';
 import { StructureSelectionHelper } from './util/structure-selection-helper';
 import { StructureOverpaintHelper } from './util/structure-overpaint-helper';
-import { PluginToastManager } from './state/toast';
+import { PluginToastManager } from './util/toast';
 import { StructureMeasurementManager } from './util/structure-measurement';
 import { ViewportScreenshotHelper } from './util/viewport-screenshot';
-import { StructureRepresentationManager } from './state/representation/structure';
-import { DataManager } from './state/manager/data';
+import { StructureRepresentationManager } from '../mol-plugin-state/representation/structure';
 import { CustomProperty } from '../mol-model-props/common/custom-property';
 import { PluginConfigManager } from './config';
 
-interface Log {
-    entries: List<LogEntry>
-    readonly entry: (e: LogEntry) => void
-    readonly error: (msg: string) => void
-    readonly message: (msg: string) => void
-    readonly info: (msg: string) => void
-    readonly warn: (msg: string) => void
-}
-
 export class PluginContext {
     private disposed = false;
     private ev = RxEventHelper.create();
     private tasks = new TaskManager();
 
     readonly state = new PluginState(this);
-    readonly commands = new PluginCommand.Manager();
+    readonly commands = new PluginCommandManager();
 
     readonly events = {
         state: {
@@ -137,10 +128,6 @@ export class PluginContext {
     readonly customStructureProperties = new CustomProperty.Registry<Structure>();
     readonly customParamEditors = new Map<string, StateTransformParameters.Class>();
 
-    readonly managers = {
-        data: new DataManager(this),
-    } as const;
-
     readonly helpers = {
         measurement: new StructureMeasurementManager(this),
         structureSelectionManager: new StructureElementSelectionManager(this),
@@ -166,7 +153,7 @@ export class PluginContext {
             this.events.canvas3d.initialized.next()
             this.events.canvas3d.initialized.isStopped = true // TODO is this a good way?
             const renderer = this.canvas3d!.props.renderer;
-            PluginCommands.Canvas3D.SetSettings.dispatch(this, { settings: { renderer: { ...renderer, backgroundColor: Color(0xFCFBF9) } } });
+            PluginCommands.Canvas3D.SetSettings(this, { settings: { renderer: { ...renderer, backgroundColor: Color(0xFCFBF9) } } });
             this.canvas3d!.animate();
             (this.helpers.viewportScreenshot as ViewportScreenshotHelper) = new ViewportScreenshotHelper(this);
             return true;
@@ -177,7 +164,7 @@ export class PluginContext {
         }
     }
 
-    readonly log: Log = {
+    readonly log = {
         entries: List<LogEntry>(),
         entry: (e: LogEntry) => this.events.log.next(e),
         error: (msg: string) => this.events.log.next(LogEntry.error(msg)),
@@ -218,12 +205,12 @@ export class PluginContext {
 
     applyTransform(state: State, a: StateTransform.Ref, transformer: StateTransformer, params: any) {
         const tree = state.build().to(a).apply(transformer, params);
-        return PluginCommands.State.Update.dispatch(this, { state, tree });
+        return PluginCommands.State.Update(this, { state, tree });
     }
 
     updateTransform(state: State, a: StateTransform.Ref, params: any) {
         const tree = state.build().to(a).update(params);
-        return PluginCommands.State.Update.dispatch(this, { state, tree });
+        return PluginCommands.State.Update(this, { state, tree });
     }
 
     private initBehaviorEvents() {

src/mol-plugin/index.ts

@@ -10,13 +10,13 @@ import { Plugin } from '../mol-plugin-ui/plugin'
 import * as React from 'react';
 import * as ReactDOM from 'react-dom';
 import { PluginSpec } from './spec';
-import { StateTransforms } from './state/transforms';
+import { StateTransforms } from '../mol-plugin-state/transforms';
 import { PluginBehaviors } from './behavior';
-import { AnimateModelIndex, AnimateAssemblyUnwind, AnimateUnitsExplode, AnimateStateInterpolation } from './state/animation/built-in';
-import { StateActions } from './state/actions';
+import { AnimateModelIndex, AnimateAssemblyUnwind, AnimateUnitsExplode, AnimateStateInterpolation } from '../mol-plugin-state/animation/built-in';
+import { StateActions } from '../mol-plugin-state/actions';
 import { InitVolumeStreaming, BoxifyVolumeStreaming, CreateVolumeStreamingBehavior } from './behavior/dynamic/volume-streaming/transformers';
 import { StructureRepresentationInteraction } from './behavior/dynamic/selection/structure-representation-interaction';
-import { TransformStructureConformation } from './state/actions/structure';
+import { TransformStructureConformation } from '../mol-plugin-state/actions/structure';
 import { VolumeStreamingCustomControls } from '../mol-plugin-ui/custom/volume';
 import { PluginConfig } from './config';
 

src/mol-plugin/layout.ts

@@ -8,7 +8,7 @@
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { PluginComponent } from './component';
 import { PluginContext } from './context';
-import { PluginCommands } from './command';
+import { PluginCommands } from './commands';
 
 const regionStateOptions = [
     ['full', 'Full'] as const,

src/mol-plugin/spec.ts

@@ -8,7 +8,7 @@
 import { StateTransformer, StateAction } from '../mol-state';
 import { StateTransformParameters } from '../mol-plugin-ui/state/common';
 import { PluginLayoutStateProps } from './layout';
-import { PluginStateAnimation } from './state/animation/model';
+import { PluginStateAnimation } from '../mol-plugin-state/animation/model';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { PluginConfigItem } from './config';
 
@@ -25,7 +25,7 @@ interface PluginSpec {
         viewport?: React.ComponentClass
     },
     components?: {
-        remoteState?: 'none' | 'default' // TODO: props for server etc
+        remoteState?: 'none' | 'default'
     },
     config?: Map<PluginConfigItem, unknown>
 }

src/mol-plugin/state.ts

@@ -5,15 +5,15 @@
  */
 
 import { State } from '../mol-state';
-import { PluginStateObject as SO } from './state/objects';
+import { PluginStateObject as SO } from '../mol-plugin-state/objects';
 import { Camera } from '../mol-canvas3d/camera';
 import { PluginBehavior } from './behavior';
-import { CameraSnapshotManager } from './state/camera';
-import { PluginStateSnapshotManager } from './state/snapshots';
+import { CameraSnapshotManager } from '../mol-plugin-state/camera';
+import { PluginStateSnapshotManager } from '../mol-plugin-state/snapshots';
 import { RxEventHelper } from '../mol-util/rx-event-helper';
 import { Canvas3DProps } from '../mol-canvas3d/canvas3d';
-import { PluginCommands } from './command';
-import { PluginAnimationManager } from './state/animation/manager';
+import { PluginCommands } from './commands';
+import { PluginAnimationManager } from '../mol-plugin-state/animation/manager';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { UUID } from '../mol-util';
 import { Interactivity } from './util/interactivity';
@@ -69,17 +69,17 @@ class PluginState {
         if (snapshot.behaviour) await this.plugin.runTask(this.behaviorState.setSnapshot(snapshot.behaviour));
         if (snapshot.data) await this.plugin.runTask(this.dataState.setSnapshot(snapshot.data));
         if (snapshot.canvas3d) {
-            if (snapshot.canvas3d.props) await PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: snapshot.canvas3d.props });
+            if (snapshot.canvas3d.props) await PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: snapshot.canvas3d.props });
         }
         if (snapshot.interactivity) {
-            if (snapshot.interactivity.props) await PluginCommands.Interactivity.SetProps.dispatch(this.plugin, { props: snapshot.interactivity.props });
+            if (snapshot.interactivity.props) await PluginCommands.Interactivity.SetProps(this.plugin, { props: snapshot.interactivity.props });
         }
         if (snapshot.cameraSnapshots) this.cameraSnapshots.setStateSnapshot(snapshot.cameraSnapshots);
         if (snapshot.animation) {
             this.animation.setSnapshot(snapshot.animation);
         }
         if (snapshot.camera) {
-            PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, {
+            PluginCommands.Camera.SetSnapshot(this.plugin, {
                 snapshot: snapshot.camera.current,
                 durationMs: snapshot.camera.transitionStyle === 'animate'
                     ? snapshot.camera.transitionDurationInMs

src/mol-plugin/util/interactivity.ts

@@ -14,7 +14,7 @@ import { StructureElementSelectionManager } from './structure-element-selection'
 import { PluginContext } from '../context';
 import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { PluginCommands } from '../command';
+import { PluginCommands } from '../commands';
 
 export { Interactivity }
 

src/mol-plugin/util/structure-complex-helper.ts

@@ -6,10 +6,10 @@
 
 import { PluginContext } from '../context';
 import { StateBuilder } from '../../mol-state';
-import { PluginStateObject } from '../state/objects';
-import { StateTransforms } from '../state/transforms';
-import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
-import { StructureComplexElementTypes } from '../state/transforms/model';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { StructureRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
+import { StructureComplexElementTypes } from '../../mol-plugin-state/transforms/model';
 
 export function createDefaultStructureComplex(
     ctx: PluginContext, root: StateBuilder.To<PluginStateObject.Molecule.Structure>

src/mol-plugin/util/structure-element-selection.ts

@@ -10,7 +10,7 @@ import { EmptyLoci, Loci } from '../../mol-model/loci';
 import { Structure, StructureElement } from '../../mol-model/structure';
 import { StateObject } from '../../mol-state';
 import { PluginContext } from '../context';
-import { PluginStateObject } from '../state/objects';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { structureElementStatsLabel } from '../../mol-theme/label';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';

src/mol-plugin/util/structure-measurement.ts

@@ -7,8 +7,8 @@
 import { StructureElement } from '../../mol-model/structure';
 import { PluginContext } from '../context';
 import { StateSelection, StateTransform } from '../../mol-state';
-import { StateTransforms } from '../state/transforms';
-import { PluginCommands } from '../command';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { PluginCommands } from '../commands';
 import { arraySetAdd } from '../../mol-util/array';
 
 export { StructureMeasurementManager }
@@ -47,7 +47,7 @@ class StructureMeasurementManager {
             .apply(StateTransforms.Representation.StructureSelectionsDistance3D)
 
         const state = this.context.state.dataState;
-        await PluginCommands.State.Update.dispatch(this.context, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(this.context, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
     async addAngle(a: StructureElement.Loci, b: StructureElement.Loci, c: StructureElement.Loci) {
@@ -75,7 +75,7 @@ class StructureMeasurementManager {
             .apply(StateTransforms.Representation.StructureSelectionsAngle3D)
 
         const state = this.context.state.dataState;
-        await PluginCommands.State.Update.dispatch(this.context, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(this.context, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
     async addDihedral(a: StructureElement.Loci, b: StructureElement.Loci, c: StructureElement.Loci, d: StructureElement.Loci) {
@@ -106,7 +106,7 @@ class StructureMeasurementManager {
             .apply(StateTransforms.Representation.StructureSelectionsDihedral3D)
 
         const state = this.context.state.dataState;
-        await PluginCommands.State.Update.dispatch(this.context, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(this.context, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
     async addLabel(a: StructureElement.Loci) {
@@ -128,7 +128,7 @@ class StructureMeasurementManager {
             .apply(StateTransforms.Representation.StructureSelectionsLabel3D)
 
         const state = this.context.state.dataState;
-        await PluginCommands.State.Update.dispatch(this.context, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(this.context, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
     async addOrientation(a: StructureElement.Loci) {
@@ -150,7 +150,7 @@ class StructureMeasurementManager {
             .apply(StateTransforms.Representation.StructureSelectionsOrientation3D)
 
         const state = this.context.state.dataState;
-        await PluginCommands.State.Update.dispatch(this.context, { state, tree: update, options: { doNotLogTiming: true } });
+        await PluginCommands.State.Update(this.context, { state, tree: update, options: { doNotLogTiming: true } });
     }
 
     constructor(private context: PluginContext) {

src/mol-plugin/util/structure-overpaint-helper.ts

@@ -4,8 +4,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginStateObject } from '../../mol-plugin/state/objects';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state';
 import { Structure, StructureElement, StructureSelection, QueryContext } from '../../mol-model/structure';
 import { PluginContext } from '../context';

src/mol-plugin/util/structure-query.ts

@@ -8,7 +8,7 @@ import Expression from '../../mol-script/language/expression';
 import { QueryFn, Structure, StructureSelection as Sel, QueryContext } from '../../mol-model/structure';
 import { Script } from '../../mol-script/script';
 import { compile } from '../../mol-script/runtime/query/compiler';
-import { PluginStateObject as SO } from '../state/objects';
+import { PluginStateObject as SO } from '../../mol-plugin-state/objects';
 
 export { StructureQueryHelper }
 namespace StructureQueryHelper {

src/mol-plugin/util/structure-representation-helper.ts

@@ -4,12 +4,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
-import { StateTransforms } from '../../mol-plugin/state/transforms';
+import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { StateTransformer, StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state';
 import { StructureElement, Structure, StructureSelection, QueryContext } from '../../mol-model/structure';
 import { PluginContext } from '../context';
-import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
+import { StructureRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
 import Expression from '../../mol-script/language/expression';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { VisualQuality } from '../../mol-geo/geometry/base';

src/mol-plugin/util/structure-selection-helper.ts

@@ -7,14 +7,14 @@
 
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { StateSelection, StateBuilder } from '../../mol-state';
-import { PluginStateObject } from '../state/objects';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { QueryContext, StructureSelection, StructureQuery, StructureElement, Structure } from '../../mol-model/structure';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { Loci } from '../../mol-model/loci';
 import { PluginContext } from '../context';
 import Expression from '../../mol-script/language/expression';
 import { BondType, ProteinBackboneAtoms, NucleicBackboneAtoms, SecondaryStructureType } from '../../mol-model/structure/model/types';
-import { StateTransforms } from '../state/transforms';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { SetUtils } from '../../mol-util/set';
 import { ValidationReport, ValidationReportProvider } from '../../mol-model-props/rcsb/validation-report';
 import { CustomProperty } from '../../mol-model-props/common/custom-property';

src/mol-plugin/util/substructure-parent-helper.ts

@@ -7,7 +7,7 @@
 import { Structure } from '../../mol-model/structure';
 import { State, StateObject, StateSelection, StateObjectCell } from '../../mol-state';
 import { PluginContext } from '../context';
-import { PluginStateObject } from '../state/objects';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 
 export { SubstructureParentHelper };
 

src/mol-plugin/state/toast.ts → src/mol-plugin/util/toast.ts

@@ -9,7 +9,7 @@
 import { PluginComponent } from '../component';
 import { OrderedMap } from 'immutable';
 import { PluginContext } from '../context';
-import { PluginCommands } from '../command';
+import { PluginCommands } from '../commands';
 
 export interface PluginToast {
     title: string,

src/mol-plugin/util/viewport-screenshot.ts

@@ -8,7 +8,7 @@
 import { PluginContext } from '../context';
 import { ImagePass } from '../../mol-canvas3d/passes/image';
 import { StateSelection } from '../../mol-state';
-import { PluginStateObject } from '../state/objects';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { Task, RuntimeContext } from '../../mol-task';
 import { canvasToBlob } from '../../mol-canvas3d/util';
 import { download } from '../../mol-util/download';

src/mol-plugin/version.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 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>
  */
 
-export const PLUGIN_VERSION = '0.5.0';
+export const PLUGIN_VERSION = '0.5.5';
 /** unix time stamp, to be filled in at bundle build time */
 declare const __PLUGIN_VERSION_TIMESTAMP__: number
 export const PLUGIN_VERSION_TIMESTAMP = __PLUGIN_VERSION_TIMESTAMP__;