diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index dbc813432bbe613347823a411199b9c24c5647fc..676ac2ac421b95b686e131a36e4c595b33c75fa7 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -88,7 +88,6 @@ async function tryLoadFromUrl(ctx: PluginContext) {
format: format as any,
isBinary,
options: params.source.params.options,
- structure: params.source.params.structure,
}
}
}));
diff --git a/src/mol-plugin-state/actions/structure.ts b/src/mol-plugin-state/actions/structure.ts
index 250f582c50f803d5a37ccf2e00b8005c1aaf61cc..40d89a724bdcceaf81f4cba694d2c8ad3543d768 100644
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -19,6 +19,7 @@ import { Download, ParsePsf } from '../transforms/data';
import { CoordinatesFromDcd, CustomModelProperties, CustomStructureProperties, TopologyFromPsf, TrajectoryFromModelAndCoordinates } from '../transforms/model';
import { DataFormatProvider, guessCifVariant } from './data-format';
import { applyTrajectoryHierarchyPreset } from '../builder/structure/hierarchy-preset';
+import { PresetStructureReprentations } from '../builder/structure/representation-preset';
// TODO make unitcell creation part of preset
@@ -36,7 +37,8 @@ export const MmcifProvider: DataFormatProvider<PluginStateObject.Data.String | P
getDefaultBuilder: (ctx: PluginContext, data, options) => {
return Task.create('mmCIF default builder', async () => {
const trajectory = await ctx.builders.structure.parseTrajectory(data, 'mmcif');
- await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, noRepresentation: !options.visuals });
+ const representationPreset = options.visuals ? 'auto' : 'empty';
+ await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, representationPreset });
})
}
}
@@ -52,7 +54,8 @@ export const PdbProvider: DataFormatProvider<any> = {
getDefaultBuilder: (ctx: PluginContext, data, options) => {
return Task.create('PDB default builder', async () => {
const trajectory = await ctx.builders.structure.parseTrajectory(data, 'pdb');
- await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, noRepresentation: !options.visuals });
+ const representationPreset = options.visuals ? 'auto' : 'empty';
+ await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, representationPreset });
})
}
}
@@ -68,7 +71,8 @@ export const GroProvider: DataFormatProvider<any> = {
getDefaultBuilder: (ctx: PluginContext, data, options) => {
return Task.create('GRO default builder', async () => {
const trajectory = await ctx.builders.structure.parseTrajectory(data, 'gro');
- await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, noRepresentation: !options.visuals });
+ const representationPreset = options.visuals ? 'auto' : 'empty';
+ await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, representationPreset });
})
}
}
@@ -84,7 +88,8 @@ export const Provider3dg: DataFormatProvider<any> = {
getDefaultBuilder: (ctx: PluginContext, data, options) => {
return Task.create('3DG default builder', async () => {
const trajectory = await ctx.builders.structure.parseTrajectory(data, '3dg');
- await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, noRepresentation: !options.visuals });
+ const representationPreset = options.visuals ? 'auto' : 'empty';
+ await applyTrajectoryHierarchyPreset(ctx, trajectory, 'first-model', { showUnitcell: options.visuals, representationPreset });
})
}
}
@@ -123,59 +128,51 @@ export const DcdProvider: DataFormatProvider<any> = {
//
-const DownloadModelRepresentationOptions = PD.Group({
+const DownloadModelRepresentationOptions = (plugin: PluginContext) => PD.Group({
type: RootStructureDefinition.getParams(void 0, 'assembly').type,
- noRepresentation: PD.Optional(PD.Boolean(false, { description: 'Omit creating default representation.' }))
-}, { isExpanded: false });
-
-const DownloadStructurePdbIdSourceOptions = PD.Group({
- // supportProps: PD.Optional(PD.Boolean(false)),
+ representation: PD.Select(PresetStructureReprentations.auto.id,
+ plugin.builders.structure.representation.getPresets().map(p => [p.id, p.display.name] as any),
+ { description: 'Which representation preset to use.' }),
asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
-});
+}, { isExpanded: false });
export { DownloadStructure };
type DownloadStructure = typeof DownloadStructure
const DownloadStructure = StateAction.build({
from: PluginStateObject.Root,
display: { name: 'Download Structure', description: 'Load a structure from the provided source and create its representation.' },
- params: {
- source: PD.MappedStatic('bcif-static', {
- 'pdbe-updated': PD.Group({
- id: PD.Text('1cbs', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
- structure: DownloadModelRepresentationOptions,
- options: DownloadStructurePdbIdSourceOptions
- }, { isFlat: true, label: 'PDBe Updated' }),
- 'rcsb': PD.Group({
- id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
- structure: DownloadModelRepresentationOptions,
- options: DownloadStructurePdbIdSourceOptions
- }, { isFlat: true, label: 'RCSB' }),
- 'pdb-dev': PD.Group({
- id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma separated ids.' }),
- structure: DownloadModelRepresentationOptions,
- options: DownloadStructurePdbIdSourceOptions
- }, { isFlat: true, label: 'PDBDEV' }),
- 'bcif-static': PD.Group({
- id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
- structure: DownloadModelRepresentationOptions,
- options: DownloadStructurePdbIdSourceOptions
- }, { isFlat: true, label: 'BinaryCIF (static PDBe Updated)' }),
- 'swissmodel': PD.Group({
- id: PD.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma separated ACs.' }),
- structure: DownloadModelRepresentationOptions,
- options: DownloadStructurePdbIdSourceOptions
- }, { isFlat: true, label: 'SWISS-MODEL', description: 'Loads the best homology model or experimental structure' }),
- 'url': PD.Group({
- url: PD.Text(''),
- format: PD.Select('mmcif', [['mmcif', 'CIF'], ['pdb', 'PDB']] as ['mmcif' | 'pdb', string][]),
- isBinary: PD.Boolean(false),
- structure: DownloadModelRepresentationOptions,
- options: PD.Group({
- // supportProps: PD.Optional(PD.Boolean(false)),
- createRepresentation: PD.Optional(PD.Boolean(true))
- })
- }, { isFlat: true, label: 'URL' })
- })
+ params: (_, plugin: PluginContext) => {
+ const options = DownloadModelRepresentationOptions(plugin);
+ return {
+ source: PD.MappedStatic('bcif-static', {
+ 'pdbe-updated': PD.Group({
+ id: PD.Text('1cbs', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
+ options
+ }, { isFlat: true, label: 'PDBe Updated' }),
+ 'rcsb': PD.Group({
+ id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
+ options
+ }, { isFlat: true, label: 'RCSB' }),
+ 'pdb-dev': PD.Group({
+ id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma separated ids.' }),
+ options
+ }, { isFlat: true, label: 'PDBDEV' }),
+ 'bcif-static': PD.Group({
+ id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma separated PDB ids.' }),
+ options
+ }, { isFlat: true, label: 'BinaryCIF (static PDBe Updated)' }),
+ 'swissmodel': PD.Group({
+ id: PD.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma separated ACs.' }),
+ options
+ }, { isFlat: true, label: 'SWISS-MODEL', description: 'Loads the best homology model or experimental structure' }),
+ 'url': PD.Group({
+ url: PD.Text(''),
+ format: PD.Select('mmcif', [['mmcif', 'CIF'], ['pdb', 'PDB']] as ['mmcif' | 'pdb', string][]),
+ isBinary: PD.Boolean(false),
+ options
+ }, { isFlat: true, label: 'URL' })
+ })
+ }
}
})(({ params, state }, plugin: PluginContext) => Task.create('Download Structure', async ctx => {
plugin.behaviors.layout.leftPanelTabName.next('data');
@@ -227,7 +224,8 @@ const DownloadStructure = StateAction.build({
default: throw new Error(`${(src as any).name} not supported.`);
}
- const createRepr = !params.source.params.structure.noRepresentation;
+ const representationPreset: any = params.source.params.options.representation || PresetStructureReprentations.auto.id;
+ const showUnitcell = representationPreset !== PresetStructureReprentations.empty.id;
await state.transaction(async () => {
if (downloadParams.length > 0 && asTrajectory) {
@@ -237,13 +235,21 @@ const DownloadStructure = StateAction.build({
}, { state: { isGhost: true } });
const trajectory = await plugin.builders.structure.parseTrajectory(blob, { formats: downloadParams.map((_, i) => ({ id: '' + i, format: 'cif' as 'cif' })) });
- await applyTrajectoryHierarchyPreset(plugin, trajectory, 'first-model', { showUnitcell: createRepr, noRepresentation: !createRepr });
+ await applyTrajectoryHierarchyPreset(plugin, trajectory, 'first-model', {
+ structure: src.params.options.type,
+ showUnitcell,
+ representationPreset
+ });
} else {
for (const download of downloadParams) {
const data = await plugin.builders.data.download(download, { state: { isGhost: true } });
const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
- await applyTrajectoryHierarchyPreset(plugin, trajectory, 'first-model', { showUnitcell: createRepr, noRepresentation: !createRepr });
+ await applyTrajectoryHierarchyPreset(plugin, trajectory, 'first-model', {
+ structure: src.params.options.type,
+ showUnitcell,
+ representationPreset
+ });
}
}
}).runInContext(ctx);
diff --git a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
index 282dc193d79b50188138a7ca6a7e311a4824d057..735f6635ffd1214430fdf4ec4b73e63801a196bd 100644
--- a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
+++ b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
@@ -32,7 +32,6 @@ const FirstModelParams = (a: PluginStateObject.Molecule.Trajectory | undefined,
model: PD.Optional(PD.Group(StateTransformer.getParamDefinition(StateTransforms.Model.ModelFromTrajectory, a, plugin))),
showUnitcell: PD.Optional(PD.Boolean(true)),
structure: PD.Optional(RootStructureDefinition.getParams(void 0, 'assembly').type),
- noRepresentation: PD.Optional(PD.Boolean(false)),
...CommonParams(a, plugin)
});
@@ -44,27 +43,20 @@ const firstModel = TrajectoryHierarchyPresetProvider({
const builder = plugin.builders.structure;
const model = await builder.createModel(trajectory, params.model);
- const modelProperties = !!params.modelProperties
- ? await builder.insertModelProperties(model, params.modelProperties) : void 0;
- const modelChildParent = modelProperties || model;
+ const modelProperties = await builder.insertModelProperties(model, params.modelProperties);
const structure = await builder.createStructure(modelProperties || model, params.structure);
- const structureProperties = !!params.structureProperties
- ? await builder.insertStructureProperties(structure, params.structureProperties) : void 0;
- const structureChildParent = structureProperties || structure;
+ const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
- const unitcell = params.showUnitcell === void 0 || !!params.showUnitcell ? await builder.tryCreateUnitcell(modelChildParent, undefined, { isHidden: true }) : void 0;
-
- const representation = !params.noRepresentation
- ? await plugin.builders.structure.representation.applyPreset(structureChildParent, params.representationPreset || 'auto')
- : void 0;
+ const unitcell = params.showUnitcell === void 0 || !!params.showUnitcell ? await builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true }) : void 0;
+ const representation = await plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto');
return {
- model: modelChildParent,
+ model: modelProperties,
modelRoot: model,
modelProperties,
unitcell,
- structure: structureChildParent,
+ structure: structureProperties,
structureRoot: structure,
structureProperties,
representation
@@ -86,10 +78,13 @@ const allModels = TrajectoryHierarchyPresetProvider({
for (let i = 0; i < tr.length; i++) {
const model = await builder.createModel(trajectory, { modelIndex: i }, { isCollapsed: true });
- const structure = await builder.createStructure(model, { name: 'deposited', params: {} });
+ const modelProperties = await builder.insertModelProperties(model, params.modelProperties);
+ const structure = await builder.createStructure(modelProperties || model, { name: 'deposited', params: {} });
+ const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
+
models.push(model);
structures.push(structure);
- await builder.representation.applyPreset(structure, params.representationPreset || 'auto', { globalThemeName: 'model-index' });
+ await builder.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { globalThemeName: 'model-index' });
}
return { models, structures };
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index aff28abea7701231797dcf3df16369c482cb741e..f665d23f8c6b8e1ef6acc25af36620c268b16720 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -67,6 +67,14 @@ function reprBuilder(plugin: PluginContext, params: CommonStructureRepresentatio
return { update, builder, color, typeParams };
}
+const empty = StructureRepresentationPresetProvider({
+ id: 'preset-structure-representation-empty',
+ display: { name: 'Empty', group: 'Preset' },
+ async apply(ref, params, plugin) {
+ return { };
+ }
+});
+
const polymerAndLigand = StructureRepresentationPresetProvider({
id: 'preset-structure-representation-polymer-and-ligand',
display: { name: 'Polymer & Ligand', group: 'Preset' },
@@ -228,6 +236,7 @@ export function presetSelectionComponent(plugin: PluginContext, structure: State
}
export const PresetStructureReprentations = {
+ empty,
auto,
'atomic-detail': atomicDetail,
'polymer-cartoon': polymerCartoon,
diff --git a/src/mol-plugin-state/builder/structure/representation.ts b/src/mol-plugin-state/builder/structure/representation.ts
index 0d071f75b6ec98a43b5ecb6498f388117929a0bd..a4671507f8f1f2ca633b44243ca8ce97b589ea92 100644
--- a/src/mol-plugin-state/builder/structure/representation.ts
+++ b/src/mol-plugin-state/builder/structure/representation.ts
@@ -54,6 +54,15 @@ export class StructureRepresentationBuilder {
return ret;
}
+ getPresetSelect(s?: PluginStateObject.Molecule.Structure): PD.Select<string> {
+ const options: [string, string][] = [];
+ for (const p of this._providers) {
+ if (s && p.isApplicable && !p.isApplicable(s, this.plugin)) continue;
+ options.push([p.id, p.display.name]);
+ }
+ return PD.Select('auto', options);
+ }
+
getPresetsWithOptions(s: PluginStateObject.Molecule.Structure) {
const options: [string, string][] = [];
const map: { [K in string]: PD.Any } = Object.create(null);
diff --git a/src/mol-plugin-state/manager/structure/component.ts b/src/mol-plugin-state/manager/structure/component.ts
index 0fbc62afabdb3496173017bd93752a58835b1948..355ed28165b473b719eb939b48d8afeebb052eed 100644
--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/src/mol-plugin-state/manager/structure/component.ts
@@ -212,24 +212,41 @@ class StructureComponentManager extends PluginComponent<StructureComponentManage
return this.plugin.updateDataState(update, { canUndo: 'Update Representation' });
}
- updateRepresentationsTheme<C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(components: ReadonlyArray<StructureComponentRef>, params: StructureComponentManager.UpdateThemeParams<C, S>): Promise<any> {
- if (components.length === 0) return Promise.resolve();
+ /**
+ * To update theme for all selected structures, use
+ * plugin.dataTransaction(async () => {
+ * for (const s of structure.hierarchy.selection.structures) await updateRepresentationsTheme(s.componets, ...);
+ * }, { canUndo: 'Update Theme' });
+ */
+ updateRepresentationsTheme<C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(components: ReadonlyArray<StructureComponentRef>, params: StructureComponentManager.UpdateThemeParams<C, S>): Promise<any> | undefined
+ updateRepresentationsTheme<C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(components: ReadonlyArray<StructureComponentRef>, params: (c: StructureComponentRef, r: StructureRepresentationRef) => StructureComponentManager.UpdateThemeParams<C, S>): Promise<any> | undefined
+ updateRepresentationsTheme(components: ReadonlyArray<StructureComponentRef>, paramsOrProvider: StructureComponentManager.UpdateThemeParams<any, any> | ((c: StructureComponentRef, r: StructureRepresentationRef) => StructureComponentManager.UpdateThemeParams<any, any>)) {
+ if (components.length === 0) return;
const update = this.dataState.build();
for (const c of components) {
for (const repr of c.representations) {
const old = repr.cell.transform.params;
- const colorTheme = params.color
- ? createStructureColorThemeParams(this.plugin, c.structure.cell.obj?.data, old?.type.name, params.color, params.colorParams)
- : void 0;
- const sizeTheme = params.color
- ? createStructureSizeThemeParams(this.plugin, c.structure.cell.obj?.data, old?.type.name, params.size, params.sizeParams)
- : void 0;
- update.to(repr.cell).update(prev => {
- if (colorTheme) prev.colorTheme = colorTheme;
- if (sizeTheme) prev.sizeTheme = sizeTheme;
- });
+ const params: StructureComponentManager.UpdateThemeParams<any, any> = typeof paramsOrProvider === 'function' ? paramsOrProvider(c, repr) : paramsOrProvider;
+
+ const colorTheme = params.color === 'default'
+ ? createStructureColorThemeParams(this.plugin, c.structure.cell.obj?.data, old?.type.name)
+ : params.color
+ ? createStructureColorThemeParams(this.plugin, c.structure.cell.obj?.data, old?.type.name, params.color, params.colorParams)
+ : void 0;
+ const sizeTheme = params.size === 'default'
+ ? createStructureSizeThemeParams(this.plugin, c.structure.cell.obj?.data, old?.type.name)
+ : params.color
+ ? createStructureSizeThemeParams(this.plugin, c.structure.cell.obj?.data, old?.type.name, params.size, params.sizeParams)
+ : void 0;
+
+ if (colorTheme || sizeTheme) {
+ update.to(repr.cell).update(prev => {
+ if (colorTheme) prev.colorTheme = colorTheme;
+ if (sizeTheme) prev.sizeTheme = sizeTheme;
+ });
+ }
}
}
@@ -392,9 +409,9 @@ namespace StructureComponentManager {
/**
* this works for any theme name (use 'name as any'), but code completion will break
*/
- color?: C,
+ color?: C | 'default',
colorParams?: ColorTheme.BuiltInParams<C>,
- size?: S,
+ size?: S | 'default',
sizeParams?: SizeTheme.BuiltInParams<S>
}
}
diff --git a/src/mol-plugin-ui/plugin.tsx b/src/mol-plugin-ui/plugin.tsx
index 52a07f76691758259f32a9e6c361ae04cfbab37e..dda09d98eb763b86c16a6813283d93ea176201ea 100644
--- a/src/mol-plugin-ui/plugin.tsx
+++ b/src/mol-plugin-ui/plugin.tsx
@@ -229,7 +229,7 @@ export class Log extends PluginUIComponent<{}, { entries: List<LogEntry> }> {
// const actions = cell.status === 'ok' && <StateObjectActionSelect state={current.state} nodeRef={ref} plugin={this.plugin} />
// if (cell.status === 'error') {
-// return <>
+// return <>
// <SectionHeader icon='flow-cascade' title={`${cell.obj?.label || transform.transformer.definition.display.name}`} desc={transform.transformer.definition.display.name} />
// <UpdateTransformControl state={current.state} transform={transform} customHeader='none' />
// {actions}
@@ -249,7 +249,7 @@ export class Log extends PluginUIComponent<{}, { entries: List<LogEntry> }> {
// </ExpandGroup>);
// }
-// return <>
+// return <>
// <SectionHeader icon='flow-cascade' title={`${parent.obj?.label || parent.transform.transformer.definition.display.name}`} desc={parent.transform.transformer.definition.display.name} />
// <UpdateTransformControl state={current.state} transform={parent.transform} customHeader='none' />
// {decorators && <div className='msp-controls-section'>{decorators}</div>}
diff --git a/src/mol-plugin-ui/state/tree.tsx b/src/mol-plugin-ui/state/tree.tsx
index e4dda875a6fabd5802057e50a76ccee1a263b9b9..f28642886e85722f12a4538aa8fd79ab757a5f06 100644
--- a/src/mol-plugin-ui/state/tree.tsx
+++ b/src/mol-plugin-ui/state/tree.tsx
@@ -14,6 +14,7 @@ import { ActionMenu } from '../controls/action-menu';
import { ApplyActionControl } from './apply-action';
import { ControlGroup } from '../controls/common';
import { UpdateTransformControl } from './update-transform';
+import { StateTreeSpine } from '../../mol-state/tree/spine';
export class StateTree extends PluginUIComponent<{ state: State }, { showActions: boolean }> {
state = { showActions: true };
@@ -254,6 +255,19 @@ class StateTreeNodeLabel extends PluginUIComponent<{ cell: StateObjectCell, dept
(item?.value as any)();
}
+ updates() {
+ const cell = this.props.cell;
+ const decoratorChain = StateTreeSpine.getDecoratorChain(cell.parent, cell.transform.ref);
+
+ const decorators = [];
+ for (let i = decoratorChain.length - 1; i >= 0; i--) {
+ const d = decoratorChain[i];
+ decorators!.push(<UpdateTransformControl key={`${d.transform.transformer.id}-${i}`} state={cell.parent} transform={d.transform} noMargin wrapInExpander />);
+ }
+
+ return decorators;
+ }
+
render() {
const cell = this.props.cell;
const n = cell.transform;
@@ -315,38 +329,11 @@ class StateTreeNodeLabel extends PluginUIComponent<{ cell: StateObjectCell, dept
let actions = this.actions;
return <div style={{ marginBottom: '1px' }}>
{row}
- <UpdateTransformControl state={cell.parent} transform={cell.transform} noMargin wrapInExpander />
+ {this.updates()}
{actions && <ActionMenu items={actions} onSelect={this.selectAction} />}
</div>
}
- // if (this.state.isCurrent) {
- // return <>
- // {row}
- // <StateTreeNodeTransform {...this.props} toggleCollapsed={this.toggleUpdaterObs} />
- // </>
- // }
-
return row;
}
-}
-
-// class StateTreeNodeTransform extends PluginUIComponent<{ nodeRef: string, state: State, depth: number, toggleCollapsed?: Observable<any> }> {
-// componentDidMount() {
-// // this.subscribe(this.plugin.events.state.object.updated, ({ ref, state }) => {
-// // if (this.props.nodeRef !== ref || this.props.state !== state) return;
-// // this.forceUpdate();
-// // });
-// }
-
-// render() {
-// const ref = this.props.nodeRef;
-// const cell = this.props.state.cells.get(ref)!;
-// const parent: StateObjectCell | undefined = (cell.sourceRef && this.props.state.cells.get(cell.sourceRef)!) || void 0;
-
-// if (!parent || parent.status !== 'ok') return null;
-
-// const transform = cell.transform;
-// return <UpdateTransformContol state={this.props.state} transform={transform} initiallyCollapsed={true} toggleCollapsed={this.props.toggleCollapsed} />;
-// }
-// }
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-plugin-ui/structure/components.tsx b/src/mol-plugin-ui/structure/components.tsx
index bc91366328502ac1eaf7c35441b3fe69187a4912..8c27c2152d545d6066b625ac33115a73cfc86198 100644
--- a/src/mol-plugin-ui/structure/components.tsx
+++ b/src/mol-plugin-ui/structure/components.tsx
@@ -81,9 +81,7 @@ class ComponentEditorControls extends PurePluginUIComponent<{}, ComponentEditorC
}
get presetActions() {
- const actions = [
- ActionMenu.Item('Clear', null),
- ];
+ const actions = [];
const pivot = this.plugin.managers.structure.component.pivotStructure;
const providers = this.plugin.builders.structure.representation.getPresets(pivot?.cell.obj)
for (const p of providers) {
diff --git a/src/mol-plugin/behavior/dynamic/selection/structure-representation-interaction.ts b/src/mol-plugin/behavior/dynamic/selection/structure-representation-interaction.ts
index 4de194b5133036f89bffbe3e65b1b909b91ba61b..eff25ffa4dabb1e51d67512f6f7ae1f6f87cd754 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-representation-interaction.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-representation-interaction.ts
@@ -55,8 +55,6 @@ const StructureRepresentationInteractionParams = (plugin: PluginContext) => {
type StructureRepresentationInteractionProps = PD.ValuesFor<ReturnType<typeof StructureRepresentationInteractionParams>>
-//PD.Values<typeof StructureRepresentationInteractionParams>
-
export enum StructureRepresentationInteractionTags {
Group = 'structure-interaction-group',
ResidueSel = 'structure-interaction-residue-sel',
@@ -213,7 +211,7 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
const state = this.plugin.state.data;
const builder = state.build();
- const all = StateSelection.Generators.root.subtree();
+ const all = StateSelection.Generators.root.subtree();
for (const repr of state.select(all.withTag(StructureRepresentationInteractionTags.ResidueRepr))) {
builder.to(repr).update(this.params.focusParams);
}
diff --git a/src/mol-plugin/util/substructure-parent-helper.ts b/src/mol-plugin/util/substructure-parent-helper.ts
index 16e703179e0a1d62fd2be066a0d7131b42c7ff77..10cfdae8a50c3054a9e204bef0140a9151670ef4 100644
--- a/src/mol-plugin/util/substructure-parent-helper.ts
+++ b/src/mol-plugin/util/substructure-parent-helper.ts
@@ -5,39 +5,91 @@
*/
import { Structure } from '../../mol-model/structure';
-import { State, StateObject, StateSelection, StateObjectCell } from '../../mol-state';
+import { State, StateObject, StateSelection, StateObjectCell, StateTransform } from '../../mol-state';
import { PluginContext } from '../context';
import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { arraySetAdd, arraySetRemove } from '../../mol-util/array';
export { SubstructureParentHelper };
class SubstructureParentHelper {
+ private decorators = new Map<string, string[]>();
private root = new Map<Structure, { ref: string, count: number }>();
private tracked = new Map<string, Structure>();
- /** Returns the root node of given structure if existing */
- get(s: Structure): StateObjectCell<PluginStateObject.Molecule.Structure> | undefined {
+ /** Returns the root node of given structure if existing, takes decorators into account */
+ get(s: Structure, ignoreDecorators = false): StateObjectCell<PluginStateObject.Molecule.Structure> | undefined {
const r = this.root.get(s);
if (!r) return;
- return this.plugin.state.data.cells.get(r.ref);
+ const decorators = this.decorators.get(r.ref);
+ if (ignoreDecorators || !decorators) return this.plugin.state.data.cells.get(r.ref);
+ return this.plugin.state.data.cells.get(this.findDeepestDecorator(r.ref, decorators));
+ }
+
+ private findDeepestDecorator(ref: string, decorators: string[]) {
+ if (decorators.length === 0) return ref;
+ if (decorators.length === 1) return decorators[0];
+
+ const cells = this.plugin.state.data.cells;
+ let depth = 0, ret = ref;
+ for (const dr of decorators) {
+ let c = cells.get(dr);
+ let d = 0;
+ while (c && c.transform.ref !== StateTransform.RootRef) {
+ d++;
+ c = cells.get(c.transform.parent);
+ }
+ if (d > depth) {
+ ret = dr;
+ depth = d;
+ }
+ }
+ return ret;
+ }
+
+ private addDecorator(root: string, ref: string) {
+ if (this.decorators.has(root)) {
+ arraySetAdd(this.decorators.get(root)!, ref);
+ } else {
+ this.decorators.set(root, [ref]);
+ }
+ }
+
+ private tryRemoveDecorator(root: string, ref: string) {
+ if (this.decorators.has(root)) {
+ const xs = this.decorators.get(root)!;
+ arraySetRemove(xs, ref);
+ if (xs.length === 0) this.decorators.delete(root);
+ }
}
private addMapping(state: State, ref: string, obj: StateObject) {
if (!PluginStateObject.Molecule.Structure.is(obj)) return;
- const parent = state.select(StateSelection.Generators.byRef(ref).rootOfType([PluginStateObject.Molecule.Structure]))[0];
this.tracked.set(ref, obj.data);
+ let parentRef;
// if the structure is already present in the tree, do not rewrite the root.
if (this.root.has(obj.data)) {
- this.root.get(obj.data)!.count++;
- return;
+ const e = this.root.get(obj.data)!;
+ parentRef = e.ref;
+ e.count++;
+ } else {
+ const parent = state.select(StateSelection.Generators.byRef(ref).rootOfType([PluginStateObject.Molecule.Structure]))[0];
+
+ if (!parent) {
+ this.root.set(obj.data, { ref, count: 1 });
+ } else {
+ parentRef = parent.transform.ref;
+ this.root.set(obj.data, { ref: parentRef, count: 1 });
+ }
}
- if (!parent) {
- this.root.set(obj.data, { ref, count : 1 });
- } else {
- this.root.set(obj.data, { ref: parent.transform.ref, count: 1 });
+ if (!parentRef) return;
+
+ const cell = state.cells.get(ref);
+ if (cell?.transform.isDecorator) {
+ this.addDecorator(parentRef, ref);
}
}
@@ -48,6 +100,9 @@ class SubstructureParentHelper {
this.tracked.delete(ref);
const root = this.root.get(s)!;
+
+ this.tryRemoveDecorator(root.ref, ref);
+
if (root.count > 1) {
root.count--;
} else {