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@@ -10,7 +10,7 @@
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import { BehaviorSubject } from 'rxjs';
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import { Plugin } from 'molstar/lib/mol-plugin-ui/plugin';
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import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
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-import { ViewerState, CollapsedState, ModelUrlProvider, LigandUrlProvider, LigandViewerState } from './types';
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+import { ViewerState, CollapsedState, ModelUrlProvider, LigandUrlProvider, LigandViewerState, LoadParams } from './types';
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import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
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import { ColorNames } from 'molstar/lib/mol-util/color/names';
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@@ -147,7 +147,7 @@ const DefaultLigandViewerProps = {
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extensions: ObjectKeys(LigandExtensions),
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layoutIsExpanded: false,
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- layoutShowControls: true,
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+ layoutShowControls: false,
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layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
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layoutShowSequence: false,
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layoutShowLog: false,
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@@ -431,7 +431,12 @@ export class LigandViewer {
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},
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camera: {
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// desirable for alignment view so that the display doesn't "jump around" as more structures get loaded
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- manualReset: o.manualReset
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+ manualReset: o.manualReset,
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+ helper: {
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+ axes: {
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+ name: 'off', params: {}
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+ }
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+ }
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}
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},
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components: {
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@@ -446,10 +451,10 @@ export class LigandViewer {
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remoteState: 'none',
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},
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config: [
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+ [PluginConfig.VolumeStreaming.Enabled, false],
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[PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
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[PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
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[PluginConfig.Viewport.ShowAnimation, false],
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- [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
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[PluginConfig.Download.DefaultPdbProvider, 'rcsb'],
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[PluginConfig.Download.DefaultEmdbProvider, 'rcsb'],
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[PluginConfig.Structure.DefaultRepresentationPreset, PresetStructureRepresentations.auto.id],
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@@ -515,27 +520,35 @@ export class LigandViewer {
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for (const provider of this.ligandUrlProviders) {
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try {
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const p = provider(id);
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- await this.customState.modelLoader.load<any, any>({ fileOrUrl: p.url, format: p.format, isBinary: p.isBinary }, undefined, undefined, ChemicalCompontentTrajectoryHierarchyPreset, { shownCoordinateType: this.customState.shownCoordinateType });
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- await this.syncHydrogenState();
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-
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- for (const s of this._plugin.managers.structure.hierarchy.current.structures) {
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- for (const c of s.components) {
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- const isHidden = c.cell.state.isHidden === true || !this.customState.showLabels;
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- await this._plugin.builders.structure.representation.addRepresentation(c.cell, { type: 'label', typeParams: { level: 'element', ignoreHydrogens: this.customState.ignoreHydrogens } }, { initialState: { isHidden } });
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- }
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- }
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+ await this.load({ fileOrUrl: p.url, format: p.format, isBinary: p.isBinary });
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} catch (e) {
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console.warn(`loading '${id}' failed with '${e}', trying next ligand-loader-provider`);
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}
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}
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}
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+ async loadLigandFromUrl(url: string, format: BuiltInTrajectoryFormat, isBinary: boolean) {
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+ await this.load({ fileOrUrl: url, format, isBinary });
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+ }
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+
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+ private async load(p: LoadParams) {
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+ await this.customState.modelLoader.load<any, any>(p, undefined, undefined, ChemicalCompontentTrajectoryHierarchyPreset, { shownCoordinateType: this.customState.shownCoordinateType, representationPresetParams: { theme: { carbonColor: 'element-symbol' } } });
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+ await this.syncHydrogenState();
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+
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+ for (const s of this._plugin.managers.structure.hierarchy.current.structures) {
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+ for (const c of s.components) {
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+ const isHidden = c.cell.state.isHidden === true || !this.customState.showLabels;
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+ await this._plugin.builders.structure.representation.addRepresentation(c.cell, { type: 'label', typeParams: { level: 'element', fontQuality: 4, borderColor: ColorNames.black, ignoreHydrogens: this.customState.ignoreHydrogens } }, { initialState: { isHidden } });
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+ }
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+ }
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+ }
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+
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async toggleHydrogen() {
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this.customState.ignoreHydrogens = !this.customState.ignoreHydrogens;
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await this.syncHydrogenState();
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}
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- async syncHydrogenState() {
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+ private async syncHydrogenState() {
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const update = this._plugin.build();
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for (const s of this._plugin.managers.structure.hierarchy.current.structures) {
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for (const c of s.components) {
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@@ -547,6 +560,7 @@ export class LigandViewer {
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}
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}
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await update.commit();
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+ this._plugin.managers.camera.reset(undefined, 100);
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}
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async toggleLabels() {
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@@ -554,7 +568,7 @@ export class LigandViewer {
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await this.syncLabelState();
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}
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- async syncLabelState() {
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+ private async syncLabelState() {
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for (const s of this._plugin.managers.structure.hierarchy.current.structures) {
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for (const c of s.components) {
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if (c.cell.state.isHidden) continue;
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@@ -564,5 +578,6 @@ export class LigandViewer {
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}
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}
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}
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+ this._plugin.managers.camera.reset(undefined, 100);
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}
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}
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Sebastian Bittrich