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@@ -12,14 +12,17 @@ import {Mat4} from "molstar/lib/mol-math/linear-algebra";
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import {BuiltInTrajectoryFormat} from "molstar/lib/mol-plugin-state/formats/trajectory";
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import {PluginState} from "molstar/lib/mol-plugin/state";
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import {
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+ ResidueIndex,
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Structure,
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StructureElement,
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StructureProperties as SP,
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- StructureSelection
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+ StructureSelection,
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+ Queries as Q,
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+ StructureQuery
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} from "molstar/lib/mol-model/structure";
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import {OrderedSet} from "molstar/lib/mol-data/int";
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import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
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-import {State, StateSelection} from "molstar/lib/mol-state";
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+import {State} from "molstar/lib/mol-state";
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import {StructureRef} from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
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import {RcsbFvSelection, ResidueSelectionInterface} from "../../RcsbFvSelection/RcsbFvSelection";
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import {AbstractPlugin} from "./AbstractPlugin";
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@@ -29,6 +32,7 @@ import {Script} from "molstar/lib/mol-script/script";
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import {MolScriptBuilder} from "molstar/lib/mol-script/language/builder";
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import {SetUtils} from "molstar/lib/mol-util/set";
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import {StructureRepresentationRegistry} from "molstar/lib/mol-repr/structure/registry";
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+import {ColorTheme} from "molstar/lib/mol-theme/color";
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export enum LoadMethod {
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loadPdbId = "loadPdbId",
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@@ -55,7 +59,7 @@ interface LoadParams {
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id?:string;
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}
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-export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterface, SaguaroPluginPublicInterface {
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+export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterface {
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private plugin: Viewer;
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private innerSelectionFlag: boolean = false;
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private loadingFlag: boolean = false;
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@@ -64,6 +68,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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private modelChangeCallbackSubs: Subscription;
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private modelMap: Map<string,string|undefined> = new Map<string, string>();
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private readonly componentSet: Set<string> = new Set<string>();
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+ private readonly componentVisibility: Map<string,boolean> = new Map<string, boolean>();
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constructor(props: RcsbFvSelection) {
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super(props);
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@@ -100,6 +105,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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await this.plugin.loadStructureFromData(config.data!, config.format!, config.isBinary!);
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}
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}
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+ this.plugin.getPlugin().selectionMode = true;
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this.loadingFlag = false;
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this.mapModels(loadConfig.params);
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this.modelChangeCallback(this.getChains());
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@@ -134,22 +140,59 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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public setBackground(color: number) {
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}
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- public selectRange(modelId:string, asymId: string, begin: number, end: number, mode: 'select'|'hover', operation:'add'|'set'): void {
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+ public select(modelId:string, asymId: string, begin: number, end: number, mode: 'select'|'hover', operation:'add'|'set'): void;
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+ public select(selection: Array<{modelId:string; asymId: string; position: number;}>, mode: 'select'|'hover', operation:'add'|'set'): void;
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+ public select(...args: any[]): void{
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+ if(args.length === 6){
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+ this.selectRange(args[0],args[1],args[2],args[3],args[4],args[5]);
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+ }else if(args.length === 3){
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+ this.selectSet(args[0],args[1],args[2]);
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+ }
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+ }
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+ private selectRange(modelId:string, asymId: string, begin: number, end: number, mode: 'select'|'hover', operation:'add'|'set'): void {
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if(mode == null || mode === 'select') {
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this.innerSelectionFlag = true;
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}
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+
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this.plugin.select(this.getModelId(modelId), asymId, begin, end, mode, operation);
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this.innerSelectionFlag = false;
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}
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- public selectSet(selection: Array<{modelId:string; asymId: string; position: number;}>, mode: 'select'|'hover', operation:'add'|'set'): void {
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+ private selectSet(selection: Array<{modelId:string; asymId: string; position: number;}>, mode: 'select'|'hover', operation:'add'|'set'): void {
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if(mode == null || mode === 'select') {
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this.innerSelectionFlag = true;
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}
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this.plugin.select(selection.map(r=>{return{modelId: this.getModelId(r.modelId), position:r.position, asymId: r.asymId}}), mode, operation);
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this.innerSelectionFlag = false;
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}
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+ public clearSelection(mode:'select'|'hover', option?:{modelId:string; labelAsymId:string;}): void {
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+ if(mode === 'select') {
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+ this.plugin.clearFocus();
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+ this.innerSelectionFlag = true;
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+ }
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+ if(option != null)
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+ this.plugin.clearSelection(mode, {modelId: this.getModelId(option.modelId), labelAsymId: option.labelAsymId});
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+ else
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+ this.plugin.clearSelection(mode);
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+ this.innerSelectionFlag = false;
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+ }
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+
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+ public setFocus(modelId: string, asymId: string, begin: number, end: number): void{
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+ this.plugin.setFocus(this.getModelId(modelId), asymId, begin, end);
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+ }
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+ public clearFocus(): void {
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+ this.plugin.clearFocus();
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+ }
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- public focusPositions(modelId: string, asymId: string, positions:Array<number>): void{
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+ public cameraFocus(modelId: string, asymId: string, positions:Array<number>): void;
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+ public cameraFocus(modelId: string, asymId: string, begin: number, end: number): void;
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+ public cameraFocus(...args: any[]): void{
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+ if(args.length === 3){
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+ this.focusPositions(args[0],args[1],args[2]);
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+ }else if(args.length === 4){
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+ this.focusRange(args[0],args[1],args[2],args[3]);
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+ }
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+ }
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+ private focusPositions(modelId: string, asymId: string, positions:Array<number>): void{
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const data: Structure | undefined = getStructureWithModelId(this.plugin.getPlugin().managers.structure.hierarchy.current.structures, this.getModelId(modelId));
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if (data == null) return;
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const sel: StructureSelection = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
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@@ -162,8 +205,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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else
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this.plugin.getPlugin().managers.camera.reset();
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}
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-
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- public focusRange(modelId: string, asymId: string, begin: number, end: number): void{
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+ private focusRange(modelId: string, asymId: string, begin: number, end: number): void{
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const seqIds: Array<number> = new Array<number>();
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for(let n = begin; n <= end; n++){
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seqIds.push(n);
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@@ -175,6 +217,8 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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public async createComponent(componentLabel: string, modelId:string, asymId: string, representationType: StructureRepresentationRegistry.BuiltIn): Promise<void>;
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public async createComponent(componentLabel: string, modelId:string, residues: Array<{asymId: string; position: number;}>, representationType: StructureRepresentationRegistry.BuiltIn): Promise<void>;
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public async createComponent(...args: any[]): Promise<void> {
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+ this.removeComponent(args[0]);
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+ this.componentVisibility.set(args[0], true);
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this.componentSet.add(args[0]);
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if(args.length === 4)
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await this.plugin.createComponent(args[0], this.getModelId(args[1]), args[2], args[3]);
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@@ -193,6 +237,17 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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return false;
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}
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+ public async colorComponent(componentLabel: string, color: ColorTheme.BuiltIn): Promise<void>{
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+ for(const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups){
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+ for(const comp of c){
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+ if(comp.cell.obj?.label === componentLabel) {
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+ await this.plugin.getPlugin().managers.structure.component.updateRepresentationsTheme([comp], { color: color });
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+ return;
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+ }
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+ }
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+ }
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+ }
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+
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public getComponentSet(): Set<string>{
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const out: Set<string> = new Set<string>();
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this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups.forEach(c=>{
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@@ -213,11 +268,57 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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this.plugin.removeComponent(id);
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})
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this.componentSet.clear();
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+ this.componentVisibility.clear();
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}else{
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this.plugin.removeComponent(componentLabel);
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this.componentSet.delete(componentLabel);
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+ this.componentVisibility.delete(componentLabel);
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+ }
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+ }
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+
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+ public displayComponent(componentLabel: string): boolean;
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+ public displayComponent(componentLabel: string, visibilityFlag: boolean): void;
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+ public displayComponent(componentLabel: string, visibilityFlag?: boolean): void|boolean {
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+ if(typeof visibilityFlag === 'boolean')
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+ return this.changeComponentDisplay(componentLabel, visibilityFlag);
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+ else
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+ return this.getComponentDisplay(componentLabel);
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+ }
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+ private changeComponentDisplay(componentLabel: string, visibilityFlag: boolean): void{
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+ if(this.isComponent(componentLabel) && !this.componentVisibility.has(componentLabel))
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+ this.componentVisibility.set(componentLabel, true);
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+ if(this.componentVisibility.get(componentLabel) != visibilityFlag) {
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+ for (const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups) {
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+ for (const comp of c) {
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+ if (comp.cell.obj?.label === componentLabel) {
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+ if(this.getComponentDisplay(componentLabel) != visibilityFlag)
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+ this.plugin.getPlugin().managers.structure.component.toggleVisibility([comp]);
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+ return void 0;
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+ }
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+ }
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+ }
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}
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}
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+ private getComponentDisplay(componentLabel: string): boolean{
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+ for (const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups) {
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+ for (const comp of c) {
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+ if (comp.cell.obj?.label === componentLabel) {
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+ return this.componentVisibility.get(componentLabel) ?? false;
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+ }
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+ }
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+ }
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+ return false;
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+ }
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+
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+ public setRepresentationChangeCallback(g:()=>void){
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+ this.plugin.getPlugin().state.events.cell.stateUpdated.subscribe(o=>{
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+ if(o.cell.obj?.type.name === "Structure" && this.componentSet.has(o.cell.obj?.label)){
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+ if(o.cell.state.isHidden != null) {
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+ this.componentVisibility.set(o.cell.obj?.label, !o.cell.state.isHidden);
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+ }
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+ }
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+ });
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+ }
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public setHoverCallback(g:()=>void){
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this.plugin.getPlugin().behaviors.interaction.hover.subscribe((r: InteractivityManager.HoverEvent)=>{
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@@ -250,6 +351,59 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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if(this.innerSelectionFlag) {
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return;
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}
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+ if(this.plugin.getPlugin().managers.structure.selection.additionsHistory.length > 0) {
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+ const currentLoci: Loci = this.plugin.getPlugin().managers.structure.selection.additionsHistory[0].loci;
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+ const loc: StructureElement.Location = StructureElement.Location.create(currentLoci.structure);
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+ StructureElement.Location.set(
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+ loc,
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+ currentLoci.structure,
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+ currentLoci.elements[0].unit,
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+ currentLoci.elements[0].unit.elements[OrderedSet.getAt(currentLoci.elements[0].indices,0)]
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+ );
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+ const currentModelId: string = this.getModelId(currentLoci.structure.model.id);
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+ if(currentLoci.elements.length > 0)
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+ if(SP.entity.type(loc) === 'non-polymer') {
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+ const resAuthId: number = SP.residue.auth_seq_id(loc);
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+ const chainLabelId: string = SP.chain.label_asym_id(loc);
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+ const query: StructureQuery = Q.modifiers.includeSurroundings(
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+ Q.generators.residues({
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+ residueTest:l=>SP.residue.auth_seq_id(l.element) === resAuthId,
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+ chainTest:l=>SP.chain.label_asym_id(l.element) === chainLabelId
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+ }),
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+ {
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+ radius: 5,
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+ wholeResidues: true
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+ });
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+ this.innerSelectionFlag = true;
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+ const sel: StructureSelection = StructureQuery.run(query, currentLoci.structure);
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+ const surroundingsLoci: Loci = StructureSelection.toLociWithSourceUnits(sel);
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+ this.plugin.getPlugin().managers.structure.selection.fromLoci('add', surroundingsLoci);
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+ const surroundingsLoc = StructureElement.Location.create(surroundingsLoci.structure);
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+ for (const e of surroundingsLoci.elements) {
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+ StructureElement.Location.set(surroundingsLoc, surroundingsLoci.structure, e.unit, e.unit.elements[0]);
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+ if(SP.entity.type(surroundingsLoc) === 'polymer'){
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+ const currentAsymId: string = SP.chain.label_asym_id(surroundingsLoc);
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+ this.selection.setLastSelection('select', {
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+ modelId: currentModelId,
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+ labelAsymId: currentAsymId,
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+ regions: []
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+ });
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+ }
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+ }
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+ this.innerSelectionFlag = false;
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+ }else if( SP.entity.type(loc) === 'polymer' ) {
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+ const currentAsymId: string = SP.chain.label_asym_id(loc);
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+ this.selection.setLastSelection('select', {
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+ modelId: currentModelId,
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+ labelAsymId: currentAsymId,
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+ regions: []
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+ });
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+ }else{
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+ this.selection.setLastSelection('select', null);
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+ }
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+ }else{
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+ this.selection.setLastSelection('select', null);
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+ }
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const sequenceData: Array<ResidueSelectionInterface> = new Array<ResidueSelectionInterface>();
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for(const structure of this.plugin.getPlugin().managers.structure.hierarchy.current.structures){
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const data: Structure | undefined = structure.cell.obj?.data;
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@@ -258,8 +412,8 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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if(StructureElement.Loci.is(loci)){
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const loc = StructureElement.Location.create(loci.structure);
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for (const e of loci.elements) {
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+ StructureElement.Location.set(loc, loci.structure, e.unit, e.unit.elements[0]);
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const seqIds = new Set<number>();
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- loc.unit = e.unit;
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for (let i = 0, il = OrderedSet.size(e.indices); i < il; ++i) {
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loc.element = e.unit.elements[OrderedSet.getAt(e.indices, i)];
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seqIds.add(SP.residue.label_seq_id(loc));
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@@ -278,17 +432,6 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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});
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}
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- public clearSelection(mode:'select'|'hover', option?:{modelId:string; labelAsymId:string;}): void {
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- if(mode === 'select') {
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- this.innerSelectionFlag = true;
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- }
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- if(option != null)
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- this.plugin.clearSelection(mode, {modelId: this.getModelId(option.modelId), labelAsymId: option.labelAsymId});
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- else
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- this.plugin.clearSelection(mode);
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- this.innerSelectionFlag = false;
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- }
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-
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public pluginCall(f: (plugin: PluginContext) => void){
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this.plugin.pluginCall(f);
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}
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bioinsilico