Ligand selection features

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [4.0.12] - 2024-08-20
+### Improvements
+- Ligand selection will always switch to the chain with most selected residues
+- Ligand selection will not select other ligands
+### Dependency update
+- rcsb-saguaro-app v6.2.5
+- audit fix
+
 ## [4.0.12] - 2024-08-20
 ### Dependency update
 - rcsb-saguaro-app v6.2.1

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-3d",
-  "version": "4.0.12",
+  "version": "4.1.0",
   "description": "RCSB Molstar/Saguaro Web App",
   "main": "build/dist/app.js",
   "files": [
@@ -90,10 +90,10 @@
   },
   "peerDependencies": {
     "@rcsb/rcsb-api-tools": "^4.3.0",
-    "@rcsb/rcsb-molstar": "^2.9.3",
+    "@rcsb/rcsb-molstar": "^2.10.3",
     "@rcsb/rcsb-saguaro": "^3.0.9",
-    "@rcsb/rcsb-saguaro-app": "^6.2.2",
-    "molstar": "^4.0.1",
+    "@rcsb/rcsb-saguaro-app": "^6.2.5",
+    "molstar": "^4.4.1",
     "react": "^18.3.1",
     "react-dom": "^18.3.1"
   },

src/RcsbFvState/RcsbFvSelectorManager.ts

@@ -7,11 +7,12 @@ export interface RegionSelectionInterface{
     source:'structure'|'sequence';
 }
 
+type typedSelection = SaguaroRegionList & {source:RegionSelectionInterface["source"]};
 //TODO this class should be interfaced
 //TODO Check how lastSelection is used. It is not linked to selection. Only label asymId is used when the value is got
 export class RcsbFvSelectorManager {
 
-    private lastSelection: SaguaroRegionList & {source:RegionSelectionInterface["source"]}| null = null;
+    private lastSelection: typedSelection | null = null;
     private selection: Array<SaguaroRegionList> = new Array<SaguaroRegionList>();
     private hover: Array<SaguaroRegionList> = new Array<SaguaroRegionList>();
 
@@ -58,11 +59,11 @@ export class RcsbFvSelectorManager {
             return this.hover;
     }
 
-    public getLastSelection(): SaguaroRegionList & {source:RegionSelectionInterface["source"]} | null{
+    public getLastSelection(): typedSelection | null{
        return this.lastSelection;
     }
 
-    public setLastSelection(selection: SaguaroRegionList & {source:RegionSelectionInterface["source"]} | null): void {
+    public setLastSelection(selection: typedSelection | null): void {
         this.lastSelection = selection;
     }
 

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarCallbackManager.ts

@@ -8,16 +8,16 @@ import {
     Structure,
     StructureElement,
     StructureProperties as SP,
-    StructureQuery,
     StructureSelection
 } from "molstar/lib/mol-model/structure";
 import {OrderedSet} from "molstar/lib/mol-data/int";
-import {Queries as Q} from "molstar/lib/mol-model/structure/query";
 import {PluginContext} from "molstar/lib/mol-plugin/context";
 import {Viewer} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {Subscription} from "rxjs";
 import {DataContainer, DataContainerReader} from "../../../Utils/DataContainer";
 import {RcsbFvStateInterface} from "../../../RcsbFvState/RcsbFvStateInterface";
+import {MolScriptBuilder as MS} from "molstar/lib/mol-script/language/builder";
+import {Script} from "molstar/lib/mol-script/script";
 
 type ModelMapType = Omit<ViewerModelMapManagerInterface<unknown,unknown>,'add'|'delete'>;
 export class MolstarCallbackManager implements ViewerCallbackManagerInterface{
@@ -29,7 +29,9 @@ export class MolstarCallbackManager implements ViewerCallbackManagerInterface{
     private readonly innerSelectionFlag: DataContainer<boolean>;
     private readonly innerReprChangeFlag: DataContainer<boolean>;
 
-    private selectSubs: Subscription;
+    private addSubs: Subscription;
+    private removeSubs: Subscription;
+    private clearSubs: Subscription;
     private hoverSubs: Subscription;
     private modelChangeSubs: Subscription;
     private reprChangeSubs: Subscription;
@@ -82,97 +84,75 @@ export class MolstarCallbackManager implements ViewerCallbackManagerInterface{
     }
 
     public subscribeSelection(): Subscription {
-        this.selectSubs = this.viewer.plugin.managers.structure.selection.events.changed.subscribe(()=>{
+        this.addSubs = this.viewer.plugin.managers.structure.selection.events.loci.add.subscribe((currentLoci)=>{
             if(this.innerSelectionFlag.get())
                 return;
-            if(this.viewer.plugin.managers.structure.selection.additionsHistory.length > 0) {
-                const currentLoci: Loci = this.viewer.plugin.managers.structure.selection.additionsHistory[0].loci;
-                const loc: StructureElement.Location = StructureElement.Location.create(currentLoci.structure);
-                StructureElement.Location.set(
-                    loc,
-                    currentLoci.structure,
-                    currentLoci.elements[0].unit,
-                    currentLoci.elements[0].unit.elements[OrderedSet.getAt(currentLoci.elements[0].indices,0)]
-                );
-                const currentModelId: string = this.modelMapManager.getModelId(currentLoci.structure.model.id);
-                if(currentLoci.elements.length > 0)
-                    if(SP.entity.type(loc) === 'non-polymer') {
-                        const resAuthId: number = SP.residue.auth_seq_id(loc);
-                        const chainLabelId: string = SP.chain.label_asym_id(loc);
-                        const query: StructureQuery = Q.modifiers.includeSurroundings(
-                            Q.generators.residues({
-                                residueTest:l=>SP.residue.auth_seq_id(l.element) === resAuthId,
-                                chainTest:l=>SP.chain.label_asym_id(l.element) === chainLabelId
-                            }),
-                            {
-                                radius: 5,
-                                wholeResidues: true
-                            });
-                        this.innerSelectionFlag.set(true);
-                        const sel: StructureSelection = StructureQuery.run(query, currentLoci.structure);
-                        const surroundingsLoci: Loci = StructureSelection.toLociWithSourceUnits(sel);
-                        this.viewer.plugin.managers.structure.selection.fromLoci('add', surroundingsLoci);
-                        const surroundingsLoc = StructureElement.Location.create(surroundingsLoci.structure);
-                        for (const e of surroundingsLoci.elements) {
-                            StructureElement.Location.set(surroundingsLoc, surroundingsLoci.structure, e.unit, e.unit.elements[0]);
-                            if(SP.entity.type(surroundingsLoc) === 'polymer'){
-                                this.stateManager.selectionState.setLastSelection({
-                                    modelId: currentModelId,
-                                    labelAsymId: SP.chain.label_asym_id(surroundingsLoc),
-                                    source:"structure",
-                                    regions: []
-                                });
-                            }
-                        }
-                        this.innerSelectionFlag.set(false);
-                    }else if( SP.entity.type(loc) === 'polymer' ) {
+            const loc: StructureElement.Location = createLocation(currentLoci);
+            const currentModelId: string = this.modelMapManager.getModelId(currentLoci.structure.model.id);
+            if(SP.entity.type(loc) === 'non-polymer') {
+                const resAuthId: number = SP.residue.auth_seq_id(loc);
+                const chainLabelId: string = SP.chain.label_asym_id(loc);
+                const surrCore = MS.struct.generator.atomGroups({
+                    'residue-test': MS.core.rel.eq([MS.ammp('auth_seq_id'), resAuthId]),
+                    'chain-test': MS.core.rel.eq([MS.ammp('label_asym_id'), chainLabelId]),
+                    'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
+                });
+                const surrExp = MS.struct.modifier.includeSurroundings({
+                    0: surrCore,
+                    radius: 5,
+                    "as-whole-residues": true
+                })
+                const polymerExp = MS.struct.generator.atomGroups({
+                    'residue-test': MS.core.rel.eq([MS.ammp('entityType'),'non-polymer'])
+                });
+                const sel: StructureSelection = Script.getStructureSelection(Q=>Q.struct.modifier.exceptBy({
+                    0: surrExp,
+                    by: polymerExp
+                }), currentLoci.structure);
+                this.innerSelectionFlag.set(true);
+                const surroundingsLoci: StructureElement.Loci = StructureSelection.toLociWithSourceUnits(sel);
+                this.viewer.plugin.managers.structure.selection.fromLoci('add', StructureSelection.toLociWithSourceUnits(sel));
+                const surroundingsLoc = StructureElement.Location.create(surroundingsLoci.structure);
+                let currentSelLength = 0;
+                for (const e of surroundingsLoci.elements) {
+                    StructureElement.Location.set(surroundingsLoc, surroundingsLoci.structure, e.unit, e.unit.elements[0]);
+                    if(SP.entity.type(surroundingsLoc) === 'polymer' && ((typeof e.indices !== "object" && currentSelLength == 0) || (e.indices as unknown as []).length >= currentSelLength)){
+                        currentSelLength = typeof e.indices !== "object" ? 0 : (e.indices as unknown as []).length;
                         this.stateManager.selectionState.setLastSelection({
                             modelId: currentModelId,
-                            labelAsymId: SP.chain.label_asym_id(loc),
-                            operatorName: SP.unit.operator_name(loc),
+                            labelAsymId: SP.chain.label_asym_id(surroundingsLoc),
                             source:"structure",
                             regions: []
                         });
-                    }else{
-                        this.stateManager.selectionState.setLastSelection(null);
                     }
-                else
-                    this.stateManager.selectionState.setLastSelection(null);
+                }
+                this.innerSelectionFlag.set(false);
+            }else if( SP.entity.type(loc) === 'polymer' ) {
+                const labelAsymId= SP.chain.label_asym_id(loc);
+                const operatorName = SP.unit.operator_name(loc);
+                this.stateManager.selectionState.setLastSelection({
+                    modelId: currentModelId,
+                    labelAsymId: labelAsymId,
+                    operatorName: operatorName,
+                    source: "structure",
+                    regions: []
+                });
             }else{
                 this.stateManager.selectionState.setLastSelection(null);
             }
-            const sequenceData: Array<SaguaroSet> = new Array<SaguaroSet>();
-            for(const structure of this.viewer.plugin.managers.structure.hierarchy.current.structures){
-                const data: Structure | undefined = structure.cell.obj?.data;
-                if(data == null) return;
-                const loci: Loci = this.viewer.plugin.managers.structure.selection.getLoci(data);
-                if(StructureElement.Loci.is(loci)){
-                    const loc = StructureElement.Location.create(loci.structure);
-                    for (const e of loci.elements) {
-                        StructureElement.Location.set(loc, loci.structure, e.unit, e.unit.elements[0]);
-                        if(SP.entity.type(loc) === 'polymer'){
-                            const seqIds = new Set<number>();
-                            for (let i = 0, il = OrderedSet.size(e.indices); i < il; ++i) {
-                                loc.element = e.unit.elements[OrderedSet.getAt(e.indices, i)];
-                                seqIds.add(SP.residue.label_seq_id(loc));
-                            }
-                            if(seqIds.size > 0)
-                                sequenceData.push({
-                                    modelId: this.modelMapManager.getModelId(data.model.id),
-                                    labelAsymId: SP.chain.label_asym_id(loc),
-                                    operatorName: SP.unit.operator_name(loc),
-                                    seqIds
-                                });
-                        }
-                    }
-                }
-            }
-            this.stateManager.selectionState.setSelectionFromResidueSelection(sequenceData, 'select', 'structure');
-            if(sequenceData.length == 0)
-                this.stateManager.selectionState.setLastSelection(null);
-            this.stateManager.next({type:"selection-change", view:"3d-view"});
+           this.updateStateManager()
         });
-        return this.selectSubs;
+        this.removeSubs = this.viewer.plugin.managers.structure.selection.events.loci.remove.subscribe(()=> {
+            if (this.innerSelectionFlag.get())
+                return;
+            this.updateStateManager();
+        });
+        this.viewer.plugin.managers.structure.selection.events.loci.clear.subscribe(()=> {
+            if (this.innerSelectionFlag.get())
+                return;
+            this.updateStateManager();
+        });
+        return this.addSubs;
     }
 
     public pluginCall(f: (plugin: PluginContext) => void){
@@ -194,10 +174,55 @@ export class MolstarCallbackManager implements ViewerCallbackManagerInterface{
     }
 
     public unsubscribe(): void {
-        this.selectSubs?.unsubscribe();
+        this.addSubs?.unsubscribe();
+        this.removeSubs?.unsubscribe();
+        this.clearSubs?.unsubscribe();
         this.modelChangeSubs?.unsubscribe();
         this.hoverSubs?.unsubscribe();
     }
 
+    private updateStateManager(): void{
+        const sequenceData: Array<SaguaroSet> = new Array<SaguaroSet>();
+        for(const structure of this.viewer.plugin.managers.structure.hierarchy.current.structures){
+            const data: Structure | undefined = structure.cell.obj?.data;
+            if(data == null) return;
+            const loci: Loci = this.viewer.plugin.managers.structure.selection.getLoci(data);
+            if(StructureElement.Loci.is(loci)){
+                const loc = StructureElement.Location.create(loci.structure);
+                for (const e of loci.elements) {
+                    StructureElement.Location.set(loc, loci.structure, e.unit, e.unit.elements[0]);
+                    if(SP.entity.type(loc) === 'polymer'){
+                        const seqIds = new Set<number>();
+                        for (let i = 0, il = OrderedSet.size(e.indices); i < il; ++i) {
+                            loc.element = e.unit.elements[OrderedSet.getAt(e.indices, i)];
+                            seqIds.add(SP.residue.label_seq_id(loc));
+                        }
+                        if(seqIds.size > 0)
+                            sequenceData.push({
+                                modelId: this.modelMapManager.getModelId(data.model.id),
+                                labelAsymId: SP.chain.label_asym_id(loc),
+                                operatorName: SP.unit.operator_name(loc),
+                                seqIds
+                            });
+                    }
+                }
+            }
+        }
+        this.stateManager.selectionState.setSelectionFromResidueSelection(sequenceData, 'select', 'structure');
+        if(sequenceData.length == 0)
+            this.stateManager.selectionState.setLastSelection(null);
+        this.stateManager.next({type:"selection-change", view:"3d-view"});
+    }
 
 }
+
+function createLocation(loci: StructureElement.Loci){
+    const loc: StructureElement.Location = StructureElement.Location.create(loci.structure);
+    StructureElement.Location.set(
+        loc,
+        loci.structure,
+        loci.elements[0].unit,
+        loci.elements[0].unit.elements[OrderedSet.getAt(loci.elements[0].indices,0)]
+    );
+    return loc;
+}

src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AssemblyRepresentationPresetProvider.ts

@@ -8,6 +8,7 @@ import {StructureElement, StructureProperties as SP} from "molstar/lib/mol-model
 import {MolScriptBuilder as MS} from "molstar/lib/mol-script/language/builder";
 import uniqid from "uniqid";
 import {PLDDTConfidenceColorThemeProvider} from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
+import { QualityAssessment } from 'molstar/lib/extensions/model-archive/quality-assessment/prop';
 import {ColorTheme} from "molstar/lib/mol-theme/color";
 import reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 import {StructureBuilder} from "molstar/lib/mol-plugin-state/builder/structure";
@@ -68,7 +69,7 @@ export const AssemblyRepresentationPresetProvider = StructureRepresentationPrese
                     quality: "auto"
                 });
                 representationMap[asymId] = builder.buildRepresentation(update, comp, {
-                    color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
+                    color: structure.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
                     type: "cartoon"
                 });
 

tsconfig.json

@@ -5,7 +5,7 @@
     "alwaysStrict": true,
     "noImplicitAny": true,
     "noImplicitThis": true,
-    "sourceMap": false,
+    "sourceMap": true,
     "noUnusedLocals": true,
     "strictNullChecks": true,
     "strictFunctionTypes": true,