fix broken reinitialize from ligend view when bm was active

src/plugin/manager.ts

@@ -21,7 +21,8 @@ class Visualization {
     // #region data properties    
     private environment: Model.Environment;
     private pdbId: string;
-    private bindingSite: Model.BindingSite;
+    private bindingSites: Model.BindingSite[];
+    private presentBindingSite: Model.BindingSite;
     private depiction: Depiction;
 
     private visualsMapper: VisualsMapper;
@@ -41,6 +42,7 @@ class Visualization {
         this.visualsMapper = new VisualsMapper(this.environment);
         this.rProvider = ResidueProvider.getInstance(this.environment);
         this.fullScreen = false;
+        this.bindingSites = new Array<Model.BindingSite>();
 
         if (uiParameters === undefined) uiParameters = new Config.UIParameters();
 
@@ -295,11 +297,13 @@ class Visualization {
 
         if (this.depiction === undefined || this.depiction.ccdId !== body.ligand.chem_comp_id) {
             this.initLigandDisplay(body.ligand.chem_comp_id).then(() => {
-                this.bindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
+                this.presentBindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
+                this.bindingSites.push(this.presentBindingSite);
                 this.setupLigandScene();
             });
         } else {
-            this.bindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
+            this.presentBindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
+            this.bindingSites.push(this.presentBindingSite);
             this.setupLigandScene();
         }
     }
@@ -316,10 +320,11 @@ class Visualization {
     public addBoundMoleculeInteractions(data: any, bmId: string) {
         let key = Object.keys(data)[0];
         this.interactionsData = data;
+        this.presentBindingSite = new Model.BindingSite().fromBoundMolecule(key, data[key][0]);
 
-        this.bindingSite = new Model.BindingSite().fromBoundMolecule(key, data[key][0]);
-        this.bindingSite.bmId = bmId;
-        let ligands = this.bindingSite.residues.filter(x => x.isLigand);
+        this.bindingSites.push(this.presentBindingSite);
+        this.presentBindingSite.bmId = bmId;
+        let ligands = this.presentBindingSite.residues.filter(x => x.isLigand);
 
         if (ligands.length === 1) this.initLigandInteractions(this.pdbId, ligands[0].authorResidueNumber, ligands[0].chainId);
         else this.setupScene();
@@ -362,7 +367,7 @@ class Visualization {
         let dataBlob = new Blob([JSON.stringify(this.interactionsData, null, 4)], { type: 'application/json' });
 
         downloadLink.href = URL.createObjectURL(dataBlob);
-        downloadLink.download = this.interactionsData === undefined ? 'no name.json' : `${this.pdbId}_${this.bindingSite.bmId}_interactions.json`;
+        downloadLink.download = this.interactionsData === undefined ? 'no name.json' : `${this.pdbId}_${this.presentBindingSite.bmId}_interactions.json`;
         document.body.appendChild(downloadLink);
         downloadLink.click();
         document.body.removeChild(downloadLink);
@@ -376,8 +381,21 @@ class Visualization {
      */
     public reinitialize() {
         
-        if (this.depiction === undefined) this.setupScene();
-        else this.setupLigandScene();
+        if (this.bindingSites.length > 1 && this.depiction !== undefined) {
+            this.presentBindingSite = this.bindingSites[0];
+            this.bindingSites.pop();
+            
+            this.depictionRoot.selectAll('*').remove();
+            this.depiction = undefined;
+            
+            this.setupScene().then(() => this.centerScene());
+        }
+        else if (this.depiction === undefined) { 
+            this.setupScene().then(() => this.centerScene());
+        }
+        else {
+            this.setupLigandScene().then(() => this.centerScene());
+        }
 
         this.hideLigandLabel();
     }
@@ -462,7 +480,7 @@ class Visualization {
     }
 
     private getSVGName(): string {
-        if (this.bindingSite !== undefined) return `${this.bindingSite.bmId}.svg`;
+        if (this.presentBindingSite !== undefined) return `${this.presentBindingSite.bmId}.svg`;
         if (this.depiction !== undefined) return `${this.depiction.ccdId}.svg`;
 
         return 'blank.svg';
@@ -562,7 +580,7 @@ class Visualization {
     private setupLinks() {
         this.links = this.linksRoot
             .selectAll()
-            .data(this.bindingSite.links)
+            .data(this.presentBindingSite.links)
             .enter().append('g');
 
         this.links
@@ -657,10 +675,10 @@ class Visualization {
         this.wipeOutVisuals();
         this.setupLinks();
 
-        this.bindingSite.interactionNodes
+        this.presentBindingSite.interactionNodes
             .filter((x: Model.InteractionNode) => !x.residue.isLigand)
             .forEach((x: Model.InteractionNode) => {
-                let lnks = this.bindingSite.links
+                let lnks = this.presentBindingSite.links
                     .filter((y: Model.LigandResidueLink) => y.containsInteractionNode(x))
                     .map((y: Model.LigandResidueLink) => [].concat.apply([], y.interaction.map(z => z.sourceAtoms)));
 
@@ -673,13 +691,13 @@ class Visualization {
 
 
         // setup nodes; wait for resources to be ready
-        this.bindingSite.interactionNodes.forEach(x => this.rProvider.downloadAnnotation(x.residue));
+        this.presentBindingSite.interactionNodes.forEach(x => this.rProvider.downloadAnnotation(x.residue));
         await Promise.all(this.rProvider.downloadPromises);
         await Promise.all([this.visualsMapper.graphicsPromise, this.visualsMapper.mappingPromise]);
 
         this.nodes = this.nodesRoot.append('g')
             .selectAll()
-            .data(this.bindingSite.interactionNodes)
+            .data(this.presentBindingSite.interactionNodes)
             .enter().append('g');
 
 
@@ -708,7 +726,7 @@ class Visualization {
         let charge = d3.forceManyBody().strength(-100).distanceMin(40).distanceMax(80);
         let collision = d3.forceCollide().radius(45);
 
-        this.simulation = d3.forceSimulation(this.bindingSite.interactionNodes)
+        this.simulation = d3.forceSimulation(this.presentBindingSite.interactionNodes)
             .force('link', forceLink)
             .force('charge', charge) //strength 
             .force('collision', collision)
@@ -732,13 +750,13 @@ class Visualization {
         this.setupLinks();
 
         // setup nodes; wait for resources to be ready
-        this.bindingSite.interactionNodes.forEach(x => ResidueProvider.getInstance(this.environment).downloadAnnotation(x.residue));
+        this.presentBindingSite.interactionNodes.forEach(x => ResidueProvider.getInstance(this.environment).downloadAnnotation(x.residue));
         await Promise.all(this.rProvider.downloadPromises);
         await Promise.all([this.visualsMapper.graphicsPromise, this.visualsMapper.mappingPromise]);
 
         this.nodes = this.nodesRoot
             .selectAll()
-            .data(this.bindingSite.interactionNodes)
+            .data(this.presentBindingSite.interactionNodes)
             .enter().append('g')
             .attr('class', (e: Model.InteractionNode) => `pdb-lig-env-svg-node pdb-lig-env-svg-${e.residue.getResidueType()}-res`)
             .on('click', (x: Model.InteractionNode, i: number, g: any) => this.selectLigand(x, i, g))
@@ -757,7 +775,7 @@ class Visualization {
         this.addNodeLabels(this.nodes);
 
         let forceLink = d3.forceLink()
-            .links(this.bindingSite.links)
+            .links(this.presentBindingSite.links)
             .distance((x: Model.Link) => (<Model.InteractionNode>x.source).residue.isLigand && (<Model.InteractionNode>x.target).residue.isLigand ? 55 : 150)
             .strength(0.5);
 
@@ -765,7 +783,7 @@ class Visualization {
         let collision = d3.forceCollide(45);
         let center = d3.forceCenter(this.parent.offsetWidth / 2, this.parent.offsetHeight / 2);
 
-        this.simulation = d3.forceSimulation(this.bindingSite.interactionNodes)
+        this.simulation = d3.forceSimulation(this.presentBindingSite.interactionNodes)
             .force('link', forceLink)
             .force('charge', charge) //strength 
             .force('collision', collision)