allow atom names to be displayed

src/plugin/config.ts

@@ -70,6 +70,7 @@ namespace Config {
         residueLabel: boolean;
         tooltip: boolean;
         menu: boolean;
+        names: boolean;
 
         constructor() {
             this.reinitialize = true;
@@ -82,6 +83,7 @@ namespace Config {
             this.residueLabel = true;
             this.tooltip = true;
             this.menu = true;
+            this.names = true;
         }
     }
 }
\ No newline at end of file

src/plugin/depiction.ts

@@ -8,10 +8,10 @@
  * @class Depiction
  * @param {string} ccdId PDB CCD id.
  * @param {Atom[]} atoms List of atoms.
- * @param {Bond[]} bonds Visual representation of bonds. 
+ * @param {Bond[]} bonds Visual representation of bonds.
  * They do not correlate 1:1 with a number of bonds!
  * @param {Vector2D} resolution x,y dimension of the image. Needs to be used
- * for a scene shift, so it is centered. 
+ * for a scene shift, so it is centered.
  */
 class Depiction {
     ccdId: string;
@@ -39,7 +39,7 @@ class Depiction {
         this.bonds = new Array<Bond>();
 
         let bds = new Set<string>();
-        
+
         data.bonds.forEach(x => {
             let atomA = this.atoms.find(e => e.name == x.bgn);
             let atomB = this.atoms.find(e => e.name == x.end);
@@ -58,14 +58,14 @@ class Depiction {
 
 
     /**
-     * Returns an initial position of Residue node bound to a list of 
+     * Returns an initial position of Residue node bound to a list of
      * atom.
-     * 
+     *
      * Present implementation sorts all the partners based on the atom
-     * degree and then gets the one with the lovest degree and places 
+     * degree and then gets the one with the lovest degree and places
      * the initial residue position along the vector pointing from it.
      *
-     * @param {string[]} atomNames list of atom names the bound residue 
+     * @param {string[]} atomNames list of atom names the bound residue
      * has a contact with.
      * @returns {Vector2D} Returns an initial placement of the residue in contact.
      * @memberof Depiction
@@ -90,11 +90,13 @@ class Depiction {
         return new Vector2D(x, y);
     }
 
-    public draw() {
+    public draw(atom_names: boolean = false) {
         this.structure.selectAll("*").remove();
 
         this.appendBondVisuals();
-        this.appendTexts();
+
+        if (atom_names) this.appendAtomNames();
+        else this.appendLabels();
     }
 
     public highlightSubgraph(atoms: Array<string>, color: string = undefined) {
@@ -145,17 +147,35 @@ class Depiction {
             .attr('d', (y: Bond) => y.coords);
     }
 
+    /**
+     * Append atom name labels to the visualization.
+     *
+     * @memberof Depiction
+     */
+    private appendAtomNames() {
+        this.structure.selectAll()
+            .data(this.atoms)
+            .enter()
+            .append('text')
+            .attr('filter', "url(#solid-background)")
+            .attr('style', 'font-size:21px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000')
+            .attr('x', x => x.position.x)
+            .attr('y', x => x.position.y)
+            .attr('dominant-baseline', 'central')
+            .attr('text-anchor', 'middle')
+            .text(x => x.name);
+    }
+
     /**
      * Append depiction labels to the visualization. Because RDKIt places
      * the labels slightly differently this information needs to be
      * consumed too, because we cannot use just atom position directly.
-     * Also there are all sorts of colorful subscripts and superscripts, 
+     * Also there are all sorts of colorful subscripts and superscripts,
      * so it is much easier to use it this way.
      *
      * @memberof Depiction
      */
-    private appendTexts(): void {
-        
+    private appendLabels() {
         let data = this.atoms
             .filter(x => x.labels.length > 0)
             ?.map(x => x.labels)
@@ -172,7 +192,6 @@ class Depiction {
             .attr('dominant-baseline', (x: any) => x['dominant-baseline'])
             .attr('text-anchor', (x: any) => x['text-anchor'])
             .each(function (x: any) {
-                
                 for (var i = 0; i < x.tspans.length; i++) {
                     d3.select(this)
                         .append('tspan')
@@ -243,7 +262,7 @@ class Atom {
     }
 
     /**
-     * 
+     *
      *
      * @param {Atom} other
      * @returns true if the atoms are equal
@@ -310,7 +329,7 @@ class Vector2D {
 
 
     /**
-     * Composes vectors to a single one. This is used in infering the 
+     * Composes vectors to a single one. This is used in infering the
      * original placement of the residue nodes.
      *
      * @static
@@ -359,7 +378,7 @@ class Bond {
     /**
      * Get the other atom for a given bond.
      *
-     * @param {Atom} other     
+     * @param {Atom} other
      * @returns {Atom} The other atom from the bond.
      * @throws {Error} if the atom is not part of that bond at all.
      * @memberof Bond

src/plugin/manager.ts

@@ -17,7 +17,7 @@ class Visualization {
     private links: any;
     // #endregion
 
-    // #region data properties    
+    // #region data properties
     private environment: Model.Environment;
     private pdbId: string;
     private bindingSites: Model.BindingSite[];
@@ -190,7 +190,7 @@ class Visualization {
     /**
      * Download bound molecule interactions data from PDBe Graph API end point
      * /pdb/bound_molecule_interactions
-     * 
+     *
      * Correct parameters can be obtained using API call:
      * /pdb/bound_molecules
      *
@@ -212,7 +212,7 @@ class Visualization {
     /**
      * Download carbohydrate interactions data from PDBe Graph API end point
      * /pdb/carbohydrate_polymer_interactions
-     * 
+     *
      * Correct parameters can be obtained using API call:
      * /pdb/bound_molecules
      *
@@ -235,10 +235,10 @@ class Visualization {
     /**
      * Download ligand interactions data from PDBe Graph API end point
      * /pdb/bound_ligand_interactions.
-     * 
+     *
      * Correct parameters can be obtained using API call:
      * /pdb/bound_molecules
-     * 
+     *
      * @param {string} pdbId pdb id
      * @param {number} resId residue number aka: auth_seq_id
      * @param {string} chainId chain id aka: auth_asym_id
@@ -256,7 +256,7 @@ class Visualization {
     }
 
     /**
-     * Download ligand structure given the anotation generated by the 
+     * Download ligand structure given the anotation generated by the
      * PDBeChem process.
      *
      * @param {string} ligandId
@@ -285,6 +285,10 @@ class Visualization {
         this.depiction.draw();
     }
 
+    public toggleDepiction(atomNames: boolean) {
+        this.depiction.draw(atomNames);
+    }
+
 
     /**
      * Add atom highlight to the ligand structure. The previous highlight
@@ -318,7 +322,7 @@ class Visualization {
     /**
      * Add ligand interactions to the canvas
      *
-     * @param {*} data Data content of the API end point 
+     * @param {*} data Data content of the API end point
      * /pdb/bound_ligand_interactions
      * @memberof Visualization
      */
@@ -344,7 +348,7 @@ class Visualization {
     /**
      * Add bound molecule interactions to the canvas.
      *
-     * @param {*} data Data content of the API end point 
+     * @param {*} data Data content of the API end point
      * /pdb/bound_molecule_interactions
      * @param {string} bmId Bound molecule id
      * @memberof Visualization
@@ -472,8 +476,8 @@ class Visualization {
 
     private computeBoundingBox(minX: number, maxX: number, minY: number, maxY: number) {
         // The width and the height of the graph
-        let molWidth = (maxX - minX) + 1; // +1 to avoid 0 division
-        let molHeight = (maxY - minY) + 1;
+        let molWidth = Math.max((maxX - minX), this.parent.offsetWidth);
+        let molHeight = Math.max((maxY - minY), this.parent.offsetHeight);
 
         // how much larger the drawing area is than the width and the height
         let widthRatio = this.parent.offsetWidth / molWidth;
@@ -495,8 +499,7 @@ class Visualization {
         this.canvas.attr('transform', `translate(${xTrans}, ${yTrans}) scale(${minRatio})`);
 
         // tell the zoomer what we did so that next we zoom, it uses the
-        // transformation we entered here        
-
+        // transformation we entered here
         let translation = d3.zoomIdentity.translate(xTrans, yTrans).scale(minRatio);
         this.zoomHandler?.transform(this.svg, translation);
     }
@@ -761,7 +764,7 @@ class Visualization {
 
         this.simulation = d3.forceSimulation(this.presentBindingSite.interactionNodes)
             .force('link', forceLink)
-            .force('charge', charge) //strength 
+            .force('charge', charge) //strength
             .force('collision', collision)
             .on('tick', () => this.simulationStep());
 
@@ -771,7 +774,7 @@ class Visualization {
 
 
     /**
-     * Setup display of interactions for bound molecule. 
+     * Setup display of interactions for bound molecule.
      * * This includes: setup of links, nodes, simulation and subscribing to relevant events.
      * No depiction is required for this step.
      *
@@ -818,7 +821,7 @@ class Visualization {
 
         this.simulation = d3.forceSimulation(this.presentBindingSite.interactionNodes)
             .force('link', forceLink)
-            .force('charge', charge) //strength 
+            .force('charge', charge) //strength
             .force('collision', collision)
             .force('center', center)
             .on('tick', () => this.simulationStep());

src/plugin/ui.ts

@@ -234,6 +234,15 @@ class UI {
                     .attr('class', 'icon icon-common icon-sync-alt')
                     .on('click', () => this.reinitialize());
             }
+
+            if (p.reinitialize) {
+                dynamicPanel.append('i')
+                    .attr('id', 'pdb-lig-env-names-btn')
+                    .attr('title', 'Show/hide atom names')
+                    .attr('class', 'icon icon-common icon-font')
+                    .classed('active', false)
+                    .on('click', () => this.showNames());
+            }
         }
 
         if (p.tooltip) {
@@ -299,6 +308,21 @@ class UI {
         }
     }
 
+    private showNames() {
+        let btn = d3.select(this.parent).select('#pdb-lig-env-names-btn');
+        let isActive = btn.classed('active');
+
+        if (isActive) {
+            this.display.toggleDepiction(true);
+            btn.style('color', '#637ca0');
+            btn.classed('active', false);
+        } else {
+            this.display.toggleDepiction(false);
+            btn.style('color', '');
+            btn.classed('active', true);
+        }
+    }
+
     private showHelp() {
         let el = d3.select(this.parent).select('#pdb-lig-env-help-container');
         let btn = d3.select(this.parent).select('#pdb-lig-env-help-btn');