Change width/height calc. Trim prmtop atom names.

Previous calculation did not account for applied scaling transformations. Now remove whitespace from prmtop atom names.
3dmol · Mar 13, 2024 · cf59124 · cf59124
1 parent 0a69191
commit cf59124
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Showing 4 changed files with 27,589 additions and 27,580 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/src/GLViewer.ts b/src/GLViewer.ts
@@ -111,30 +111,39 @@ export class GLViewer {
     private spinInterval: any;
 
 
-    //reimplement jquery getwidth/height
-    private getRect() {
+    private getWidth() {
         let div = this.container;
-        let rect = div.getBoundingClientRect();
-        if (rect.width == 0 && rect.height == 0 && div.style.display === 'none') {
+        //offsetwidth accounts for scaling
+        let w = div.offsetWidth; 
+        if(w == 0 && div.style.display === 'none') {
             let oldpos = div.style.position;
             let oldvis = div.style.visibility;
             div.style.display = 'block';
             div.style.visibility = 'hidden';
             div.style.position = 'absolute';
-            rect = div.getBoundingClientRect();
+            w = div.offsetWidth;
             div.style.display = 'none';
             div.style.visibility = oldvis;
-            div.style.position = oldpos;
+            div.style.position = oldpos;            
         }
-        return rect;
-    };
-
-    private getWidth() {
-        return this.getRect().width;
+        return w;
     };
 
     private getHeight() {
-        return this.getRect().height;
+        let div = this.container;
+        let h = div.offsetHeight; 
+        if(h == 0 && div.style.display === 'none') {
+            let oldpos = div.style.position;
+            let oldvis = div.style.visibility;
+            div.style.display = 'block';
+            div.style.visibility = 'hidden';
+            div.style.position = 'absolute';
+            h = div.offsetHeight;
+            div.style.display = 'none';
+            div.style.visibility = oldvis;
+            div.style.position = oldpos;            
+        }
+        return h;
     };
 
     private setupRenderer() {

diff --git a/src/parsers/PRMTOP.ts b/src/parsers/PRMTOP.ts
@@ -45,8 +45,8 @@ export function PRMTOP(str: string /*, options*/) {
         atom.x = 0;
         atom.y = 0;
         atom.z = 0;
-        atom.atom = lines[index + 1].slice(col[1] * j, col[1] * (j + 1));
-        atom.elem = lines[index + 1].slice(col[1] * j, col[1] * j + 1);
+        atom.atom = lines[index + 1].slice(col[1] * j, col[1] * (j + 1)).trim();
+        atom.elem = lines[index + 1].slice(col[1] * j, col[1] * j + 1).trim();
         atom.properties = properties;
         atom.bonds = [];
         atom.bondOrder = [];