From ff3757c35cc25b235e152b75d698a18cb3c0ce63 Mon Sep 17 00:00:00 2001
From: superstar54 <xingwang1991@gmail.com>
Date: Sat, 23 Nov 2024 22:17:08 +0100
Subject: [PATCH] only update the selected atoms if there are selected atoms

---
 src/atoms/AtomsViewer.js  |  1 +
 src/atoms/plugins/atom.js | 16 +++++++++++-----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/atoms/AtomsViewer.js b/src/atoms/AtomsViewer.js
index e1b57b0..acce1e4 100644
--- a/src/atoms/AtomsViewer.js
+++ b/src/atoms/AtomsViewer.js
@@ -198,6 +198,7 @@ class AtomsViewer {
     this._cell = null;
     this._atoms = null;
     this._currentFrame = 0;
+    this.selectedAtomsIndices = [];
     // set cell
     this.cellManager.cell = this.atoms.cell;
     // initialize the bond settings
diff --git a/src/atoms/plugins/atom.js b/src/atoms/plugins/atom.js
index dfc54b6..66c1254 100644
--- a/src/atoms/plugins/atom.js
+++ b/src/atoms/plugins/atom.js
@@ -188,25 +188,31 @@ export class AtomManager {
   // Method to update the scale of atoms
   updateAtomScale() {
     let mesh = this.meshes["atom"];
-    this.updateMeshScale(mesh, this.viewer.atoms.symbols, this.viewer.atomScale);
+    // only update the selected atoms if there are selected atoms
+    const indices = this.viewer.selectedAtomsIndices.length > 0 ? this.viewer.selectedAtomsIndices : [...Array(this.viewer.atoms.positions.length).keys()];
+    this.updateMeshScale(mesh, indices, this.viewer.atoms.symbols, this.viewer.atomScale);
     // update the boundary atoms
     mesh = this.meshes["image"];
     if (mesh) {
       const symbols = [];
+      const imageAtomsIndices = [];
       for (let i = 0; i < this.viewer.imageAtomsList.length; i++) {
         symbols.push(this.viewer.atoms.symbols[this.viewer.imageAtomsList[i][0]]);
+        if (this.viewer.selectedAtomsIndices.includes(this.viewer.imageAtomsList[i][0])) {
+          imageAtomsIndices.push(i);
+        }
       }
-      this.updateMeshScale(mesh, symbols, this.viewer.atomScale);
+      this.updateMeshScale(mesh, imageAtomsIndices, symbols, this.viewer.atomScale);
     }
   }
 
-  updateMeshScale(mesh, symbols, atomScale) {
+  updateMeshScale(mesh, indices, symbols, atomScale) {
     const position = new THREE.Vector3();
     const rotation = new THREE.Quaternion();
     const scale = new THREE.Vector3();
     console.log("settings: ", this.settings);
 
-    for (let i = 0; i < mesh.count; i++) {
+    indices.forEach((i) => {
       const instanceMatrix = new THREE.Matrix4();
       console.log("symbols[i]: ", symbols[i]);
       const radius = this.settings[symbols[i]].radius || 1;
@@ -218,7 +224,7 @@ export class AtomManager {
       // Recompose the matrix with the new scale
       instanceMatrix.compose(position, rotation, scale);
       mesh.setMatrixAt(i, instanceMatrix);
-    }
+    });
     mesh.instanceMatrix.needsUpdate = true;
   }
 }