superstar54 · superstar54 · Mar 24, 2024 · Mar 18, 2024 · Mar 24, 2024
diff --git a/README.md b/README.md
@@ -60,6 +60,12 @@ npm run build
 npx playwright test
 ```
 
+Run the test with the title
+
+```
+npx playwright test -g "Animation"
+```
+
 If the snapshots need to be updated:
 
 ```

diff --git a/demo/demo.js b/demo/demo.js
@@ -1,5 +1,7 @@
 import { WEAS, Atoms, Species, parseXYZ, parseCIF, parseCube } from "../src/index.js"; // Adjust the path as necessary
+import * as THREE from "three";
 
+window.THREE = THREE;
 window.WEAS = WEAS;
 window.Atoms = Atoms;
 window.Species = Species;

diff --git a/examples/h2o.html b/examples/h2o.html
@@ -2,6 +2,7 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
+    <link rel="stylesheet" href="https://unpkg.com/weas/dist/style.css" />
     <title>WEAS Molecule</title>
   </head>
   <body>

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "weas",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "WEAS (Web Environment for Atomic Structures) is a JavaScript library to visualize and manipulate the atomistic structures directly in the web browser",
   "main": "src/index.js",
   "scripts": {

diff --git a/src/atoms/AtomsViewer.js b/src/atoms/AtomsViewer.js
@@ -445,8 +445,10 @@ class AtomsViewer {
     }
     this.atomColors = getAtomColors(this.atoms, this.colorBy, { colorType: this.colorType, colorRamp: this._colorRamp });
     this.drawBalls();
-    this.bondManager.drawBonds();
-    this.polyhedraManager.drawPolyhedras();
+    const bondMesh = this.bondManager.drawBonds();
+    this.atomsMesh.add(bondMesh);
+    const polyhedraMesh = this.polyhedraManager.drawPolyhedras();
+    this.atomsMesh.add(polyhedraMesh);
     this.isosurfaceManager.drawIsosurfaces();
     if (this.showVectorField) {
       this.VFManager.drawVectorFields();
@@ -459,6 +461,7 @@ class AtomsViewer {
   drawBalls() {
     // draw atoms
     this.atomsMesh = drawAtoms({ scene: this.tjs.scene, atoms: this.atoms, atomScales: this.atomScales, colors: this.atomColors, radiusType: this.radiusType, materialType: this._materialType });
+    this.tjs.scene.add(this.atomsMesh);
     // atoms to be drawn, boundary atoms, and the bonded atoms
     // merge the boundaryList and the bondedAtoms
     this.imageAtomsList = this.bondedAtoms["atoms"].concat(this.boundaryList);
@@ -473,7 +476,16 @@ class AtomsViewer {
         atomScales[i] = this.atomScales[this.imageAtomsList[i][0]];
       }
       const atomColors = getAtomColors(imageAtomsList, this.colorBy, { colorType: this.colorType, defaultColor: "#0xffffff", colorRamp: this._colorRamp });
-      this.boundaryAtomsMesh = drawAtoms({ scene: this.tjs.scene, atoms: imageAtomsList, atomScales: atomScales, colors: atomColors, radiusType: this.radiusType, materialType: this._materialType });
+      this.boundaryAtomsMesh = drawAtoms({
+        scene: this.tjs.scene,
+        atoms: imageAtomsList,
+        atomScales: atomScales,
+        colors: atomColors,
+        radiusType: this.radiusType,
+        materialType: this._materialType,
+        data_type: "boundary",
+      });
+      this.atomsMesh.add(this.boundaryAtomsMesh);
     }
   }
 
@@ -482,8 +494,16 @@ class AtomsViewer {
     const atomScales = new Array(this.atoms.getAtomsCount()).fill(0);
     // use yellow color to highlight the selected atoms
     const atomColors = new Array(this.atoms.getAtomsCount()).fill(new THREE.Color(0xffff00));
-    this.highlightAtomsMesh = drawAtoms({ scene: this.tjs.scene, atoms: this.atoms, atomScales: atomScales, colors: atomColors, radiusType: this.radiusType, materialType: "Basic" });
-    this.tjs.scene.add(this.highlightAtomsMesh);
+    this.highlightAtomsMesh = drawAtoms({
+      scene: this.tjs.scene,
+      atoms: this.atoms,
+      atomScales: atomScales,
+      colors: atomColors,
+      radiusType: this.radiusType,
+      materialType: "Basic",
+      data_type: "highlight",
+    });
+    this.atomsMesh.add(this.highlightAtomsMesh);
     this.highlightAtomsMesh.material.opacity = 0.6;
     this.updateHighlightAtomsMesh(this.selectedAtomsIndices);
   }

diff --git a/src/atoms/draw_atoms.js b/src/atoms/draw_atoms.js
@@ -4,7 +4,7 @@ import { materials } from "../tools/materials.js";
 
 const Radii = { Covalent: covalentRadii, VDW: vdwRadii };
 
-export function drawAtoms({ scene, atoms, atomScales, colors, radiusType = "Covalent", materialType = "Standard" }) {
+export function drawAtoms({ atoms, atomScales, colors, radiusType = "Covalent", materialType = "Standard", data_type = "atom" }) {
   console.time("drawAtoms Time");
   // console.log("atomScales: ", atomScales);
   console.log("Draw Atoms: ", +atoms.symbols.length, " atoms");
@@ -45,7 +45,7 @@ export function drawAtoms({ scene, atoms, atomScales, colors, radiusType = "Cova
     // Set color
     instancedMesh.setColorAt(globalIndex, colors[globalIndex]);
   });
-  instancedMesh.userData.type = "atom";
+  instancedMesh.userData.type = data_type;
   instancedMesh.userData.uuid = atoms.uuid;
   // the default objectMode for atoms is "edit"
   instancedMesh.userData.objectMode = "edit";
@@ -57,7 +57,6 @@ export function drawAtoms({ scene, atoms, atomScales, colors, radiusType = "Cova
     instancedMesh.instanceColor.needsUpdate = true;
   }
 
-  scene.add(instancedMesh);
   console.timeEnd("drawAtoms Time");
   return instancedMesh;
 }
diff --git a/src/atoms/plugins/bond.js b/src/atoms/plugins/bond.js
@@ -130,7 +130,7 @@ export class BondManager {
       atomColors = this.viewer.atomColors;
     }
     this.bondMesh = drawStick(this.viewer.atoms, this.bondList, this.buildBondDict(), this.viewer.bondRadius, this.viewer._materialType, atomColors);
-    this.scene.add(this.bondMesh);
+    return this.bondMesh;
   }
 
   updateBondMesh(atomIndex = null, atoms = null) {

diff --git a/src/atoms/plugins/isosurface.js b/src/atoms/plugins/isosurface.js
@@ -94,6 +94,7 @@ export class Isosurface {
   drawIsosurfaces() {
     /* Draw isosurfaces */
     if (this.volumetricData === null) {
+      console.log("No volumetric data is set");
       return;
     }
     console.log("drawIsosurfaces");

diff --git a/src/atoms/plugins/polyhedra.js b/src/atoms/plugins/polyhedra.js
@@ -27,7 +27,8 @@ export class PolyhedraManager {
     this.viewer = viewer;
     this.scene = this.viewer.tjs.scene;
     this.settings = [];
-    this.meshes = [];
+    // create a group to store the polyhedra meshes
+    this.meshes = new THREE.Group();
     this.init();
   }
 
@@ -81,9 +82,7 @@ export class PolyhedraManager {
 
   clearMeshes() {
     /* Remove highlighted atom meshes from the selectedAtomsMesh group */
-    this.meshes.forEach((mesh) => {
-      clearObject(this.scene, mesh);
-    });
+    clearObject(this.scene, this.meshes);
   }
 
   drawPolyhedras() {
@@ -92,10 +91,11 @@ export class PolyhedraManager {
     if (this.viewer.debug) {
       console.log("polyhedras: ", polyhedras);
     }
-    this.meshes = drawPolyhedras(this.viewer.atoms, polyhedras, this.viewer.bondManager.bondList, this.viewer._colorType, this.viewer._materialType);
-    this.meshes.forEach((mesh) => {
-      this.scene.add(mesh);
+    const meshes = drawPolyhedras(this.viewer.atoms, polyhedras, this.viewer.bondManager.bondList, this.viewer._colorType, this.viewer._materialType);
+    meshes.forEach((mesh) => {
+      this.meshes.add(mesh);
     });
+    return this.meshes;
   }
 
   updatePolyhedraMesh(atomIndex = null, atoms = null) {

diff --git a/src/controls/TransformControls.js b/src/controls/TransformControls.js
@@ -27,7 +27,6 @@ export class TransformControls {
     this.centroidNDC = new THREE.Vector2();
     this.initialAtomPositions = new Map(); // To store initial positions of selected atoms
     this.initialObjectState = new Map(); // To store initial state of selected objects
-    this.viewerRect = this.tjs.containerElement.getBoundingClientRect();
     // Get the camera's forward direction (negative z-axis in world space)
     this.cameraDirection = new THREE.Vector3(0, 0, -1);
   }
@@ -43,6 +42,7 @@ export class TransformControls {
   enterMode(mode, mousePosition) {
     this.mode = mode;
     console.log("Enter mode: ", this.mode);
+    this.cameraDirection = new THREE.Vector3(0, 0, -1);
     this.cameraDirection.applyQuaternion(this.tjs.camera.quaternion);
     if (this.mode === "translate") {
       // Get the camera's forward direction (negative z-axis in world space)
@@ -74,17 +74,15 @@ export class TransformControls {
     // Create a translate operation
     if (this.mode === "translate") {
       const translateVector = this.getTranslateVector(this.eventHandler.currentMousePosition, this.initialMousePosition);
-      console.log("Translate vector: ", translateVector);
-      const translateOperation = new TranslateOperation(this.weas, translateVector);
+      const translateOperation = new TranslateOperation({ weas: this.weas, vector: translateVector });
       this.weas.ops.execute(translateOperation, false);
     } else if (this.mode === "rotate") {
       const rotationAngle = this.getRotationAngle(this.eventHandler.currentMousePosition, this.initialMousePosition);
-      const rotateOperation = new RotateOperation(this.weas, this.cameraDirection, rotationAngle);
+      const rotateOperation = new RotateOperation({ weas: this.weas, axis: this.cameraDirection, angle: rotationAngle });
       this.weas.ops.execute(rotateOperation, false);
     } else if (this.mode === "scale") {
       const scaleVector = this.getScaleVector(this.eventHandler.currentMousePosition, this.initialMousePosition);
-      console.log("Scale vector: ", scaleVector);
-      const scaleOperation = new ScaleOperation(this.weas, scaleVector);
+      const scaleOperation = new ScaleOperation({ weas: this.weas, scale: scaleVector });
       this.weas.ops.execute(scaleOperation, false);
     } else {
       console.log("Invalid mode");
@@ -175,9 +173,15 @@ export class TransformControls {
     this.weas.objectManager.translateSelectedObjects(translateVector);
   }
 
+  getNDC(mousePosition) {
+    return new THREE.Vector2(((mousePosition.x - this.tjs.viewerRect.left) / this.tjs.viewerRect.width) * 2 - 1, -((mousePosition.y - this.tjs.viewerRect.top) / this.tjs.viewerRect.height) * 2 + 1);
+  }
+
   getTranslateVector(currentMousePosition, previousMousePosition) {
-    const currentWorldPosition = getWorldPositionFromScreen(currentMousePosition.x, currentMousePosition.y, this.tjs.camera, this.translatePlane);
-    const previousWorldPosition = getWorldPositionFromScreen(previousMousePosition.x, previousMousePosition.y, this.tjs.camera, this.translatePlane);
+    const newNDC = this.getNDC(currentMousePosition);
+    const currentWorldPosition = getWorldPositionFromScreen(this.tjs.camera, newNDC, this.translatePlane);
+    const initialNDC = this.getNDC(previousMousePosition);
+    const previousWorldPosition = getWorldPositionFromScreen(this.tjs.camera, initialNDC, this.translatePlane);
     return currentWorldPosition.sub(previousWorldPosition);
   }
 
@@ -200,15 +204,8 @@ export class TransformControls {
   }
 
   getScaleVector(currentMousePosition, previousMousePosition) {
-    const initialNDC = new THREE.Vector2(
-      ((previousMousePosition.x - this.viewerRect.left) / this.viewerRect.width) * 2 - 1,
-      -((previousMousePosition.y - this.viewerRect.top) / this.viewerRect.height) * 2 + 1,
-    );
-
-    const newNDC = new THREE.Vector2(
-      ((currentMousePosition.x - this.viewerRect.left) / this.viewerRect.width) * 2 - 1,
-      -((currentMousePosition.y - this.viewerRect.top) / this.viewerRect.height) * 2 + 1,
-    );
+    const initialNDC = this.getNDC(previousMousePosition);
+    const newNDC = this.getNDC(currentMousePosition);
     if (initialNDC.equals(newNDC)) {
       return; // Skip further processing
     }
@@ -221,15 +218,8 @@ export class TransformControls {
   }
 
   getRotationAngle(currentMousePosition, previousMousePosition) {
-    const initialNDC = new THREE.Vector2(
-      ((previousMousePosition.x - this.viewerRect.left) / this.viewerRect.width) * 2 - 1,
-      -((previousMousePosition.y - this.viewerRect.top) / this.viewerRect.height) * 2 + 1,
-    );
-
-    const newNDC = new THREE.Vector2(
-      ((currentMousePosition.x - this.viewerRect.left) / this.viewerRect.width) * 2 - 1,
-      -((currentMousePosition.y - this.viewerRect.top) / this.viewerRect.height) * 2 + 1,
-    );
+    const initialNDC = this.getNDC(previousMousePosition);
+    const newNDC = this.getNDC(currentMousePosition);
     if (initialNDC.equals(newNDC)) {
       console.log("No mouse movement detected, skipping rotation.");
       return; // Skip further processing

diff --git a/src/core/Camera.js b/src/core/Camera.js
@@ -0,0 +1,39 @@
+import * as THREE from "three";
+
+export class OrthographicCamera extends THREE.OrthographicCamera {
+  constructor(left, right, top, bottom, near, far, tjs = null) {
+    super(left, right, top, bottom, near, far);
+    this.tjs = tjs;
+  }
+
+  // Custom method to update zoom
+  updateZoom(value) {
+    if (this.zoom !== value) {
+      this.zoom = value;
+      this.updateProjectionMatrix(); // Required to apply the zoom change
+      this.dispatchObjectEvent({
+        data: value,
+        action: "zoom",
+        catalog: "camera",
+      });
+    }
+  }
+
+  // Custom method to update position
+  updatePosition(x, y, z) {
+    const newPos = new THREE.Vector3(x, y, z);
+    if (!this.position.equals(newPos)) {
+      this.position.copy(newPos);
+      this.dispatchObjectEvent({
+        data: [x, y, z],
+        action: "position",
+        catalog: "camera",
+      });
+    }
+  }
+
+  dispatchObjectEvent(data) {
+    const event = new CustomEvent("weas", { detail: data });
+    this.tjs.containerElement.dispatchEvent(event);
+  }
+}
diff --git a/src/core/ObjectManager.js b/src/core/ObjectManager.js
@@ -5,33 +5,42 @@ export class ObjectManager {
   constructor(weas) {
     this.weas = weas;
     this.selectionManager = weas.selectionManager;
-    this.sceneManager = weas.tjs.sceneManager;
+    this.scene = weas.tjs.scene;
   }
 
-  translateSelectedObjects(translateVector) {
-    this.selectionManager.selectedObjects.forEach((object) => {
+  translateSelectedObjects(translateVector, selectedObjects = null) {
+    if (selectedObjects === null) {
+      selectedObjects = this.selectionManager.selectedObjects;
+    }
+    selectedObjects.forEach((object) => {
       const initialPosition = object.position.clone();
       object.position.copy(initialPosition.add(translateVector));
     });
   }
 
-  rotateSelectedObjects(rotationAxis, rotationAngle) {
+  rotateSelectedObjects(rotationAxis, rotationAngle, selectedObjects = null) {
+    if (selectedObjects === null) {
+      selectedObjects = this.selectionManager.selectedObjects;
+    }
     rotationAxis = rotationAxis.normalize();
     rotationAngle = THREE.MathUtils.degToRad(rotationAngle);
-    this.selectionManager.selectedObjects.forEach((object) => {
+    selectedObjects.forEach((object) => {
       object.rotateOnAxis(rotationAxis, -rotationAngle);
     });
   }
 
   deleteSelectedObjects() {
     this.selectionManager.selectedObjects.forEach((object) => {
-      clearObject(this.sceneManager.scene, object);
+      clearObject(this.scene, object);
     });
     this.selectionManager.clearSelection();
   }
 
-  scaleSelectedObjects(scale) {
-    this.selectionManager.selectedObjects.forEach((object) => {
+  scaleSelectedObjects(scale, selectedObjects = null) {
+    if (selectedObjects === null) {
+      selectedObjects = this.selectionManager.selectedObjects;
+    }
+    selectedObjects.forEach((object) => {
       object.scale.multiply(scale);
     });
   }
@@ -41,7 +50,7 @@ export class ObjectManager {
     this.selectionManager.selectedObjects.forEach((object) => {
       const clone = object.clone();
       clone.position.add(new THREE.Vector3(1, 1, 1));
-      this.sceneManager.scene.add(clone);
+      this.scene.add(clone);
       newObjects.push(clone);
     });
     this.selectionManager.selectedObjects = newObjects;