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fix bond clear method #53

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merged 3 commits into from
Nov 24, 2024
Merged

fix bond clear method #53

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61d3eca
fix bond clear method
superstar54 Nov 23, 2024
ff3757c
only update the selected atoms if there are selected atoms
superstar54 Nov 23, 2024
20846fe
fix atomScale
superstar54 Nov 24, 2024
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144 changes: 78 additions & 66 deletions src/atoms/AtomsViewer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ class AtomsViewer {
this._showBondedAtoms = viewerSettings._showBondedAtoms;
this._showCell = viewerSettings._showCell;
this._boundary = viewerSettings._boundary;
this.atomScale = viewerSettings.atomScale;
this._atomScale = viewerSettings._atomScale;
this.backgroundColor = viewerSettings.backgroundColor;
this._selectedAtomsIndices = new Array(); // Store selected atoms
this.debug = viewerSettings.debug;
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -255,64 +256,7 @@ class AtomsViewer {
set modelStyle(newValue) {
newValue = parseInt(newValue);
this.logger.debug("updateModelStyle: ", newValue);
if (this.selectedAtomsIndices.length > 0) {
if (newValue === 0) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 1;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
} else if (newValue === 1) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0.4;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
} else if (newValue === 2) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0.4;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 1;
});
} else if (newValue === 3) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
} else if (newValue === 4) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
}
} else {
this._modelStyle = parseInt(newValue);
// clear this.models
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(0);
this.modelPolyhedras = new Array(this.atoms.getAtomsCount()).fill(0);
if (this._modelStyle === 0) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(1);
} else if (this._modelStyle === 1) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0.4);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(1);
} else if (this._modelStyle === 2) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0.4);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(2);
this.modelPolyhedras = new Array(this.atoms.getAtomsCount()).fill(1);
} else if (this._modelStyle === 3) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(3);
} else if (this._modelStyle === 4) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(4);
}
}
// avoid the recursive loop
if (this.guiManager.modelStyleController && this.guiManager.modelStyleController.getValue() !== newValue) {
this.guiManager.modelStyleController.setValue(newValue); // Update the GUI
}
this.updateModelStyles(newValue);
this.weas.eventHandlers.dispatchViewerUpdated({ modelStyle: newValue });
}

Expand All @@ -321,14 +265,13 @@ class AtomsViewer {
}

set radiusType(newValue) {
this._radiusType = newValue;
if (this.guiManager.radiusTypeController && this.guiManager.radiusTypeController.getValue() !== newValue) {
this.guiManager.radiusTypeController.setValue(newValue); // Update the GUI
if (this._radiusType !== newValue) {
this._radiusType = newValue;
this.weas.eventHandlers.dispatchViewerUpdated({ radiusType: newValue });
this.atomManager.init();
this.bondManager.init();
this.polyhedraManager.init();
}
this.weas.eventHandlers.dispatchViewerUpdated({ radiusType: newValue });
this.atomManager.init();
this.bondManager.init();
this.polyhedraManager.init();
}

get colorBy() {
Expand Down Expand Up @@ -447,6 +390,18 @@ class AtomsViewer {
this.weas.eventHandlers.dispatchViewerUpdated({ showBondedAtoms: newValue });
}

get atomScale() {
return this._atomScale;
}

set atomScale(newValue) {
if (this._atomScale !== newValue) {
this._atomScale = newValue;
this.weas.eventHandlers.dispatchViewerUpdated({ atomScale: newValue });
this.atomManager.updateAtomScale(newValue);
}
}

get atomScales() {
return this._atomScales;
}
Expand Down Expand Up @@ -728,6 +683,63 @@ class AtomsViewer {
atoms.newAttribute(name, values, domain);
});
}

updateModelStyles(newValue) {
if (this.selectedAtomsIndices.length > 0) {
if (newValue === 0) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 1;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
} else if (newValue === 1) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0.4;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
} else if (newValue === 2) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0.4;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 1;
});
} else if (newValue === 3) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
} else if (newValue === 4) {
this.selectedAtomsIndices.forEach((atomIndex) => {
this.atomScales[atomIndex] = 0;
this.modelSticks[atomIndex] = newValue;
this.modelPolyhedras[atomIndex] = 0;
});
}
} else {
// clear this.models
this._modelStyle = newValue;
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(0);
this.modelPolyhedras = new Array(this.atoms.getAtomsCount()).fill(0);
if (newValue === 0) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(1);
} else if (newValue === 1) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0.4);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(1);
} else if (newValue === 2) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0.4);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(2);
this.modelPolyhedras = new Array(this.atoms.getAtomsCount()).fill(1);
} else if (newValue === 3) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(3);
} else if (newValue === 4) {
this.atomScales = new Array(this.atoms.getAtomsCount()).fill(0);
this.modelSticks = new Array(this.atoms.getAtomsCount()).fill(4);
}
}
}
}

export { AtomsViewer };
86 changes: 82 additions & 4 deletions src/atoms/atomsGui.js
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,11 @@ class AtomsGUI {
this.div = document.createElement("div");
this.viewer.tjs.containerElement.appendChild(this.div);

// Listen to viewer events
this.viewer.tjs.containerElement.addEventListener("viewerUpdated", (event) => {
this.updateViewerControl(event.detail);
});

if (this.guiConfig.controls.atomsControl) {
this.addAtomsControl();
}
Expand Down Expand Up @@ -50,12 +55,12 @@ class AtomsGUI {

// Radius Type Control
this.radiusTypeController = atomsFolder
.add({ radiusType: this.viewer.radiusType }, "radiusType", radiusTypes)
.add(this.viewer, "radiusType", radiusTypes)
.name("Radius Type")
.onChange((value) => {
this.viewer.radiusType = value;
this.viewer.drawModels();
})
.name("Radius Type");
});

// Atom Label Control
this.atomLabelTypeController = atomsFolder
Expand All @@ -75,7 +80,12 @@ class AtomsGUI {
.name("Material Type");

// Atom Scale Control
atomsFolder.add(this.viewer, "atomScale", 0.1, 2.0).onChange(this.viewer.atomManager.updateAtomScale.bind(this.viewer.atomManager)).name("Atom Scale");
this.atomScaleController = atomsFolder
.add(this.viewer, "atomScale", 0.1, 2.0)
.name("Atom Scale")
.onChange((value) => {
this.viewer.atomScale = value; // Viewer setter handles the update
});

// Show Cell Control
this.showCellController = atomsFolder
Expand Down Expand Up @@ -325,6 +335,74 @@ class AtomsGUI {
legendContainer.style.left = position.includes("left") ? "10px" : "";
legendContainer.style.right = position.includes("right") ? "10px" : "";
}

updateViewerControl(detail) {
// detail is a object containing the updated viewer properties
// Update the GUI controls with the new values
Object.entries(detail).forEach(([key, value]) => {
switch (key) {
case "modelStyle":
this.updateModelStyle(value);
break;
case "radiusType":
this.updateRadiusType(value);
break;
case "atomLabelType":
// this.updateAtomLabelType(value);
break;
case "materialType":
// this.updateMaterialType(value);
break;
case "atomScale":
this.updateAtomScale(value);
break;
case "showCell":
// this.updateShowCell(value);
break;
case "showBondedAtoms":
// this.updateShowBondedAtoms(value);
break;
case "colorBy":
// this.updateColorBy(value);
break;
case "colorType":
// this.updateColorType(value);
break;
case "backgroundColor":
// this.updateBackgroundColor(value);
break;
case "isPlaying":
// this.updateIsPlaying(value);
break;
case "currentFrame":
// this.updateCurrentFrame(value);
break;
case "boundary":
// this.updateBoundary(value);
break;
default:
break;
}
});
}
updateAtomScale(newValue) {
if (this.atomScaleController && this.atomScaleController.getValue() !== newValue) {
this.atomScaleController.setValue(newValue);
}
}

updateModelStyle(newValue) {
if (this.modelStyleController && this.modelStyleController.getValue() !== newValue) {
this.modelStyleController.setValue(newValue);
this.viewer.drawModels();
}
}

updateRadiusType(newValue) {
if (this.radiusTypeController && this.radiusTypeController.getValue() !== newValue) {
this.radiusTypeController.setValue(newValue);
}
}
}

export { AtomsGUI };
22 changes: 16 additions & 6 deletions src/atoms/plugins/atom.js
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Original file line number Diff line number Diff line change
Expand Up @@ -186,27 +186,37 @@ export class AtomManager {
}
}
// Method to update the scale of atoms
updateAtomScale() {
updateAtomScale(value) {
if (value === undefined) {
value = this.viewer.atomScale;
}
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, value);
// 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, value);
}
this.viewer.tjs.render();
}

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;
Expand All @@ -218,7 +228,7 @@ export class AtomManager {
// Recompose the matrix with the new scale
instanceMatrix.compose(position, rotation, scale);
mesh.setMatrixAt(i, instanceMatrix);
}
});
mesh.instanceMatrix.needsUpdate = true;
}
}
11 changes: 7 additions & 4 deletions src/atoms/plugins/bond.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import { elementsWithPolyhedra, covalentRadii, elementColors, default_bond_pairs
import { convertColor } from "../utils.js";
import { kdTree } from "../../geometry/kdTree.js";
import { searchBoundary } from "./boundary.js";
import { clearObject } from "../../utils.js";

// default bond radius
export const defaultBondRadius = 0.1;
Expand Down Expand Up @@ -42,7 +43,7 @@ export class BondManager {
this.viewer = viewer;
this.scene = this.viewer.tjs.scene;
this.settings = {};
this.meshes = [];
this.meshes = {};
this.hideLongBonds = hideLongBonds;
this.showHydrogenBonds = showHydrogenBonds;
this.bondRadius = 0.1;
Expand Down Expand Up @@ -134,10 +135,12 @@ export class BondManager {

clearMeshes() {
/* Remove highlighted atom meshes from the selectedAtomsMesh group */
this.meshes.forEach((mesh) => {
clearObject(this.scene, mesh);
Object.values(this.meshes).forEach((mesh) => {
if (mesh) {
clearObject(this.scene, mesh);
}
});
this.meshes = [];
this.meshes = {};
}

drawBonds() {
Expand Down
2 changes: 1 addition & 1 deletion src/config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ const defaultViewerSettings = {
[0, 1],
[0, 1],
],
atomScale: 0.4, // Default atom scale
_atomScale: 0.4, // Default atom scale
backgroundColor: "#ffffff", // Default background color (white)
logLevel: "warn", // Default log level
};
Expand Down
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