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index.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>PYMOL in Pyodide</title>
<style>
#canvas {
display: block;
margin: 0 auto;
border:1px solid black;
}
</style>
<style>
#loading-container {
position: relative;
width:150px;
height:150px;
margin: 100px;
}
#loading{
position:absolute;
transform:translate(-50%,-50%);
border:4px solid #E5EDFF;
border-left-color:#f39c12;
border-radius:50%;
width:90%;
height:90%;
animation:spinner1 1.2s linear infinite
}
#loading-progress{
position:absolute;
top:50%;
left:50%;
transform:translate(-50%,-50%);
font-size:20px;
color:#f39c12;
}
@keyframes spinner1{
0%{
transform:rotate(0)
}
100%{
transform:rotate(360deg)
}
}
#main-content {
display: none;
}
body {
display: flex;
flex-direction: column;
align-items: center;
}
#load-pdb-area {
display: flex;
flex-direction: row;
justify-content: center;
align-items: center;
}
#load-pdb-area span.separator {
margin: 0 20px;
font-size: 24px;
}
#load-pdb-area span#load-message {
margin: 0 20px;
font-size: 18px;
color: red;
}
#DBID {
width: 200px;
text-align: center;
}
#drop-area1 {
border: 2px dashed #ccc;
border-radius: 20px;
width: 500px;
height: 70px;
margin: 20px 0;
display: flex;
align-items: center;
justify-content: center;
font-size: 24px;
text-align: center;
}
#pymol-control-area {
display: flex;
flex-direction: column;
justify-content: space-around;
align-items: center;
}
#pymol-control-area > * {
margin: 5px;
}
#cmdInput {
margin: 5px;
width: 300px;
}
</style>
</head>
<body>
<div id="loading-container"><div id="loading"></div><span id="loading-progress">0%</span></div>
<div id="main-content">
<canvas id="canvas" width="1024" height="600"></canvas>
<div id="load-pdb-area">
<div id="drop-area1">Drag and drop pdb file here, or click to select pdb file</div>
<span class="separator">or</span>
<div>
<div>
<input type="text" id="DBID" placeholder="e.g. 1BDD or AF-P38507-F1">
<button type="button" id="fetch-button">load by PDB ID or AFDB ID</button>
</div>
<span id="load-message"></span>
</div>
</div>
<div id="pymol-control-area">
<button id="my-button">Press here to launch PyMOL after selecting PDB file</button>
<button id="ray-button">Press here to ray</button>
<button id="download-button">Press here to download current session</button>
</div>
<div id="pymol-console">
<center><input type="text" id="cmdInput" placeholder="> Enter PyMOL command"></center>
</div>
</div>
<p>
<script type="module" src="https://cdn.jsdelivr.net/pyodide/v0.22.1/full/pyodide.js"></script>
<script src="https://cdn.jsdelivr.net/npm/pako/dist/pako.min.js"></script>
<script>
let inputFiles=[];
let pdb1="";
let filename1="dummy1.pdb";
const dropArea1 = document.getElementById('drop-area1');
dropArea1.addEventListener('dragenter', handleDragEnter1, false);
dropArea1.addEventListener('dragleave', handleDragLeave1, false);
dropArea1.addEventListener('dragover', handleDragOver1, false);
dropArea1.addEventListener('drop', handleDrop1, false);
dropArea1.addEventListener('click', handleClick1, false);
function handleDragEnter1(event) {
event.stopPropagation();
event.preventDefault();
dropArea1.style.background = '#eee';
}
function handleDragLeave1(event) {
event.stopPropagation();
event.preventDefault();
dropArea1.style.background = '#fff';
}
function handleDragOver1(event) {
event.stopPropagation();
event.preventDefault();
dropArea1.style.background = '#eee';
}
async function readFile(file) {
let pdb1 = null;
let filename1 = null;
return new Promise((resolve, reject) => {
const reader = new FileReader();
// Check if the file name ends with ".gz"
if (file.name.endsWith('.gz')) {
reader.onload = function (event) {
const compressedData = event.target.result;
// Decompress the data using Pako
const decompressed = pako.inflate(compressedData, { to: 'string' });
////console.log(decompressed);
// Store the decompressed data
pdb1 = decompressed;
filename1 = file.name.replace("\.gz","");
resolve({ pdb1, filename1 });
};
// Read the file as an array buffer
reader.readAsArrayBuffer(file);
} else if (file.name.endsWith('.pse')){
const fileReader = new FileReader();
// Read the file as an ArrayBuffe
fileReader.onload = () => {
const arrayBuffer = fileReader.result;
// Convert the ArrayBuffer to a Uint8Array
pdb1 = new Uint8Array(arrayBuffer);
filename1 = file.name
resolve({ pdb1, filename1 });
// Write the binary data to the Pyodide virtual file system
}
fileReader.readAsArrayBuffer(file);
// Read the file as an array buffer
}else{
reader.onload = function (event) {
const content = event.target.result;
// Output the file contents to the ////console
////console.log(content);
// Store the file contents
pdb1 = content;
filename1 = file.name
resolve({ pdb1, filename1 });
};
// Read the file as text
reader.readAsText(file);
}
});
}
async function handleDrop1(event) {
event.stopPropagation();
event.preventDefault();
dropArea1.style.background = '#fff';
inputFiles = await Promise.all(Array.from(event.dataTransfer.files).map((file) => readFile(file)));
filename1 = inputFiles[0].filename1;
dropArea1.textContent = inputFiles.map((obj)=>obj.filename1).join();
}
function handleClick1(event) {
const input = document.createElement('input');
input.type = 'file';
input.multiple = true;
input.onchange = async function (event) {
inputFiles = await Promise.all(Array.from(event.target.files).map((file) => readFile(file)));
filename1 = inputFiles[0].filename1;
dropArea1.textContent = inputFiles.map((obj)=>obj.filename1).join();
}
input.click();
}
const fetchButton = document.getElementById('fetch-button');
fetchButton.addEventListener('click', async function(){
const DBID = document.getElementById('DBID').value;
const loadMessage = document.getElementById('load-message');
if (DBID.length == 0) {
loadMessage.textContent = 'Please input ID';
return;
}
//https://alphafold.ebi.ac.uk/files/AF-P38507-F1-model_v4.cif
const response = DBID.startsWith("AF-")
? await fetch(`https://alphafold.ebi.ac.uk/files/${DBID}-model_v4.cif`)
: await fetch(`https://files.rcsb.org/download/${DBID}.cif`);
if (!response.ok) {
loadMessage.textContent = 'File not found';
return;
}
loadMessage.textContent = '';
const content = await response.text();
pdb1 = content;
filename1 = DBID+".cif";
inputFiles = [{ pdb1, filename1 }];
dropArea1.textContent = filename1;
const myButton = document.getElementById('my-button');
myButton.click();
});
</script>
<script type="module">
const cv = document.getElementById("canvas");
let rect = cv.getBoundingClientRect();
let OriginX = parseInt(rect.left);
let OriginY = parseInt(rect.top);
let loaded = false;
const width = 1024;
const height = 600;
const gui_width= 220;
async function loadPyMOL() {
const loadingProgress = document.getElementById('loading-progress');
const pyodide = await loadPyodide();
await pyodide.loadPackage("numpy");
loadingProgress.textContent = '50%';
await pyodide.loadPackage("https://yakomaxa.github.io/PyMOL-Wasm/pymol-2.6.0a0-cp39-cp39-emscripten_3_1_46_wasm32.whl");
loadingProgress.textContent = '75%';
// Run PyMOL code
await pyodide.globals.set("originX",OriginX);
await pyodide.globals.set("originY",OriginY);
await pyodide.globals.set("width",width);
await pyodide.globals.set("gui_width",gui_width);
await pyodide.globals.set("height",height);
await pyodide.runPythonAsync(`
class SelfProxy:
def __init__(self, proxied, _self):
self._self = _self
self.proxied = proxied
def __getattr__(self, key):
v = getattr(self.proxied, key)
def wrapper(*a, **k):
k['_self'] = self._self
return v(*a, **k)
return wrapper
import pymol2 as p2
_p = p2.PyMOL()
# need for letting wizarding.py or something to recognize the PyMOL instance
import pymol
pymol.cmd = _p.cmd
_p.start()
import pymol.util
_p.util = SelfProxy(pymol.util, _p.cmd)
import pymol.preset
_p.preset = SelfProxy(pymol.preset, _p.cmd)
_p.cmd.set("internal_gui",1)
_p.cmd.set("internal_feedback", 1)
_p.cmd.bg_color("black")
_p.initEmscriptenContext(0,0,0,0,0)
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
`
);
document.getElementById("main-content").style.display = "block";
document.getElementById("loading-container").style.display = "none";
const myButton = document.getElementById('my-button');
myButton.addEventListener('click', async function(){
setTimeout(async () => {
try {
for (const { pdb1, filename1 } of inputFiles) {
await pyodide.FS.writeFile(filename1, pdb1);
await pyodide.runPythonAsync(`
_p.cmd.load("${filename1}")
`);
}
if (!loaded) {
await pyodide.runPythonAsync(`
_p.cmd.set("label_font_id", 10)
_p.cmd.set("label_size", 30)
_p.cmd.set("sphere_mode", 0)
_p.cmd.set("use_shader",0)
_p.cmd.set("render_as_cylinders", "off")
_p.cmd.set("dot_density", 25)
_p.cmd.set("dot_lighting","off")
_p.cmd.set("line_width",5)
_p.cmd.set("trilines","on")
_p.cmd.set("dash_as_cylinders","on")
_p.cmd.set("nonbonded_as_cylinders","off")
_p.cmd.set("nb_spheres_use_shader", 2)
#_p.cmd.set("nonbonded_use_shader",1)
_p.cmd.set("internal_gui",1)
_p.cmd.set("internal_gui_width",gui_width)
_p.cmd.set("internal_feedback", 0)
_p.cmd.set("internal_gui_control_size", 30)
_p.cmd.bg_color("black")
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.draw()`
);
cv.addEventListener('click', onClick);
document.addEventListener('mousemove', onMouseMove);
document.addEventListener('mousemove', onMouseMove4Stop);
//cv.addEventListener('mousestop', onMouseStop);
cv.addEventListener('mousedown', onMouseDown);
cv.addEventListener('mouseup', onMouseUp);
cv.addEventListener('contextmenu', onContextMenu);
//cv.addEventListener('dblclick', onDoubleClick);
document.addEventListener('keydown', onKeyDown);
document.addEventListener('keyup', onKeyUp);
cv.addEventListener("wheel", (event) => {
if (event.wheelDeltaY < 0) {
onWheelRollUp(event);
} else if (event.wheelDeltaY > 0) {
onWheelRollDown(event);
}
})
// To take input for wizard (especially renaming)
document.addEventListener('keydown', async function(event) {
// prevent capturing keypresses from input fields
if (event.target.tagName === "INPUT") {
return;
}
// calling this will prevent ctrl+ R from reloading the page
//event.preventDefault();
let key = event.key;
let keyCode = null;
if (event.shiftKey && key.length === 1) {
keyCode = key.toUpperCase().charCodeAt(0);
} else if(key.length === 1){
keyCode = key.toLowerCase().charCodeAt(0);
} else {
keyCode = event.keyCode;
}
await pyodide.globals.set('keyCode',keyCode)
await pyodide.runPythonAsync(`
wiz = _p.cmd.get_wizard()
if (wiz != None):
wiz.do_key(keyCode,0,0,0)
`)
frameCounterLong = 0;
animatingLong = true;
animateLong()
});
}
loaded=true;
} catch (error) {
}
}, 100);
})
const rayButton = document.getElementById('ray-button');
rayButton.addEventListener('click', async function(){
setTimeout(async () => {
try {
await pyodide.runPythonAsync(`
_p.cmd.bg_color("white")
_p.cmd.set("antialias",2)
#_p.cmd.set("ray_trace_mode",2)
_p.cmd.set("ray_opaque_background",0)
#_p.cmd.set("fog",0)
#_p.cmd.set("ambient",0.66)
#_p.cmd.set("reflect",0)
#_p.cmd.set("spec_reflect",0.08)
#_p.cmd.set("light_count", 2)
# cartoon representation
#_p.cmd.set("cartoon_oval_width", 0.46)
#_p.cmd.set("cartoon_oval_length", 1.35)
#_p.cmd.set("cartoon_loop_radius", 0.46)
#_p.cmd.set("cartoon_oval_quality", 25)
#_p.cmd.set("cartoon_loop_quality", 100)
_p.cmd.png("/test.png",ray=1)
_p.cmd.bg_color("black")
_p.cmd.set("antialias",0)
_p.cmd.set("ray_trace_mode",0)
_p.cmd.set("ray_opaque_background",0)
print("DONE")
`).then(async ()=>{
var data = await pyodide.FS.readFile('/test.png');
var blob = new Blob([data], { type: 'application/octet-stream' });
var url = URL.createObjectURL(blob);
var link = document.createElement('a');
link.href = url;
link.download = filename1+".png"; // Change the filename as needed
document.body.appendChild(link); // Add link to DOM
link.click();
}
);
} catch (error) {
}
}, 100);
})
const downloadButton = document.getElementById('download-button');
downloadButton.addEventListener('click', async function(){
await pyodide.runPythonAsync(`
_p.cmd.save("save.pse")
`).then(async ()=>{
const data = await pyodide.FS.readFile('save.pse');
const blob = new Blob([data], { type: 'application/octet-stream' });
const url = URL.createObjectURL(blob);
const now = new Date();
const postfix = `${now.toLocaleDateString('sv-SE')}_${now.getHours()}_${now.getMinutes()}_${now.getSeconds()}`;
const link = document.createElement('a');
link.href = url;
link.download = `${filename1}.${postfix}.pse`; // Change the filename as needed
document.body.appendChild(link); // Add link to DOM
link.click();
}
);
});
var cmdinput = document.getElementById("cmdInput");
cmdinput.addEventListener("keypress", async function(event) {
if (event.key === "Enter" && loaded) {
event.preventDefault(); // Prevent the default action (if any)
setTimeout(async () => {
try {
var command = document.getElementById("cmdInput").value;
//document.getElementById("commandline").innerText = command;
await pyodide.globals.set("command",command);
await pyodide.runPythonAsync(`
_p.cmd.do(command)
_p.idle()
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
`)
cmdInput.value = ""
} catch (error) {
}
}, 100);
}
});
let lastMouseX = null;
let lastMouseY = null;
let mouseStoppedTimeout = null;
let leftButtonCallNum = 0;
let middleButtonCallNum = 0;
let rightButtonCallNum = 0;
let leftButtonCallNum_ctrl = 0;
let mouseButtonDown = false;
let key_ctrl = false;
var goLeftDown=false;
async function onKeyDown(event){
key_ctrl = ((event.ctrlKey && !event.metaKey) || (!event.ctrlKey && event.metaKey));
}
async function onKeyUp(event){
key_ctrl = ((event.ctrlKey && !event.metaKey) || (!event.ctrlKey && event.metaKey));
}
async function Left(flag){
if (flag==0){
//console.log("Left reserved");
await pyodide.runPythonAsync( `
_p.button(0, 0, int(x), int(height - y), 0)
`);
if (!animating) {
animating = true;
frameCounter = 0;
animate();
}
}else{
//console.log("Left unlocked");
await pyodide.runPythonAsync( `
_p.button(0, 1, int(x), int(height - y), 0)
`);
if (!animating) {
animating = true;
frameCounter = 0;
animate();
}
}
}
async function Right(flag){
if (flag==0){
//console.log("Right reserved");
await pyodide.runPythonAsync( `_p.button(2, 0, int(x), int(height - y), 0)`);
}else{
//console.log("Right unlocked");
await pyodide.runPythonAsync( `_p.button(2, 1, int(x), int(height - y), 0)`);
}
}
async function Middle(flag){
if (flag==0){
//console.log("Middle reserved");
await pyodide.runPythonAsync( `_p.button(1, 0, int(x), int(height - y), 0)`);
}else{
//console.log("Middle unlocked");
await pyodide.runPythonAsync( `_p.button(1, 1, int(x), int(height - y), 0)`);
}
}
async function onMouseMove(event) {
if (!loaded){
return;
}
event.preventDefault();
var key_ctrl_here = ((event.ctrlKey && !event.metaKey) || (!event.ctrlKey && event.metaKey));
let rect = cv.getBoundingClientRect();
let OriginX = parseInt(rect.left);
let OriginY = parseInt(rect.top);
var mouseX = event.clientX - OriginX;
var mouseY = event.clientY - OriginY;
await pyodide.globals.set("x",mouseX);
await pyodide.globals.set("y",mouseY);
// set middle button state
if (isLeftButtonDown && key_ctrl_here ){
isMiddleButtonDown = true;
//console.log("M down");
}
if (!(isLeftButtonDown && key_ctrl_here )){
isMiddleButtonDown = false;
//console.log("M up");
}
// set left button ON
if ((isLeftButtonDown && !( key_ctrl_here) && leftButtonCallNum == 0) ) {
//console.log("AA begin")
if (middleButtonCallNum==1){
Middle(1);
}
Left(0);
mouseButtonDown=true;
leftButtonCallNum = 1;
middleButtonCallNum = 0;
//console.log("AA end")
} // OFF
if (!isLeftButtonDown && !(key_ctrl_here) && leftButtonCallNum == 1){
//console.log("BB begin")
Left(1);
mouseButtonDown=false;
leftButtonCallNum = 0;
middleButtonCallNum = 0;
//console.log("BB end")
}
// set middle button ON
if (isMiddleButtonDown && middleButtonCallNum == 0 || isMiddleButtonDown_real && middleButtonCallNum == 0){
console.log("CC begin");
if (leftButtonCallNum==1){
Left(1);
}
Middle(0);
mouseButtonDown=true;
middleButtonCallNum = 1
leftButtonCallNum = 0;
console.log("CC end");
} // OFF
if ((!isMiddleButtonDown && middleButtonCallNum == 1) && (!isMiddleButtonDown_real && middleButtonCallNum == 1)){
console.log("DD begin");
Middle(1);
mouseButtonDown=false;
middleButtonCallNum = 0;
leftButtonCallNum = 0;
console.log("DD end");
}
// set right button ON
if (isRightButtonDown && rightButtonCallNum == 0){
//console.log("EE begin");
Right(0);
mouseButtonDown=true;
rightButtonCallNum = 1
//console.log("EE end");
}
if ((!isRightButtonDown && rightButtonCallNum == 1)){
//console.log("FF begin");
Right(1);
mouseButtonDown=false;
rightButtonCallNum = 0;
//console.log("FF end");
}
if(mouseButtonDown){
Dragging=true
}
if (Dragging){
await pyodide.runPythonAsync(`
_p.idle()
_p.drag(x, height-y, 0)
`);
}else{
}
if (!animating) {
animating = true;
frameCounter = 0;
animate();
}
}
function onMouseStop(event) {
if (!animating) {
animating = true;
frameCounter = 0;
animate();
}
//console.log('Mouse stopped at:', event.detail.x, event.detail.y);
}
function onContextMenu(event) {
event.preventDefault();
}
let isLeftButtonDown = false;
let isMiddleButtonDown = false;
let isMiddleButtonDown_real = false;
let isRightButtonDown = false;
let Dragging=false;
async function onMouseDown(event) {
event.preventDefault();
if (event.button == 0 ) {
isLeftButtonDown=true;
}
if (event.button == 1) {
isMiddleButtonDown_real=true;
}
if (event.button == 2) {
isRightButtonDown=true;
}
}
async function onMouseUp(event) {
event.preventDefault();
frameCounterLong = 0;
animatingLong = true;
animateLong()
if (event.button == 0) {
isLeftButtonDown=false;
}
if (event.button == 1) {
isMiddleButtonDown_real=false;
}
if (event.button == 2) {
isRightButtonDown=false;
}
}
async function onWheelRollUp(event) {
await event.preventDefault();
let rect = cv.getBoundingClientRect();
let OriginX = parseInt(rect.left);
let OriginY = parseInt(rect.top);
await pyodide.globals.set("originX",OriginX);
await pyodide.globals.set("originY",OriginY);
var mouseX = event.clientX - OriginX;
var mouseY = event.clientY - OriginY;
await pyodide.globals.set("x",mouseX);
await pyodide.globals.set("y",mouseY);
await pyodide.runPythonAsync(`
_p.button(4, 0, int(x), int(height - y), 0)
_p.idle()
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
`);
}
async function onWheelRollDown(event) {
await event.preventDefault();
let rect = cv.getBoundingClientRect();
let OriginX = parseInt(rect.left);
let OriginY = parseInt(rect.top);
await pyodide.globals.set("originX",OriginX);
await pyodide.globals.set("originY",OriginY);
var mouseX = event.clientX - OriginX;
var mouseY = event.clientY - OriginY;
await pyodide.globals.set("x",mouseX);
await pyodide.globals.set("y",mouseY);
await pyodide.runPythonAsync(`
_p.button(3, 0, int(x), int(height - y), 0)
_p.idle()
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
`)
}
let clickcount=0;
async function onClick(event) {
event.preventDefault();
if (!mouseStop){
return;
}
let rect = cv.getBoundingClientRect();
let OriginX = parseInt(rect.left);
let OriginY = parseInt(rect.top);
await pyodide.globals.set("originX",OriginX);
await pyodide.globals.set("originY",OriginY);
var mouseX = event.clientX - OriginX;
var mouseY = event.clientY - OriginY;
await pyodide.globals.set("x",mouseX);
await pyodide.globals.set("y",mouseY);
await pyodide.runPythonAsync(`
_p.button(0, 0, int(x), int(height - y), 0)
_p.idle()
_p.drag(x, height-y, 0)
_p.idle()
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
_p.button(0, 1, int(x-1), int(height - y-1), 0)
_p.idle()
_p.drag(x, height-y, 0)
_p.idle()
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
_p.idle()
`)
}
const frameLimit = 2;
let frameCounter = 0;
let animating = false;
const frameLimitLong = 50;
let frameCounterLong = 0;
let animatingLong = false;
async function animate() {
if (frameCounter >= frameLimit) {
animating = false;
return;
}
// Update the animation here
await pyodide.runPythonAsync(`
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
`);
frameCounter++;
requestAnimationFrame(animate);
}
async function animateLong() {
if (frameCounterLong >= frameLimitLong) {
animatingLong = false;
return;
}
// Update the animation here
await pyodide.runPythonAsync(`
_p._cmd.glViewport(0, 0, width,height)
_p.cmd.viewport(width-gui_width,height)
_p.idle()
_p.draw()
`);
frameCounterLong++;
requestAnimationFrame(animateLong);
}
let mouseStop=false
let mouseStopTimeout;
function onMouseMove4Stop() {
clearTimeout(mouseStopTimeout);
//console.log('Mouse is moving...');
mouseStop=false;
mouseStopTimeout = setTimeout(() => {
//console.log('Mouse stopped');
mouseStop=true;
}, 100); // Adjust the delay as needed
}
}
loadPyMOL();
</script>
<a href="https://github.com/yakomaxa/PyMOL-Wasm"> GitHub repository for this project (binary and javascript only at this moment) </a>
</body>
</html>