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import gradio as gr
import urllib
import re
import sys
import warnings
import torch
import torch.nn as nn
import ipywidgets as widgets
from ipywidgets import interact, fixed
from utils.helpers import *
from utils.voxelization import processStructures
from utils.model import Model
import numpy as np
import os
import moleculekit
print(moleculekit.__version__)
def update(inp, file, mode, custom_resids, clustering_threshold, distance_cutoff):
try:
filepath = file.name
except:
print("using pdbfile")
try:
pdb_file = inp
if (
re.match(
"[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}",
pdb_file,
).group()
== pdb_file
):
urllib.request.urlretrieve(
f"https://alphafold.ebi.ac.uk/files/AF-{pdb_file}-F1-model_v2.pdb",
f"files/{pdb_file}.pdb",
)
filepath = f"files/{pdb_file}.pdb"
except AttributeError:
if len(inp) == 4:
pdb_file = inp
urllib.request.urlretrieve(
f"http://files.rcsb.org/download/{pdb_file.lower()}.pdb1",
f"files/{pdb_file}.pdb",
)
filepath = f"files/{pdb_file}.pdb"
else:
return "pdb code must be 4 letters or Uniprot code does not match", ""
identifier = os.path.basename(filepath)
if mode == "All residues":
print("using all residues")
ids = get_all_protein_resids(filepath)
elif len(custom_resids) != 0:
print("using listed residues", custom_resids)
ids = get_all_resids_from_list(filepath, custom_resids.replace(",", " "))
else:
print("using metalbinding")
ids = get_all_metalbinding_resids(filepath)
print(filepath)
print(ids)
try:
voxels, prot_centers, prot_N, prots = processStructures(filepath, ids)
except Exception as e:
print(e)
return (
"Error",
f"""<div class="text-center mt-4"> Something went wrong with the voxelization, reset custom residues and other input fiels and check error message <br> <br> <code>{e}</code></div>""",
)
voxels.to(device)
with warnings.catch_warnings():
warnings.filterwarnings("ignore")
output = model(voxels)
print(output.shape)
prot_v = np.vstack(prot_centers)
output_v = output.flatten().cpu().detach().numpy()
bb = get_bb(prot_v)
gridres = 0.5
grid, box_N = create_grid_fromBB(bb, voxelSize=gridres)
probability_values = get_probability_mean(grid, prot_v, output_v)
print(probability_values.shape)
write_cubefile(
bb,
probability_values,
box_N,
outname=f"output/metal_{identifier}.cube",
gridres=gridres,
)
message = find_unique_sites(
probability_values,
grid,
writeprobes=True,
probefile=f"output/probes_{identifier}.pdb",
threshold=distance_cutoff,
p=clustering_threshold,
)
del voxels
torch.cuda.empty_cache()
return message, molecule(
filepath,
f"output/probes_{identifier}.pdb",
f"output/metal_{identifier}.cube",
)
def read_mol(molpath):
with open(molpath, "r") as fp:
lines = fp.readlines()
mol = ""
for l in lines:
mol += l
return mol
def molecule(pdb, probes, cube):
mol = read_mol(pdb)
probes = read_mol(probes)
cubefile = read_mol(cube)
x = (
"""<!DOCTYPE html>
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
<link rel="stylesheet" href="https://unpkg.com/flowbite@1.4.5/dist/flowbite.min.css" />
<style>
body{
font-family:sans-serif
}
.mol-container {
width: 100%;
height: 600px;
position: relative;
}
.slider{
width:80%;
margin:0 auto
}
.slidercontainer{
display:flex;
}
.slidercontainer > * + * {
margin-left: 0.5rem;
}
#isovalue{
text-align:right}
</style>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.3/jquery.min.js" integrity="sha512-STof4xm1wgkfm7heWqFJVn58Hm3EtS31XFaagaa8VMReCXAkQnJZ+jEy8PCC/iT18dFy95WcExNHFTqLyp72eQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/rangeslider.js/2.3.3/rangeslider.min.js" integrity="sha512-BUlWdwDeJo24GIubM+z40xcj/pjw7RuULBkxOTc+0L9BaGwZPwiwtbiSVzv31qR7TWx7bs6OPTE5IyfLOorboQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
</head>
<body>
<div class="slidercontainer my-8">
<span>Isovalue </span>
<span id="isovalue">0.5</span>
<input class="slider text-blue-400" type="range" id="rangeslider" min="0" max="1" step="0.05" value=0.5>
</div>
<div id="container" class="mol-container"></div>
<div class="flex items-center justify-center my-4">
<div class="px-4">
<label for="sidechain" class="relative inline-flex items-center mb-4 cursor-pointer ">
<input id="sidechain"type="checkbox" class="sr-only peer">
<div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
<span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show side chains</span>
</label>
</div>
<div class="px-4">
<label for="pdbmetal" class="relative inline-flex items-center mb-4 cursor-pointer ">
<input id="pdbmetal" type="checkbox" class="sr-only peer">
<div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
<span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show PDB metals</span>
</label>
</div>
<div class="px-4">
<label for="probes" class="relative inline-flex items-center mb-4 cursor-pointer ">
<input id="probes" type="checkbox" class="sr-only peer" checked>
<div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
<span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show Probes</span>
</label>
</div>
</div>
<div class="flex items-center justify-center my-4">
<button type="button" class="text-gray-900 bg-white hover:bg-gray-100 border border-gray-200 focus:ring-4 focus:outline-none focus:ring-gray-100 font-medium rounded-lg text-sm px-5 py-2.5 text-center inline-flex items-center dark:focus:ring-gray-600 dark:bg-gray-800 dark:border-gray-700 dark:text-white dark:hover:bg-gray-700 mr-2 mb-2" id="download">
<svg class="w-6 h-6 mr-2 -ml-1" fill="none" stroke="currentColor" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M4 16v1a3 3 0 003 3h10a3 3 0 003-3v-1m-4-4l-4 4m0 0l-4-4m4 4V4"></path></svg>
Download predictions
</button>
</div>
<script>
let viewer = null;
let voldata = null;
let shape = null;
let sidechain = null;
let metal = null;
$(document).ready(function () {
let element = $("#container");
let config = { backgroundColor: "white" };
viewer = $3Dmol.createViewer( element, config );
viewer.ui.initiateUI();
let data = `"""
+ mol
+ """`
viewer.addModel( data, "pdb" );
let cubefile = `"""
+ cubefile
+ """`
voldata = new $3Dmol.VolumeData(cubefile, "cube");
shape = viewer.addIsosurface(voldata, { isoval: 0.5 , color: "blue", alpha: 0.85, smoothness: 1 });
viewer.getModel(0).setStyle({}, {cartoon: {}});
let probes =`"""
+ probes
+ """`
viewer.addModel(probes, "pdb");
viewer.getModel(1).setStyle({ "resn": "ZN" }, { "sphere": { }});
viewer.getModel(1).setHoverable({}, true,
function (atom, viewer, event, container) {
if (!atom.label) {
atom.label = viewer.addLabel("ZN p=" + atom.pdbline.substring(55, 60), { position: atom, backgroundColor: "mintcream", fontColor: "black" });
}
},
function (atom, viewer) {
if (atom.label) {
viewer.removeLabel(atom.label);
delete atom.label;
}
}
);
viewer.zoomTo();
viewer.render();
viewer.zoom(0.8, 2000);
$("#sidechain").change(function () {
if (this.checked) {
BB = ["C", "O", "N"]
viewer.getModel(0).setStyle( {"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {hidden:false, colorscheme: "WhiteCarbon", radius: 0.3}, cartoon: {}});
viewer.render()
$("#pdbmetal").prop( "checked", false );
} else {
BB = ["C", "O", "N"]
viewer.getModel(0).setStyle({"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {colorscheme: "WhiteCarbon",hidden:true, radius: 0.3}, cartoon: {}});
viewer.render()
$("#pdbmetal").prop( "checked", false );
}
});
$("#pdbmetal").change(function () {
if (this.checked) {
viewer.getModel(0).setStyle({ "resn": ["ZN","MG","NA","FE", "NI","MN","CA", "CU", "CU1"] }, { "sphere": {hidden:false}});
viewer.render()
} else {
viewer.getModel(0).setStyle({ "resn": ["ZN","MG","NA","FE","NI", "MN","CA", "CU", "CU1"] }, { "sphere": {hidden:true}});
viewer.render()
}
});
$("#probes").change(function () {
if (this.checked) {
viewer.getModel(1).setStyle({ "resn": "ZN" }, { "sphere": { }});
viewer.addStyle()
viewer.render()
} else {
viewer.getModel(1).setStyle({});
viewer.render()
}
});
$("#download").click(function () {
download("protein.pdb", data);
download("metaldensity.cube", cubefile);
download("probes.pdb", probes);
})
});
function download(filename, text) {
var element = document.createElement("a");
element.setAttribute("href", "data:text/plain;charset=utf-8," + encodeURIComponent(text));
element.setAttribute("download", filename);
element.style.display = "none";
document.body.appendChild(element);
element.click();
document.body.removeChild(element);
}
</script>
<script>
$("#rangeslider").rangeslider().on("change", function (el) {
isoval = parseFloat(el.target.value);
$("#isovalue").text(el.target.value)
console.log("Change isosurface to "+el.target.value)
viewer.removeShape(shape)
shape=viewer.addIsosurface(voldata, { isoval: parseFloat(el.target.value), color: "blue", alpha: 0.85, smoothness: 1 });
viewer.render();
});
</script>
</body></html>"""
)
return f"""<iframe style="width: 100%; height: 1000px" name="result" allow="midi; geolocation; microphone; camera;
display-capture; encrypted-media;" sandbox="allow-modals allow-forms
allow-scripts allow-same-origin allow-popups
allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
def set_examples(example):
n, code, resids = example
return [n, code, resids]
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model = Model()
model.to(device)
model.load_state_dict(
torch.load(
"weights/metal_0.5A_v3_d0.2_16Abox.pth",
map_location=torch.device("cuda" if torch.cuda.is_available() else "cpu"),
)
)
model.eval()
metal3d = gr.Blocks()
with metal3d:
gr.Markdown("# Metal3D")
gr.Markdown(
""" <em>Inference using CPU-only, can be quite slow for more than 20 residues. Use [Colab notebook](https://colab.research.google.com/github/lcbc-epfl/metal-site-prediction/blob/main/Metal3D/ColabMetal.ipynb) for GPU acceleration or use the docker image locally </em>
<small><code>docker run -it -p 7860:7860 --platform=linux/amd64 registry.hf.space/simonduerr-metal3d:latest python app.py</code></small>
"""
)
with gr.Tabs():
with gr.TabItem("Input"):
inp = gr.Textbox(
placeholder="PDB Code or Uniprot identifier or upload file below",
label="Input molecule",
)
file = gr.File(file_count="single", type="file")
with gr.TabItem("Settings"):
with gr.Row():
mode = gr.Radio(
["All metalbinding residues (ASP, CYS, GLU, HIS)", "All residues"],
label="Residues to use for prediction",
)
custom_resids = gr.Textbox(
placeholder="Comma separated list of residues",
label="Custom residues",
)
with gr.Row():
clustering_threshold = gr.Slider(
minimum=0.15,
maximum=1,
value=0.15,
step=0.05,
label="Clustering threshold",
)
distance_cutoff = gr.Slider(
minimum=1,
maximum=10,
value=7,
step=0.5,
label="Clustering distance cutoff",
)
btn = gr.Button("Run")
n = gr.Textbox(label="Label", visible=False)
examples = gr.Dataset(
components=[n, inp, custom_resids],
samples=[
["HCA2", "2CBA", ""],
["Nickel in GB1 dimer", "6F5N", ""],
["Zebrafish palmitoyltransferase ZDHHC15B PDB", "6BMS", ""],
[
"Human palmitoyltransferase ZDHHC23 AlphaFold",
"Q8IYP9",
"280,273,263,260,274,277,274,287",
],
],
)
examples.click(fn=set_examples, inputs=examples, outputs=examples.components)
gr.Markdown("# Output")
out = gr.Textbox(label="status")
mol = gr.HTML()
btn.click(
fn=update,
inputs=[inp, file, mode, custom_resids, clustering_threshold, distance_cutoff],
outputs=[out, mol],
)
metal3d.launch()
|