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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() | |