Spaces:
Runtime error
Runtime error
| import gradio as gr | |
| from shutil import copyfile | |
| ## Modify to match format username-spacename | |
| ## Only works for hosted spaces on Huggingface, for local spaces or spaces hosted on Colab you need to use the gradio.live url with share=True as described in the last two lines | |
| public_link = "https://simonduerr-molstar-gradio.hf.space" | |
| import gradio as gr | |
| import os | |
| def get_pdb(upload_choice="PDB Code", pdb_code="", filepath=""): | |
| urls = { | |
| "PDB Code": {"base":"https://files.rcsb.org/view/", "suffix":".pdb"}, | |
| "AlphaFold DB": {"base":"https://alphafold.ebi.ac.uk/files/AF-", "suffix": "-F1-model_v4.pdb"}, | |
| "ESM Atlas": {"base": "https://api.esmatlas.com/fetchPredictedStructure/", "suffix":".pdb"} | |
| } | |
| if upload_choice=="local file": | |
| try: | |
| #move file to home folder to have it accessible from the web | |
| copyfile(filepath.name, os.path.join(os.getcwd(), os.path.basename(filepath.name))) | |
| return os.path.join(os.getcwd(), os.path.basename(filepath.name)) | |
| except AttributeError as e: | |
| return None | |
| else: | |
| os.system(f"wget -qnc {urls[upload_choice]['base']}{pdb_code}{urls[upload_choice]['suffix']}") | |
| return f"{pdb_code}{urls[upload_choice]['suffix']}" | |
| def read_mol(molpath): | |
| with open(molpath, "r") as fp: | |
| lines = fp.readlines() | |
| mol = "" | |
| for l in lines: | |
| mol += l | |
| return mol | |
| def molecule(input_pdb, public_link): | |
| print(input_pdb) | |
| print(public_link+'/file='+os.path.basename(input_pdb)) | |
| link = public_link+"/file="+os.path.basename(input_pdb) | |
| x ="""<!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8" /> | |
| <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0"> | |
| <title>PDBe Molstar - Helper functions</title> | |
| <!-- Molstar CSS & JS --> | |
| <link rel="stylesheet" type="text/css" href="https://www.ebi.ac.uk/pdbe/pdb-component-library/css/pdbe-molstar-light-3.1.0.css"> | |
| <script type="text/javascript" src="https://www.ebi.ac.uk/pdbe/pdb-component-library/js/pdbe-molstar-plugin-3.1.0.js"></script> | |
| <style> | |
| * { | |
| margin: 0; | |
| padding: 0; | |
| box-sizing: border-box; | |
| } | |
| .msp-plugin ::-webkit-scrollbar-thumb { | |
| background-color: #474748 !important; | |
| } | |
| .viewerSection { | |
| margin: 120px 0 0 0px; | |
| } | |
| #myViewer{ | |
| float:left; | |
| width:100%; | |
| height: 600px; | |
| position:relative; | |
| } | |
| </style> | |
| </head> | |
| <body> | |
| <div class="viewerSection"> | |
| <!-- Molstar container --> | |
| <div id="myViewer"></div> | |
| </div> | |
| <script> | |
| //Create plugin instance | |
| var viewerInstance = new PDBeMolstarPlugin(); | |
| //Set options (Checkout available options list in the documentation) | |
| var options = { | |
| customData: { | |
| url: \""""+link+"""\", | |
| format: "pdb" | |
| }, | |
| alphafoldView: true, | |
| bgColor: {r:255, g:255, b:255}, | |
| //hideCanvasControls: ["selection", "animation", "controlToggle", "controlInfo"] | |
| } | |
| //Get element from HTML/Template to place the viewer | |
| var viewerContainer = document.getElementById("myViewer"); | |
| //Call render method to display the 3D view | |
| viewerInstance.render(viewerContainer, options); | |
| </script> | |
| </body> | |
| </html>""" | |
| return f"""<iframe style="width: 100%; height: 720px" 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 update(upload_choice, inp, file, public_link): | |
| pdb_path = get_pdb(upload_choice, inp, file) | |
| return molecule(pdb_path, public_link) | |
| def toggle_upload_input(choice): | |
| if choice != "local file": | |
| return gr.update(visible=True, placeholder=choice), gr.update(visible=False, value=None) | |
| elif choice == "local file": | |
| return gr.update(visible=False), gr.update(visible=True, value=None) | |
| demo = gr.Blocks() | |
| with demo: | |
| gr.Markdown("# PDB viewer using Mol*") | |
| gr.Markdown("""If using please cite | |
| > David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; 10.1093/nar/gkab31.""") | |
| public_link = gr.Variable(value=public_link) | |
| with gr.Row(): | |
| with gr.Box(): | |
| upload_choice = gr.Radio(["PDB Code", "AlphaFold DB", "ESM Atlas","local file"], label="File source", value='PDB Code') | |
| inp = gr.Textbox( | |
| placeholder="PDB Code", label="Input structure" | |
| ) | |
| file = gr.File(file_count="single", visible=False) | |
| upload_choice.change(fn=toggle_upload_input, | |
| inputs=[upload_choice], | |
| outputs=[inp, file], | |
| queue=False) | |
| btn = gr.Button("View structure") | |
| gr.Examples([["PDB Code", "2CBA"],["AlphaFold DB", "A0A1U8FD60"], ["ESM Atlas", "MGYP001531319262"]], [upload_choice,inp]) | |
| mol = gr.HTML() | |
| btn.click(fn=update, inputs=[upload_choice, inp, file, public_link], outputs=mol) | |
| _, _, pl = demo.launch() # use public link with share=True locally and uncomment below | |
| #public_link = pl |