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Parent(s):
3a2fa2f
Create app.py
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app.py
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import gradio as gr
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import gradio as gr
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import os
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def get_pdb(pdb_code="", filepath=""):
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if pdb_code is None or pdb_code == "":
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try:
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return filepath.name
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except AttributeError as e:
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return None
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else:
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os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
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return f"{pdb_code}.pdb"
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def read_mol(molpath):
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with open(molpath, "r") as fp:
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lines = fp.readlines()
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mol = ""
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for l in lines:
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mol += l
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return mol
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def molecule(input_pdb):
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mol = read_mol(input_pdb)
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html ="""<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
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<title>PDBe Molstar - Helper functions</title>
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<!-- Molstar CSS & JS -->
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<link rel="stylesheet" type="text/css" href="https://www.ebi.ac.uk/pdbe/pdb-component-library/css/pdbe-molstar-light-3.1.0.css">
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<script type="text/javascript" src="https://www.ebi.ac.uk/pdbe/pdb-component-library/js/pdbe-molstar-plugin-3.1.0.js"></script>
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<style>
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* {
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margin: 0;
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padding: 0;
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box-sizing: border-box;
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}
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.msp-plugin ::-webkit-scrollbar-thumb {
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background-color: #474748 !important;
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}
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.viewerSection {
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margin: 120px 0 0 50px;
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}
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#myViewer{
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float:left;
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width:400px;
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height: 400px;
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position:relative;
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}
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</style>
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</head>
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<body>
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<h4>PDBe Mol* AlphaFold Demo</h4>
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<div class="viewerSection">
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<!-- Molstar container -->
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<div id="myViewer"></div>
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</div>
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<script>
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//Create plugin instance
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var viewerInstance = new PDBeMolstarPlugin();
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//Set options (Checkout available options list in the documentation)
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var options = {
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customData: {
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url: "https://alphafold.ebi.ac.uk/files/AF-O15552-F1-model_v1.cif",
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format: "cif"
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},
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alphafoldView: true,
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bgColor: {r:255, g:255, b:255},
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hideCanvasControls: ["selection", "animation", "controlToggle", "controlInfo"]
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}
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//Get element from HTML/Template to place the viewer
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var viewerContainer = document.getElementById("myViewer");
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//Call render method to display the 3D view
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viewerInstance.render(viewerContainer, options);
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</script>
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</body>
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</html>"""
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return f"""<iframe style="width: 100%; height: 600px" name="result" allow="midi; geolocation; microphone; camera;
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms
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allow-scripts allow-same-origin allow-popups
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
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def update(inp, file, request: gr.Request):
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pdb_path = get_pdb(inp, file)
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print("Request headers dictionary:", request.headers)
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print("IP address:", request.client.host)
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return molecule(pdb_path)
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demo = gr.Blocks()
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with demo:
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gr.Markdown("# PDB viewer using Molstar")
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gr.Markdown("""If using please cite
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> 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.""")
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with gr.Row():
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with gr.Box():
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inp = gr.Textbox(
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placeholder="PDB Code or upload file below", label="Input structure"
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)
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file = gr.File(file_count="single")
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gr.Examples(["2CBA", "6VXX"], inp)
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btn = gr.Button("View structure")
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mol = gr.HTML()
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btn.click(fn=update, inputs=[inp, file], outputs=mol)
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demo.launch()
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