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Runtime error
Update app.py
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app.py
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@@ -5,6 +5,69 @@ from proteins_viz import *
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import gradio as gr
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import spaces
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def convert_outputs_to_pdb(outputs):
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final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs)
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outputs = {k: v.to("cpu").numpy() for k, v in outputs.items()}
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@@ -50,18 +113,19 @@ def fold_protein(test_protein):
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with open("output_structure.pdb", "w") as f:
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f.write("".join(pdb))
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image = take_care("output_structure.pdb")
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-
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iface = gr.Interface(
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title="everything-ai-proteinfold",
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fn=fold_protein,
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inputs=gr.Textbox(
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label="Protein Sequence",
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info="Find sequences examples below, and complete examples with images at: https://github.com/AstraBert/proteinviz/tree/main/examples.md; if you input a sequence, you're gonna get the static image and the
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lines=5,
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value=f"Paste or write amino-acidic sequence here",
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),
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outputs=[gr.Image(label="Protein static image"), gr.
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examples=[
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"MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
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"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS",
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import gradio as gr
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import spaces
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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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x = (
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"""<!DOCTYPE html>
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<html>
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
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<style>
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body{
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font-family:sans-serif
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}
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.mol-container {
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width: 100%;
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height: 600px;
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position: relative;
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}
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.mol-container select{
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background-image:None;
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}
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</style>
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<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>
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<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
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</head>
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<body>
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<div id="container" class="mol-container"></div>
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<script>
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let pdb = `"""
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+ mol
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+ """`
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$(document).ready(function () {
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let element = $("#container");
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let config = { backgroundColor: "white" };
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let viewer = $3Dmol.createViewer(element, config);
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viewer.addModel(pdb, "pdb");
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viewer.getModel(0).setStyle({}, { cartoon: { colorscheme:"whiteCarbon" } });
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viewer.zoomTo();
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viewer.render();
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viewer.zoom(0.8, 2000);
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})
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</script>
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</body></html>"""
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)
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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 convert_outputs_to_pdb(outputs):
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final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs)
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outputs = {k: v.to("cpu").numpy() for k, v in outputs.items()}
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with open("output_structure.pdb", "w") as f:
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f.write("".join(pdb))
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image = take_care("output_structure.pdb")
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html = molecule("output_structure.pdb")
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return image, html
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iface = gr.Interface(
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title="everything-ai-proteinfold",
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fn=fold_protein,
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inputs=gr.Textbox(
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label="Protein Sequence",
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info="Find sequences examples below, and complete examples with images at: https://github.com/AstraBert/proteinviz/tree/main/examples.md; if you input a sequence, you're gonna get the static image and the 3D model to explore and play with",
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lines=5,
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value=f"Paste or write amino-acidic sequence here",
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),
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outputs=[gr.Image(label="Protein static image"), gr.HTML(label="Protein 3D model")],
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examples=[
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"MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
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"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS",
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