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19b831b
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Parent(s):
3f3335c
Create app.py
Browse files
app.py
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import gradio as gr
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import os
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import requests
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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://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 update(sequence):
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headers = {
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'Content-Type': 'application/x-www-form-urlencoded',
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}
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response = requests.post('https://api.esmatlas.com/foldSequence/v1/pdb/', headers=headers, data=sequence)
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name = sequence[:3] + sequence[-3:]
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pdb_filename = "test.pdb"
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pdb_string = response.content.decode('utf-8')
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with open(pdb_filename, "w") as out:
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out.write(pdb_string)
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return molecule(pdb_filename)
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demo = gr.Blocks()
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with demo:
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gr.Markdown("# PDB viewer using 3Dmol.js")
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with gr.Row():
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with gr.Box():
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inp = gr.Textbox(label="Protein sequence"), gr.Examples(["GENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN"])
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btn = gr.Button("Predict structure")
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mol = gr.HTML()
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btn.click(fn=update, inputs=inp, outputs=mol)
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demo.launch()
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