i_vorobyev
commited on
Commit
·
9f2073b
1
Parent(s):
fde5663
add 2dmoljs
Browse files
app.py
CHANGED
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@@ -1,26 +1,99 @@
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import gradio as gr
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from igfold import IgFoldRunner
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def pred_seq(seq):
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}
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)
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def greet(name):
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return "Hello " + name + "!!"
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iface.launch()
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import gradio as gr
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from igfold import IgFoldRunner
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import os
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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 validate(seq):
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alphabet = set('ACDEFGHIKLMNPQRSTVWY')
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leftover = set(seq.upper()) - alphabet
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return not leftover
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def pred_seq(seq):
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is_valid = validate(seq)
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if is_valid:
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sequences = {
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"H": "QVQLQESGGGLVQAGGSLTLSCAVSGLTFSNYAMGWFRQAPGKEREFVAAITWDGGNTYYTDSVKGRFTISRDNAKNTVFLQMNSLKPEDTAVYYCAAKLLGSSRYELALAGYDYWGQGTQVTVS"
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}
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pred_pdb = "my_nanobody1.pdb"
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igfold = IgFoldRunner()
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igfold.fold(
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pred_pdb,
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sequences=sequences,
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do_refine=False,
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do_renum=False,
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)
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molecule(pred_pdb)
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else:
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html = "<p color = 'red'>ERROR! Not valid sequence</p>"
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return (html)
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iface = gr.Interface(fn=pred_seq,
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inputs="text", outputs=gr.HTML())
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iface.launch()
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