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import gradio as gr
from igfold import IgFoldRunner
import os
import random
import base64
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):
mol = read_mol(input_pdb)
byte_content = mol.encode('utf-8')
base64_content = base64.b64encode(byte_content).decode('utf-8')
x = (
"""<!DOCTYPE html>
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
<style>
body{
font-family:sans-serif
}
.mol-container {
width: 100%;
height: 600px;
position: relative;
}
.mol-container select{
background-image:None;
}
</style>
<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>
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
</head>
<body>
<div id="container" class="mol-container"></div>
<script>
let pdb = `"""
+ mol
+ """`
$(document).ready(function () {
let element = $("#container");
let config = { backgroundColor: "white" };
let viewer = $3Dmol.createViewer(element, config);
viewer.addModel(pdb, "pdb");
viewer.getModel(0).setStyle({}, {cartoon:{color:"spectrum"}});
viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity: 0.4, color: "lightblue"});
viewer.zoomTo();
viewer.render();
viewer.zoom(0.8, 2000);
})
</script>
</body></html>"""
)
return f"""<iframe style="width: 100%; height: 600px" 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>
<div style="position: absolute; top: 10px; right: 10px; background-color: white; padding: 10px; border: 1px solid black;">
<div style="display: flex; justify-content: space-between; margin-top: 5px;">
<span>High Energy</span>
</div>
<div style="height: 150px; background: linear-gradient(to bottom, red, yellow, green, blue);"></div>
<div style="display: flex; justify-content: space-between; margin-top: 5px;">
<span>Low Energy</span>
</div>
<div style="display: flex; justify-content: space-between; margin-top: 5px;">
<a href="data:application/octet-stream;base64,{base64_content}" download="structure.pdb">Download File</a>
</div>
</div>
"""
def validate(seq):
alphabet = set('ACDEFGHIKLMNPQRSTVWY')
leftover = set(seq.upper()) - alphabet
return not leftover
def pred_seq(h_seq, l_seq):
h_seq = h_seq.upper().replace(' ', '')
l_seq = l_seq.upper().replace(' ', '')
print(h_seq)
h_is_valid = validate(h_seq)
l_is_valid = validate(l_seq)
if h_is_valid and l_is_valid:
sequences = {
"H": h_seq,
"L": l_seq
}
f_name = ''.join([random.choice("ACDEFGHIKLMNPQRSTVWY") for _ in range(15)])
pred_pdb = f"{f_name}.pdb"
igfold = IgFoldRunner()
igfold.fold(
pred_pdb,
sequences=sequences,
do_refine=False,
do_renum=False,
)
html = molecule(pred_pdb)
else:
html = "<p>ERROR! Not valid sequence</p>"
return (html)
ex_seq = "QVQLVESGGGSVQAGGSLRLSCTASGYTIGPYCMGWFRQAPGGEREAVAAINMGGGITYYADSVKGRFTISRDNAKNTVTLQMNLKPEDTAMYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSS"
h_chain_example = "EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS"
l_chain_example = "DVVMTQTPFSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIK"
with gr.Blocks() as demo:
gr.Markdown('# Antibody Structure Prediction')
gr.Markdown("## Examples")
html = """
<p>
<strong>H-chain:</strong> <tt>QVQLKESGPGLVAPSQSLSITCTVSGFSLSSYGVSWVRQPPGKGLEWLGVIWGDGSTNYHPNLMSRLSISKDISKSQVLFKLNSLQTDDTATYYCVTLDYWGQGTSVTVSS</tt>
<br/>
<strong>L-chain:</strong> <tt>DVVMTQTPLSLPVSLGDQASISCRSSQSLVHRNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYFCFQTTYVPNTFGGGTKLEIK</tt>
</p>
<p>
<strong>H-chain:</strong> <tt>EVQLLESGGGLVQPGGSLRLSCAASGFTFSLYWMGWVRQAPGKGLEWVSSISSSGGVTPYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLGELGWFDPWGQGTLVTVSS</tt>
<br/>
<strong>L-chain:</strong> <tt>DIQMTQSPSSLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYYASNLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIK</tt>
</p>
<p>
H-chain: <tt>EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS</tt>
<br/>
L-chain: <tt>EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTKLEIK</tt>
</p>
"""
gr.HTML(value = html)
h_text = gr.Textbox(lines=5, label="Heavy chain")
l_text = gr.Textbox(lines=5, label="Light chain")
btn = gr.Button(value="Submit")
btn.click(pred_seq, inputs=[h_text, l_text], outputs=gr.HTML())
if __name__ == "__main__":
demo.launch()
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