File size: 5,632 Bytes
580db5b b0cb70d 9f2073b 289b045 0014c63 b0cb70d 9f2073b 26ee080 9f2073b 0014c63 9f2073b b0cb70d 9f2073b efd57a2 9f2073b ea99d62 45f9208 54f71b6 ea99d62 9f2073b 3856e63 83bb191 54f71b6 9f2073b b0cb70d 5a255ae e26a5c3 9f2073b 1f3c26c ebd6115 ead6b80 fc7924f ead6b80 27a7049 1f3c26c 580db5b 9f2073b c9bfe79 5267d12 db18d4d 26ee080 fb540ae e90417a 9f2073b c8cad2c 9f2073b 289b045 9f2073b fcdae55 9f2073b fcdae55 9f2073b 26ee080 9f2073b 64f9281 9f2073b 41bea22 dbcc60e fc7924f dbcc60e fc7924f ce2e28f fc7924f dbcc60e fc7924f ce2e28f fc7924f c664e5c fc7924f ce2e28f fc7924f 04edd53 41bea22 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 |
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, h_seq, l_seq):
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 h_seq = `"""
+ h_seq
+ """`
let l_seq = `"""
+ l_seq
+ """`
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({chain: "H"}, {cartoon:{color:"red"}});
viewer.getModel(0).setStyle({chain: "L"}, {cartoon:{color:"blue"}});
viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity: 0.4, color: "lightblue"});
viewer.addResLabels(h_seq, {chain: "H"});
viewer.addResLabels(l_seq, {chain: "L"});
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="width: 20px; height: 20px; background-color: red; display: inline-block;"></div>
<span style="margin-left: 5px;">Heavy chain</span><br>
<div style="width: 20px; height: 20px; background-color: blue; display: inline-block;"></div>
<span style="margin-left: 5px;">Light chain</span>
<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)
print(l_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(num_models = 1)
igfold.fold(
pred_pdb,
sequences=sequences,
do_refine=False,
do_renum=False
)
html = molecule(pred_pdb, h_seq, l_seq)
else:
html = "<p>ERROR! Not valid sequence</p>"
return (html)
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>
<strong>H-chain:</strong> <tt>EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS</tt>
<br/>
<strong>L-chain: </strong> <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()
|