File size: 3,506 Bytes
580db5b b0cb70d 9f2073b 289b045 0014c63 b0cb70d 9f2073b 0014c63 9f2073b b0cb70d 9f2073b efd57a2 9f2073b 1742c86 1714685 9f2073b b0cb70d 5a255ae e26a5c3 9f2073b 1f3c26c 0014c63 1f3c26c 580db5b 9f2073b c9bfe79 fb540ae e90417a 9f2073b c8cad2c 9f2073b 289b045 9f2073b a10eab8 9f2073b 64f9281 9f2073b 6839858 9f2073b 6839858 61ecdb3 6839858 289b045 |
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 |
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: 0.7, 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>
<a href="data:application/octet-stream;base64,{base64_content}" download="example.txt">Download File</a>
"""
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()
l_seq = l_seq.upper()
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)
inputs = [gr.Textbox(lines=5, label="Heavy chain"),
gr.Textbox(lines=5, label="Light chain")
]
iface = gr.Interface(fn=pred_seq,
inputs=inputs,
outputs=gr.HTML(),
title="Antibody structure prediction")
iface.launch(share = True) |