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2b68bae 0f80091 2b68bae 0f80091 2b68bae | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 | import gradio as gr
import os
import requests
DEFAULT_SEQ = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"
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)
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: 380px;
position: relative;
}
.mol-container select{
background-image:None;
}
</style>
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
</head>
<body style="overflow: hidden;">
<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);
let colorAlpha = function (atom) {
if (atom.b < 0.5) {
return "OrangeRed";
} else if (atom.b < 0.7) {
return "Gold";
} else if (atom.b < 0.9) {
return "MediumTurquoise";
} else {
return "Blue";
}
};
viewer.addModel(pdb, "pdb");
// set plddt coloring
viewer.getModel(0).setStyle({cartoon: { colorfunc: colorAlpha }});
// display pLDDT tooltips when hovering over atoms
viewer.getModel(0).setHoverable({}, true,
function (atom, viewer, event, container) {
if (!atom.label) {
atom.label = viewer.addLabel(atom.resn + atom.resi + " pLDDT=" + atom.b, { position: atom, backgroundColor: "mintcream", fontColor: "black" });
}
},
function (atom, viewer) {
if (atom.label) {
viewer.removeLabel(atom.label);
delete atom.label;
}
}
);
viewer.zoomTo();
viewer.render();
viewer.zoom(1.2, 2000);
})
</script>
</body></html>"""
)
return f"""<iframe style="width: 100%; height: 380px" 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>"""
import tempfile
def update(sequence=DEFAULT_SEQ):
headers = {
'Content-Type': 'application/x-www-form-urlencoded',
}
response = requests.post('https://api.esmatlas.com/foldSequence/v1/pdb/', headers=headers, data=sequence)
name = sequence[:3] + sequence[-3:]
pdb_string = response.content.decode('utf-8')
tmp = tempfile.NamedTemporaryFile()
with open(tmp.name, "w") as f:
f.write(pdb_string)
print("File name", tmp.name)
return molecule(tmp.name), tmp.name
def suggest(option):
if option == "Plastic degradation protein":
suggestion = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"
elif option == "Antifreeze protein":
suggestion = "QCTGGADCTSCTGACTGCGNCPNAVTCTNSQHCVKANTCTGSTDCNTAQTCTNSKDCFEANTCTDSTNCYKATACTNSSGCPGH"
elif option == "AI Generated protein":
suggestion = "MSGMKKLYEYTVTTLDEFLEKLKEFILNTSKDKIYKLTITNPKLIKDIGKAIAKAAEIADVDPKEIEEMIKAVEENELTKLVITIEQTDDKYVIKVELENEDGLVHSFEIYFKNKEEMEKFLELLEKLISKLSGS"
elif option == "7-bladed propeller fold":
suggestion = "VKLAGNSSLCPINGWAVYSKDNSIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNSRFESVAWSASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKMEKGKVVKSVELDAPNYHYEECSCYPNAGEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGAYGVKGFSFKYGNGVWIGRTKSTNSRSGFEMIWDPNGWTETDSSFSVKQDIVAITDWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK"
else:
suggestion = ""
return suggestion
demo = gr.Blocks()
with demo:
gr.HTML("""<div style="text-align: center; max-width: 700px; margin: 0 auto;">
<div
style="
display: inline-flex;
align-items: center;
gap: 0.8rem;
font-size: 1.75rem;
"
>
<h1 style="font-weight: 900; margin-bottom: 7px; margin-top: 5px;">
ESMFold Protein Folding demo
</h1>
</div>
<p style="margin-bottom: 10px; font-size: 94%">
You can input a single protein sequence and you get the predicted protein structure
</p>
</div>""")
name = gr.Dropdown(label="Choose a Sample Protein", value="Plastic degradation protein", choices=["Antifreeze protein", "Plastic degradation protein", "AI Generated protein", "7-bladed propeller fold", "custom"])
with gr.Row():
inp = gr.Textbox(label="Protein sequence", lines=3, value=DEFAULT_SEQ, placeholder="Write your protein sequence here...")
btn = gr.Button("🔬 Predict Structure ").style(full_width=False)
mol = gr.HTML(update)
download = gr.File(label="Download file")
btn.click(fn=update, inputs=inp, outputs=[mol, download])
name.change(fn=suggest, inputs=name, outputs=inp)
name.change(fn=lambda :"", inputs=None, outputs=mol)
inp.change(fn=update, inputs=inp, outputs=mol)
gr.Markdown("A demo of [ESM](https://esmatlas.com/about) by Meta using the API. You can also use ESM in Hugging Face `transformers` as shown [here](https://github.com/huggingface/notebooks/blob/ab81a52182acf691e6743a50bc47bd1c1622086f/examples/protein_folding.ipynb), which is supported since [v4.24](https://github.com/huggingface/transformers/releases/tag/v4.24.0).")
demo.launch(debug=True) |