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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 < 50) { | |
return "OrangeRed"; | |
} else if (atom.b < 70) { | |
return "Gold"; | |
} else if (atom.b < 90) { | |
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>""" | |
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_filename = "test.pdb" | |
pdb_string = response.content.decode('utf-8') | |
with open(pdb_filename, "w") as out: | |
out.write(pdb_string) | |
return molecule(pdb_filename) | |
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("π¬ Predict Structure ").style(full_width=False) | |
mol = gr.HTML(update) | |
btn.click(fn=update, inputs=inp, outputs=mol) | |
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() |