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import gradio as gr
import os
import py3Dmol
def display_pdb_by_pdb(pdb):
# function to display pdb in py3dmol
# ref: https://huggingface.co/spaces/AIGE/A_B
view = py3Dmol.view(width=500, height=500)
view.addModel(pdb, "pdb")
view.setStyle({'cartoon': {'color': 'spectrum'}})
view.zoomTo()
output = view._make_html().replace("'", '"')
x = f"""<!DOCTYPE html><html></center> {output} </center></html>""" # do not use ' in this input
return f"""<iframe height="500px" width="100%" 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 get_pdb(sequence):
retries = 0
pdb_str = None
url = "https://api.esmatlas.com/foldSequence/v1/pdb/"
while retries < 3 and pdb_str is None:
response = requests.post(url, data=sequence, verify=False)
pdb_str = response.text
if pdb_str == "INTERNAL SERVER ERROR":
retries += 1
time.sleep(0.1)
pdb = str = None
return pdb_str
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, verify=False) #verify=false jw 0425 work around for SSL certificate
pdb_string = get_pdb(sequence)
name = sequence[:3] + sequence[-3:]
outpath = (
Path.cwd() / f"PDB-{name}.pdb")
with open(outpath.name, "w") as f:
f.write(pdb_string)
outpath_str = str(outpath)
html_view = display_pdb_by_pdb(pdb_string)
return outpath_str, html_view
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
DEFAULT_SEQ = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"
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 Structure
</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="Paste your protein sequence here...")
btn = gr.Button("Plot Predicted Structure ").style(full_width=False)
with gr.Row():
PDB_string = gr.Textbox(
lines=4,
max_lines=120,
label="PDB_string Output"
)
with gr.Row():
output_file = gr.File(
label="Download PDB Structure as Text File",
file_count="single",
type="filepath",
interactive=False,
)
output_viewer = gr.HTML()
btn.click(fn=update, inputs=inp, outputs=[output_file, output_viewer])
name.change(fn=suggest, inputs=name, outputs=inp)
inp.change(fn=update, inputs=inp, outputs=output_file)
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() |