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import gradio as gr |
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import os |
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import py3Dmol |
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import requests |
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from pathlib import Path |
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DEFAULT_SEQ = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ" |
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def display_pdb_by_pdb(pdb): |
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view = py3Dmol.view(width=500, height=500) |
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view.addModel(pdb, "pdb") |
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view.setStyle({'cartoon': {'color': 'spectrum'}}) |
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view.zoomTo() |
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output = view._make_html().replace("'", '"') |
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x = f"""<!DOCTYPE html><html></center> {output} </center></html>""" |
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return f"""<iframe height="500px" width="100%" name="result" allow="midi; geolocation; microphone; camera; |
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms |
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allow-scripts allow-same-origin allow-popups |
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" |
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>""" |
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def get_pdb(sequence): |
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retries = 0 |
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pdb_str = None |
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url = "https://api.esmatlas.com/foldSequence/v1/pdb/" |
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while retries < 3 and pdb_str is None: |
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response = requests.post(url, data=sequence, verify=False) |
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pdb_str = response.text |
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if pdb_str == "INTERNAL SERVER ERROR": |
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retries += 1 |
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time.sleep(0.1) |
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pdb = str = None |
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return pdb_str |
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def update(sequence=DEFAULT_SEQ): |
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headers = { |
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'Content-Type': 'application/x-www-form-urlencoded', |
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} |
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response = requests.post('https://api.esmatlas.com/foldSequence/v1/pdb/', headers=headers, data=sequence, verify=False) |
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pdb_string = get_pdb(sequence) |
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name = sequence[:3] + sequence[-3:] |
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outpath = ( |
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Path.cwd() / f"PDB-{name}.pdb") |
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with open(outpath.name, "w") as f: |
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f.write(pdb_string) |
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outpath_str = str(outpath) |
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html_view = display_pdb_by_pdb(pdb_string) |
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return outpath_str, html_view |
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def suggest(option): |
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if option == "Plastic degradation protein": |
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suggestion = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ" |
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elif option == "Antifreeze protein": |
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suggestion = "QCTGGADCTSCTGACTGCGNCPNAVTCTNSQHCVKANTCTGSTDCNTAQTCTNSKDCFEANTCTDSTNCYKATACTNSSGCPGH" |
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elif option == "AI Generated protein": |
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suggestion = "MSGMKKLYEYTVTTLDEFLEKLKEFILNTSKDKIYKLTITNPKLIKDIGKAIAKAAEIADVDPKEIEEMIKAVEENELTKLVITIEQTDDKYVIKVELENEDGLVHSFEIYFKNKEEMEKFLELLEKLISKLSGS" |
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elif option == "7-bladed propeller fold": |
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suggestion = "VKLAGNSSLCPINGWAVYSKDNSIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNSRFESVAWSASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKMEKGKVVKSVELDAPNYHYEECSCYPNAGEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGAYGVKGFSFKYGNGVWIGRTKSTNSRSGFEMIWDPNGWTETDSSFSVKQDIVAITDWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK" |
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else: |
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suggestion = "" |
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return suggestion |
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demo = gr.Blocks() |
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with demo: |
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gr.HTML("""<div style="text-align: center; max-width: 700px; margin: 0 auto;"> |
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<div |
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style=" |
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display: inline-flex; |
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align-items: center; |
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gap: 0.8rem; |
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font-size: 1.75rem; |
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" |
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> |
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<h1 style="font-weight: 900; margin-bottom: 7px; margin-top: 5px;"> |
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ESMFold Protein Folding Structure |
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</h1> |
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</div> |
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<p style="margin-bottom: 10px; font-size: 94%"> |
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You can input a single protein sequence and you get the predicted protein structure |
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</p> |
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</div>""") |
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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"]) |
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with gr.Row(): |
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inp = gr.Textbox(label="Protein sequence", lines=3, value=DEFAULT_SEQ, placeholder="Paste your protein sequence here...") |
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btn = gr.Button("Plot Predicted Structure ") |
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with gr.Row(): |
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PDB_string = gr.Textbox( |
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lines=4, |
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max_lines=120, |
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label="PDB_string Output" |
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) |
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with gr.Row(): |
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output_file = gr.File( |
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label="Download PDB Structure as Text File", |
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file_count="single", |
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type="filepath", |
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interactive=False, |
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) |
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output_viewer = gr.HTML() |
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btn.click(fn=update, inputs=inp, outputs=[output_file, output_viewer]) |
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name.change(fn=suggest, inputs=name, outputs=inp) |
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inp.change(fn=update, inputs=inp, outputs=output_file) |
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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).") |
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demo.launch() |
