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ESM_ShowProteinStructure

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wangjin2000 commited on May 6

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Create app.py

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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()