import gradio as gr import os import py3Dmol DEFAULT_SEQ = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ" 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""" {output} """ # do not use ' in this input return f"""""" 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 demo = gr.Blocks() with demo: gr.HTML("""

ESMFold Protein Folding Structure

You can input a single protein sequence and you get the predicted protein structure

""") 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 ") #btn = gr.Button("🔬 Predict 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()