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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 < 0.5) { | |
| return "OrangeRed"; | |
| } else if (atom.b < 0.7) { | |
| return "Gold"; | |
| } else if (atom.b < 0.9) { | |
| 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>""" | |
| import tempfile | |
| 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_string = response.content.decode('utf-8') | |
| tmp = tempfile.NamedTemporaryFile() | |
| with open(tmp.name, "w") as f: | |
| f.write(pdb_string) | |
| print("File name", tmp.name) | |
| return molecule(tmp.name) | |
| 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("🔬 Predict Structure ").style(full_width=False) | |
| mol = gr.HTML(update) | |
| #download = gr.File(label="Download file") | |
| 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(debug=True) |