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import gradio as gr |
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from igfold import IgFoldRunner |
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import os |
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import random |
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import base64 |
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import socket |
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import re |
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def read_mol(molpath): |
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with open(molpath, "r") as fp: |
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lines = fp.readlines() |
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mol = "" |
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for l in lines: |
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mol += l |
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return mol |
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def molecule(input_pdb, h_seq, l_seq): |
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mol = read_mol(input_pdb) |
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byte_content = mol.encode('utf-8') |
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base64_content = base64.b64encode(byte_content).decode('utf-8') |
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x = ( |
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"""<!DOCTYPE html> |
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<html> |
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<head> |
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<meta http-equiv="content-type" content="text/html; charset=UTF-8" /> |
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<style> |
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body{ |
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font-family:sans-serif |
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} |
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.mol-container { |
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width: 100%; |
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height: 600px; |
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position: relative; |
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} |
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.mol-container select{ |
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background-image:None; |
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} |
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</style> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.3/jquery.min.js" integrity="sha512-STof4xm1wgkfm7heWqFJVn58Hm3EtS31XFaagaa8VMReCXAkQnJZ+jEy8PCC/iT18dFy95WcExNHFTqLyp72eQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script> |
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<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script> |
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</head> |
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<body> |
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<div id="container" class="mol-container"></div> |
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<script> |
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let h_seq = `""" |
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+ h_seq |
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+ """` |
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let l_seq = `""" |
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+ l_seq |
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+ """` |
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let pdb = `""" |
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+ mol |
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+ """` |
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$(document).ready(function () { |
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let element = $("#container"); |
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let config = { backgroundColor: "white" }; |
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let viewer = $3Dmol.createViewer(element, config); |
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viewer.addModel(pdb, "pdb"); |
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viewer.getModel(0).setStyle({chain: "H"}, {cartoon:{color:"red"}}); |
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viewer.getModel(0).setStyle({chain: "L"}, {cartoon:{color:"blue"}}); |
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viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity: 0.4, color: "lightblue"}); |
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viewer.zoomTo(); |
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viewer.render(); |
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viewer.zoom(0.8, 2000); |
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}) |
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</script> |
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</body></html>""" |
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) |
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return f"""<iframe style="width: 100%; height: 600px" 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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<div style="position: absolute; top: 10px; right: 10px; background-color: white; padding: 10px; border: 1px solid black;"> |
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<div style="width: 20px; height: 20px; background-color: red; display: inline-block;"></div> |
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<span style="margin-left: 3px;">Heavy chain</span><br> |
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<div style="width: 20px; height: 20px; background-color: blue; display: inline-block;"></div> |
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<span style="margin-left: 3px;">Light chain</span> |
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<div style="display: flex; justify-content: space-between; margin-top: 5px;"> |
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<a href="data:application/octet-stream;base64,{base64_content}" download="structure.pdb">Download File</a> |
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</div> |
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</div> |
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""" |
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def validate(seq): |
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alphabet = set('ACDEFGHIKLMNPQRSTVWY') |
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leftover = set(seq.upper()) - alphabet |
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return not leftover |
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def clean_sequence(seq): |
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return re.sub(r'\s+', '', seq) |
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def pred_seq(h_seq, l_seq): |
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h_seq = clean_sequence(h_seq).upper() |
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l_seq = clean_sequence(l_seq).upper() |
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print("Logs","___"*10) |
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print(f"Heavy chain: {h_seq}") |
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print(f"Light chain: {l_seq}") |
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hostname = socket.gethostname() |
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ip_address = socket.gethostbyname(hostname) |
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print(f"Hostname: {hostname}") |
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print(f"IP Address: {ip_address}") |
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print("___"*10) |
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h_is_valid = validate(h_seq) |
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l_is_valid = validate(l_seq) |
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if h_is_valid and l_is_valid: |
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sequences = { |
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"H": h_seq, |
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"L": l_seq |
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} |
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f_name = ''.join([random.choice("ACDEFGHIKLMNPQRSTVWY") for _ in range(15)]) |
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pred_pdb = f"{f_name}.pdb" |
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igfold = IgFoldRunner(num_models = 1) |
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igfold.fold( |
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pred_pdb, |
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sequences=sequences, |
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do_refine=False, |
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do_renum=False |
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) |
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html = molecule(pred_pdb, h_seq, l_seq) |
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else: |
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html = "<p>ERROR! Not valid sequence. Please use only standard amino acid letters (ACDEFGHIKLMNPQRSTVWY)</p>" |
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return html |
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examples = [ |
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[ |
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"QVQLKESGPGLVAPSQSLSITCTVSGFSLSSYGVSWVRQPPGKGLEWLGVIWGDGSTNYHPNLMSRLSISKDISKSQVLFKLNSLQTDDTATYYCVTLDYWGQGTSVTVSS", |
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"DVVMTQTPLSLPVSLGDQASISCRSSQSLVHRNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYFCFQTTYVPNTFGGGTKLEIK" |
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], |
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[ |
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"EVQLLESGGGLVQPGGSLRLSCAASGFTFSLYWMGWVRQAPGKGLEWVSSISSSGGVTPYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLGELGWFDPWGQGTLVTVSS", |
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"DIQMTQSPSSLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYYASNLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIK" |
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], |
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[ |
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"EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS", |
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"EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTKLEIK" |
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] |
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] |
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with gr.Blocks() as demo: |
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gr.Markdown('# Antibody Structure Prediction') |
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gr.Markdown("## Examples") |
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with gr.Row(): |
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h_text = gr.Textbox(lines=5, label="Heavy chain", |
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placeholder="Enter heavy chain sequence (e.g. QVQLKESGP...)") |
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l_text = gr.Textbox(lines=5, label="Light chain", |
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placeholder="Enter light chain sequence (e.g. DVVMTQTPL...)") |
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gr.Examples( |
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examples=examples, |
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inputs=[h_text, l_text], |
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label="Click on any example to paste it into the input fields", |
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fn=pred_seq, |
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outputs=gr.HTML() |
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) |
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btn = gr.Button(value="Submit") |
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output_html = gr.HTML() |
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btn.click(pred_seq, inputs=[h_text, l_text], outputs=output_html) |
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if __name__ == "__main__": |
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demo.launch() |
