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| import gradio as gr | |
| import os | |
| def get_pdb(pdb_code="", filepath=""): | |
| if pdb_code is None or pdb_code == "": | |
| try: | |
| return filepath.name | |
| except AttributeError as e: | |
| return None | |
| else: | |
| os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb") | |
| return f"{pdb_code}.pdb" | |
| 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: 600px; | |
| position: relative; | |
| } | |
| .mol-container select{ | |
| background-image:None; | |
| } | |
| </style> | |
| <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> | |
| <script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script> | |
| </head> | |
| <body> | |
| <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); | |
| viewer.addModel(pdb, "pdb"); | |
| viewer.getModel(0).setStyle({}, { cartoon: { colorscheme:"whiteCarbon" } }); | |
| viewer.zoomTo(); | |
| viewer.render(); | |
| viewer.zoom(0.8, 2000); | |
| }) | |
| </script> | |
| </body></html>""" | |
| ) | |
| return f"""<iframe style="width: 100%; height: 600px" 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 update(inp, file): | |
| pdb_path = get_pdb(inp, file) | |
| return molecule(pdb_path) | |
| demo = gr.Blocks() | |
| with demo: | |
| gr.Markdown("# PDB viewer using 3Dmol.js") | |
| gr.Markdown("""If using please cite: | |
| > 3Dmol.js: molecular visualization with WebGL, Nicholas Rego, David Koes , Bioinformatics, Volume 31, Issue 8, April 2015, Pages 1322–1324, https://doi.org/10.1093/bioinformatics/btu829""") | |
| with gr.Row(): | |
| with gr.Box(): | |
| inp = gr.Textbox( | |
| placeholder="PDB Code or upload file below", label="Input structure" | |
| ) | |
| file = gr.File(file_count="single") | |
| gr.Examples(["2CBA", "6VXX"], inp) | |
| btn = gr.Button("View structure") | |
| mol = gr.HTML() | |
| btn.click(fn=update, inputs=[inp, file], outputs=mol) | |
| demo.launch() | |