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| import gradio as gr | |
| import torch | |
| import pydssp | |
| import py3Dmol | |
| import os | |
| def get_pdb(pdb_code="", filepath=""): | |
| try: | |
| return filepath.name | |
| except AttributeError as e: | |
| if pdb_code is None or pdb_code == "": | |
| return None | |
| else: | |
| os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb") | |
| return f"{pdb_code}.pdb" | |
| def get_offset(pdb): | |
| pdb_multiline = pdb.split("\n") | |
| for line in pdb_multiline: | |
| if line.startswith("ATOM"): | |
| return int(line[22:27]) | |
| def predict(pdb_code, pdb_file, helix, sheet, loop): | |
| path_to_pdb = get_pdb(pdb_code=pdb_code, filepath=pdb_file) | |
| pdb = open(path_to_pdb, "r").read() | |
| offset = get_offset(pdb) | |
| coord = torch.tensor(pydssp.read_pdbtext(pdb)) | |
| secondary_struct = pydssp.assign(coord) | |
| view = py3Dmol.view(width=400, height=400) | |
| view.addModel(pdb, "pdb") | |
| colormap = {"H": helix, "E": sheet, "-": loop} | |
| colors = {i + offset: colormap[resi] for i, resi in enumerate(secondary_struct)} | |
| view.setStyle({"cartoon": {"colorscheme": {"prop": "resi", "map": colors}}}) | |
| view.zoomTo() | |
| output = view._make_html().replace("'", '"') | |
| x = f"""<!DOCTYPE html><html> {output} </html>""" # do not use ' in this input | |
| return f"""<iframe style="width: 100%; height:420px" 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>""" | |
| with gr.Blocks() as demo: | |
| gr.Markdown("# Secondary structure using pyDSSP") | |
| pdb_code = gr.Textbox(label="PDB Code") | |
| pdb_file = gr.File(label="PDB File Upload") | |
| with gr.Row(): | |
| helix = gr.ColorPicker(label="helix") | |
| sheet = gr.ColorPicker(label="sheet") | |
| loop = gr.ColorPicker(label="loop") | |
| btn = gr.Button(label="Run") | |
| html = gr.HTML() | |
| btn.click( | |
| fn=predict, inputs=[pdb_code, pdb_file, helix, sheet, loop], outputs=[html] | |
| ) | |
| gr.Examples( | |
| [["1QYS", "#ff0000", "#00ff00", "#0000ff"]], | |
| inputs=[pdb_code, helix, sheet, loop], | |
| fn=predict, | |
| ) | |
| demo.launch() | |