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| import py3Dmol | |
| import requests | |
| from pathlib import Path | |
| 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.setBackgroundColor('black'); | |
| view.addModel(pdb, "pdb") | |
| view.setStyle({'cartoon': {'color': 'spectrum'}}) | |
| view.zoomTo() | |
| output = view._make_html().replace("'", '"') | |
| x = f"""<!DOCTYPE html><html></center> {output} </center></html>""" # do not use ' in this input | |
| return f"""<iframe height="500px" width="100%" 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 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 plot_struc(sequence): | |
| 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 |