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Upload plot_pdb.py
Browse files- plot_pdb.py +56 -0
plot_pdb.py
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import py3Dmol
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import requests
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from pathlib import Path
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def display_pdb_by_pdb(pdb):
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# function to display pdb in py3dmol
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# ref: https://huggingface.co/spaces/AIGE/A_B
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view = py3Dmol.view(width=500, height=500)
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view.setBackgroundColor('black');
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view.addModel(pdb, "pdb")
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view.setStyle({'cartoon': {'color': 'spectrum'}})
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view.zoomTo()
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output = view._make_html().replace("'", '"')
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x = f"""<!DOCTYPE html><html></center> {output} </center></html>""" # do not use ' in this input
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return f"""<iframe height="500px" width="100%" 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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def get_pdb(sequence):
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retries = 0
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pdb_str = None
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url = "https://api.esmatlas.com/foldSequence/v1/pdb/"
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while retries < 3 and pdb_str is None:
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response = requests.post(url, data=sequence, verify=False)
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pdb_str = response.text
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if pdb_str == "INTERNAL SERVER ERROR":
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retries += 1
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time.sleep(0.1)
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pdb = str = None
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return pdb_str
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def plot_struc(sequence):
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headers = {
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'Content-Type': 'application/x-www-form-urlencoded',
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}
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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
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pdb_string = get_pdb(sequence)
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name = sequence[:3] + sequence[-3:]
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outpath = (
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Path.cwd() / f"PDB-{name}.pdb")
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with open(outpath.name, "w") as f:
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f.write(pdb_string)
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outpath_str = str(outpath)
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html_view = display_pdb_by_pdb(pdb_string)
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return outpath_str, html_view
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