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import py3Dmol
import requests
from pathlib import Path
import Bio.PDB
def display_pdb_by_pdb(pdb_string,pdb_filename,color_map="pLDDT"):
# function to display pdb in py3dmol
# ref: https://huggingface.co/spaces/AIGE/A_B
#get pdb column values
p = Bio.PDB.PDBParser()
structure = p.get_structure('myStructureName', pdb_filename)
ids = [a.get_id() for a in structure.get_atoms()]
pLDDTs = [a.get_bfactor() for a in structure.get_atoms()]
plddt_bands = ['#FF7D45','#FFDB13','#65CBF3','#0053D6']
style = "cartoon"
#plot 3D structure
view = py3Dmol.view(width=500, height=500)
view.setBackgroundColor('black');
view.addModel(pdb_string, "pdb")
if color_map == "spectrum":
view.setStyle({'cartoon': {'color': 'spectrum'}})
else:
for i,plddt in enumerate(pLDDTs):
if plddt >0.90:
color = plddt_bands[3]
elif plddt >0.70:
color = plddt_bands[2]
elif plddt >0.50:
color = plddt_bands[1]
else:
color = plddt_bands[0]
'''
if style == "cartoon" and show_sidechains == True:
view.setStyle({'model': -1, 'serial': i+1}, {style: {'color': color},"stick":{}})
else:
view.setStyle({'model': -1, 'serial': i+1}, {style: {'color': color}})
'''
view.setStyle({'model': -1, 'serial': i+1}, {style:{'color': color}})
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 = None #pdb = str = None
#save a pdb format file
name = sequence[:3] + sequence[-3:] #combine the firt and last 3 AAs of sequence as a filename.
outpath = (
Path.cwd() / f"PDB-{name}.pdb")
with open(outpath.name, "w") as f:
f.write(pdb_str)
outpath_str = str(outpath)
return pdb_str, outpath_str
def plot_struc(sequence):
pdb_string, pdb_filename = get_pdb(sequence)
html_view = display_pdb_by_pdb(pdb_string, pdb_filename, color_map = "spectrum")
return pdb_filename, html_view |