I am attempting to use the python urllib.request library to download .pdb (protein data bank) files with the full predicted molecular structure of a given protein from the alphafold website. In this example, I am attempting to download a protein with a uniprot ID of Q9BY15. The entry https://alphafold.ebi.ac.uk/entry/Q9BY15 contains a download link to the pdb file of the protein as shown below;
And the manually downloaded file has the following naming format;
Here is the block of code I am using (in its simplest form)
import os
import urllib
import urllib.request
url = 'https://alphafold.ebi.ac.uk/entry/'
prot = 'Q9BY15'
alphaname = 'AF-' + prot + '-F1-model_v2.pdb'
urllib.request.urlretrieve(url + prot, alphaname)
And here is the file that I get when I run the code;
As you can see, the file is far smaller than the actual size of the real file (despite having the exact same name), and is effectively empty when viewing it through protein identification programs. How would I rewrite this code to pull the actual file?
