Hi all,
How do I use urllib.request module in Python 3.7 to open a pdb file?
The URL I’m using is http://files.rcsb.org/download/1N5O.pdb.
I’ve read about the need for SSL support but I’m not too sure how to write a code which incorporates those principles.
Here is how my code looks like thus far:
import urllib.request req= urllib.request.Request("http://files.rcsb.org/download/1N5O.pdb")
with urllib.request.urlopen(req) as response:
the_page= response.read()
print (the_page)
Any advice on the above would be much appreciated. Thank you!
(For more accurate formatting, I've attached my picture here in [1]:
•
written
by
konstanzeta •
You wouldn't need SSL or https support to do an http GET request over an unencrypted connection.
That said, you could do something like:
#!/usr/bin/env python
import sys
import requests
url = 'http://files.rcsb.org/download/1N5O.pdb'
localFn = '1N5O.pdb'
try:
r = requests.get(url, stream=True)
with open(localFn, 'wb') as f:
for chunk in r.iter_content(chunk_size=1024*1024):
if chunk:
f.write(chunk)
except requests.exceptions.ChunkedEncodingError as cee:
sys.stderr.write('Error: Could not get data')
sys.exit(-1)
See: http://docs.python-requests.org/en/master/user/advanced/ for a discussion of SSL/https GET requests.
NB: This will overwrite any existing file with the name 1N5O.pdb. Use os.path.exists if you want to do something a little more robust.
Hi Alex,
Thank you very much for your help.
I have applied these to my code, and its working fine now.
Have a good week ahead.
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