#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
import urllib3
except:
print('BlastPDB requires urllib3')
[docs]
class BlastPDB:
"""BlastPDB - run Blast online on the PDB database.
This can be used in Jupiter based RNA notebooks, e.g.
https://github.com/mmagnus/rna-pdb-tools/blob/master/rp18.ipynb
Warning: getBlastPDB1 has been permanently removed as part of our announced shutdown on December 9th, 2020.
https://www.rcsb.org/pdb/rest/getBlastPDB1
Usage::
>>> p = BlastPDB('GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG')
>>> p.search()
>>> p.result #doctest: +ELLIPSIS
u'<HTML>\\n<TITLE>BLAST Search Results</TITLE>...
:param seq: string
"""
def __init__(self, seq):
self.seq = seq
self.result = ''
[docs]
def search(self):
"""Search online the seq."""
http = urllib3.PoolManager()
response = http.request('GET', 'http://www.rcsb.org/pdb/rest/getBlastPDB1?sequence=' +
self.seq +
'&eCutOff=10.0&matrix=BLOSUM62&outputFormat=HTML')
if response.status == 200:
self.result = response.data.decode()
# main
if __name__ == '__main__':
import doctest
doctest.testmod()