#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the `pypath` python module
#
# Copyright 2014-2023
# EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
# Authors: see the file `README.rst`
# Contact: Dénes Türei (turei.denes@gmail.com)
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# https://www.gnu.org/licenses/gpl-3.0.html
#
# Website: https://pypath.omnipathdb.org/
#
import re
try:
import urllib2
except:
import urllib.request as urllib2
import gzip
import bs4
try:
from cStringIO import StringIO
except:
try:
from StringIO import StringIO
except:
from io import StringIO
[docs]
class ResidueMapper(object):
"""
This class stores and serves the PDB --> UniProt
residue level mapping. Attempts to download the
mapping, and stores it for further use. Converts
PDB residue numbers to the corresponding UniProt ones.
"""
[docs]
def __init__(self):
self.url = 'http://pdb.org/pdb/rest/das/pdb_uniprot_mapping/alignment?query=%s'
self.pdb_lst = 'ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/'\
'pdb_chain_uniprot.tsv.gz'
self.uniprot_pdb = None
self.clean()
self.download_errors = []
def load_mapping(self, pdb):
data = None
non_digit = re.compile(r'[^\d.-]+')
pdb = pdb.lower()
url = self.url % pdb
for i in range(5):
try:
data = urllib2.urlopen(url, timeout=60)
break
except:
continue
if not data:
self.download_errors.append(pdb)
mapper = {}
soup = bs4.BeautifulSoup(data.read())
for block in soup.find_all('block'):
seg = block.find_all('segment')
chain = seg[0]['intobjectid'].split('.')[1]
uniprot = seg[1]['intobjectid']
pdbstart = int(non_digit.sub('', seg[0]['start']))
pdbend = int(non_digit.sub('', seg[0]['end']))
uniprotstart = int(non_digit.sub('', seg[1]['start']))
uniprotend = int(non_digit.sub('', seg[1]['end']))
if chain not in mapper:
mapper[chain] = {}
mapper[chain][pdbend] = {
'uniprot': uniprot,
'pdbstart': pdbstart,
'uniprotstart': uniprotstart,
'uniprotend': uniprotend
}
if uniprot not in mapper:
mapper[uniprot] = {}
if chain not in mapper[uniprot]:
mapper[uniprot][chain] = {}
mapper[uniprot][chain][uniprotend] = {
'pdbstart': pdbstart,
'pdbend': pdbend,
'uniprotstart': uniprotstart
}
self.mappers[pdb] = mapper
def chains(self, chains):
if type(chains) in [str, unicode]:
chains = [chains]
if type(chains) is list:
chains = list(set(chains))
return chains
def pdb2uniprot(self, pdb, resnum, chains=None):
chains = self.chains(chains)
results = {}
pdb = pdb.lower()
if pdb not in self.mappers:
self.load_mapping(pdb)
if pdb in self.mappers:
for ch, data in self.mappers[pdb].iteritems():
if len(ch) == 1 and (chains is None or ch in chains):
pdbends = data.keys()
if resnum <= max(pdbends):
pdbend = min([
x for x in [e - resnum for e in pdbends] if x >= 0
]) + resnum
seg = data[pdbend]
if seg['pdbstart'] <= resnum:
offset = seg['uniprotstart'] - seg['pdbstart']
residue = {
'resnum': resnum + offset,
'offset': offset,
'uniprot': seg['uniprot']
}
results[ch] = residue
return results
def uniprot2pdb(self, uniprot, resnum, chains=None, pdbs=None):
chains = self.chains(chains)
if self.uniprot_pdb is None:
self.get_pdb_chains()
results = {}
# one uniprot can occure in more pdbs, first
# we need to find out, which pdb files should we look at:
if pdbs is None:
pdbs = []
if uniprot in self.uniprot_pdb:
for updb in self.uniprot_pdb[uniprot]:
pdbs.append(updb['pdb'])
elif type(pdbs) in [str, unicode]:
pdbs = [pdbs]
pdbs = list(set(pdbs))
# now find the residue number in each of the pdb's:
for pdb in pdbs:
if pdb not in self.mappers:
self.load_mapping(pdb)
if pdb in self.mappers and uniprot in self.mappers[pdb]:
for ch, up in self.mappers[pdb][uniprot].iteritems():
if chains is None or ch in chains:
uniprotends = up.keys()
if resnum <= max(uniprotends):
uniprotend = min([
x for x in [e - resnum for e in uniprotends]
if x >= 0
]) + resnum
seg = up[uniprotend]
if seg['uniprotstart'] <= resnum:
offset = seg['pdbstart'] - seg['uniprotstart']
residue = {
'resnum': resnum + offset,
'offset': offset
}
if pdb not in results:
results[pdb] = {}
results[pdb][ch] = residue
return results
def get_residue(self, ac, resnum, chains=None, pdbs=None):
if len(ac.strip()) == 4:
return self.pdb2uniprot(ac, resnum, chains)
else:
return self.uniprot2pdb(ac, resnum, chains, pdbs)
[docs]
def clean(self):
'''
Removes cached mappings, freeing up memory.
'''
self.mappers = {}
self.uniprot_pdb = None
self.pdb_uniprot = None
def get_pdb_chains(self):
gzfile = urllib2.urlopen(self.pdb_lst)
buff = StringIO(gzfile.read())
chains = gzip.GzipFile(fileobj=buff, mode='rb').read()
chains = chains.replace('\r', '').split('\n')
del chains[0]
del chains[0]
self.pdb_uniprot = {}
self.uniprot_pdb = {}
non_digit = re.compile(r'[^\d.-]+')
for l in chains:
l = l.split('\t')
if len(l) > 8:
if l[0] not in self.pdb_uniprot:
self.pdb_uniprot[l[0]] = {}
self.pdb_uniprot[l[0]][l[1]] = {
'uniprot': l[2],
'chain_beg': int(non_digit.sub('', l[3])),
'chain_end': int(non_digit.sub('', l[4])),
'pdb_beg': int(non_digit.sub('', l[5])),
'pdb_end': int(non_digit.sub('', l[6])),
'uniprot_beg': int(non_digit.sub('', l[7])),
'uniprot_end': int(non_digit.sub('', l[8]))
}
if self.pdb_uniprot[l[0]][l[1]]['pdb_end'] - \
self.pdb_uniprot[l[0]][l[1]]['pdb_beg'] == \
self.pdb_uniprot[l[0]][l[1]]['uniprot_end'] - \
self.pdb_uniprot[l[0]][l[1]]['uniprot_beg']:
self.pdb_uniprot[l[0]][l[1]]['offset'] = \
(self.pdb_uniprot[l[0]][l[1]]['uniprot_beg'] -
self.pdb_uniprot[l[0]][l[1]]['pdb_beg'])
else:
self.pdb_uniprot[l[0]][l[1]]['offset'] = None
if l[2] not in self.uniprot_pdb:
self.uniprot_pdb[l[2]] = []
self.uniprot_pdb[l[2]].append({
'pdb': l[0],
'chain': l[1],
'chain_beg': int(non_digit.sub('', l[3])),
'chain_end': int(non_digit.sub('', l[4])),
'pdb_beg': int(non_digit.sub('', l[5])),
'pdb_end': int(non_digit.sub('', l[6])),
'uniprot_beg': int(non_digit.sub('', l[7])),
'uniprot_end': int(non_digit.sub('', l[8])),
'offset': self.pdb_uniprot[l[0]][l[1]]['offset']
})
