#!/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/
#
from __future__ import annotations
from future.utils import iteritems
from past.builtins import xrange, range
import json
import os
import sys
import textwrap
import bs4
import pypath.share.progress as progress
import pypath.share.curl as curl
import pypath.share.common as common
import pypath.inputs.unichem as unichem_input
[docs]
class Unichem(object):
"""
Client for the UniChem drug compound identifier translation service
(https://www.ebi.ac.uk/unichem/).
"""
[docs]
def __init__(self):
sys.stdout.write(
'\n\tType `Unichem_instance.usage()` to get help.\n\n'
)
sys.stdout.flush()
# from unichem id to db name
self.uc_dict = unichem_input.unichem_sources()
# from db name to unichem id
self.name_dict = common.swap_dict(self.uc_dict)
self.url_stem = 'https://www.ebi.ac.uk/unichem/rest/src_compound_id'
self.inchi_stem = 'https://www.ebi.ac.uk/unichem/rest/inchikey/%s'
self.chembl_url = (
'http://www.ebi.ac.uk/chemblws/compounds/smiles/{0}.json'
)
self.cpd_search = 'http://www.ebi.ac.uk/unichem/rest/{0}/{1}/{2}{3}'
self.result = {}
[docs]
def usage(self):
"""
Prints usage information and examples to the standard output.
"""
msg = '''
List of identifier types can be read above.
To query UniChem, give either names or numbers of the
ID types you wish to translate from and to.
E.g.
>>> u = unichem.Unichem()
>>> u.translate('pubchem', 'chembl', list_of_pubchems)
For example, the PubChem CID of Aspirin is 2244. Translate it to
ChEMBL:
>>> u.translate('pubchem', 'chembl', '2244')
>>> u.result
{'2244': ['CHEMBL25']}
We can translate multiple identifiers the same way:
>>>
>>> u.translate('pubchem', 'chembl', ['2244', '4091'])
>>> u.result
{'2244': ['CHEMBL25'], '4091': ['CHEMBL1431']}
Additional ways of translation are from SMILEs to ChEMBL IDs, and
from InChiKeys to any ID. These are translated not by the UniChem,
but by the ChEMBL webservice.
>>> u.translate('smiles', 'chembl', list_of_smiles)
>>> u.translate('inchikey', 'chembl', list_of_inchikeys)
Other option to search is connectivity search from UniChem.
A-G parameters can be defined optionally. See description at
https://www.ebi.ac.uk/unichem/info/widesearchInfo
>>> u.connectivity_search(list_of_zincs, 'zinc', parameters=[1,0,0,0,0,1,0])
InChiKeys can be used in connectivity search too:
>>> u.connectivity_search(list_of_inchikeys, 'inchikey', parameters=[1,0,0,0,0,1,0])
You can also call directly functions accessing ChEMBL webservice, with the
same result as you would call `translate()` or `connectivity_search()`:
>>> u.smiles2chembl(list_of_smiles)
>>> u.inchikey2anything('chembl', list_of_inchikeys)
Find the dict in `u.result`. Untranslated items have value `None`.
Every call overwrites previous result!
For an up to date list of identifier types see
https://www.ebi.ac.uk/unichem/ucquery/listSources or
call `Unichem.info(<source>)`:
>>> Unichem.info('chembl')
'''
sys.stdout.write(os.linesep)
id_types = sorted(
self.uc_dict.items(),
key = lambda x: int(x[0])
)
if len(id_types) % 2:
id_types.append(('',) * 2)
nrows = len(id_types) // 2
for i in xrange(nrows):
sys.stdout.write(
''.join((
' ' * 8,
id_types[i][0].rjust(2),
' ' * 3,
id_types[i][1].ljust(20),
id_types[i + nrows][0].rjust(2),
' ' * 3,
id_types[i + nrows][1].ljust(20),
os.linesep,
))
)
sys.stdout.write(msg + os.linesep)
sys.stdout.flush()
[docs]
@staticmethod
def info(source):
"""
Print information about one source.
Args
source (int,str): The numeric or string ID of one source.
"""
unichem_input.info(source)
[docs]
def translate(self, source, target, lst):
"""
Translate one drug compound identifier to another identifier type
using the UniChem web service. For an up to date list of identifier
types see https://www.ebi.ac.uk/unichem/ucquery/listSources.
Args
source (str,int): The source ID type, either as a string label
or as a number, as used in UniChem.
target (str,int): The target ID type, either as a string label
or as a number, as used in UniChem.
lst (str,set): One or more identifiers to translate.
Returns
Returns None, the results are stored in the `result` attribute
of this object.
"""
lst = common.to_set(lst)
self.result = {}
if source == 'inchikey':
self.inchikey2anything(target, lst)
return None
if source == 'smiles':
self.smiles2chembl(lst)
return None
source = (
str(source)
if type(source) is int else
self.name_dict[source]
)
target = (
str(target)
if type(target) is int else
self.name_dict[target]
)
prg = progress.Progress(
total=len(lst),
name='Translating compound identifiers',
interval=1,
)
for comp in lst:
url = '/'.join([self.url_stem, comp, source, target])
c = curl.Curl(url, large = False)
result = c.result
self.result[comp] = []
if result is not None:
data = json.loads(result)
for d in data:
self.result[comp].append(d['src_compound_id'])
prg.step()
prg.terminate()
[docs]
def inchikey2anything(self, target, lst):
"""
Translate InChi keys to another identifier type using the ChEMBL
web service.
Args
target (str,int): The target ID type, either as a string label
or as a number, as used in UniChem.
lst (str,set): One or more InChi keys.
Returns
Returns None, the results are stored in the `result` attribute
of this object.
"""
lst = common.to_set(lst)
self.result = {}
target = (
str(target)
if type(target) is int else
self.name_dict[target]
)
prg = progress.Progress(
total=len(lst),
name='Translating InChi-Keys',
interval=1,
)
for inchik in lst:
url = self.inchi_stem % inchik
c = curl.Curl(url, large = False)
result = c.result
if result is not None:
data = json.loads(result)
self.result[inchik] = [
d['src_compound_id']
for d in data
if d['src_id'] == target
]
prg.step()
prg.terminate()
[docs]
def smiles2chembl(self, smiles):
"""
Translate SMILES to ChEMBL ID using the ChEMBL web service.
Args
smiles (str,list): One or more SMILES.
Returns
Returns None, the results are stored in the `result` attribute
of this object.
"""
smiles = common.to_set(smiles)
self.result = {}
prg = progress.Progress(
total=len(smiles),
name='Translating SMILEs',
interval=1
)
for sml in smiles:
url = self.chembl_url.format(sml)
c = curl.Curl(url, large = False)
result = c.result
self.result[sml] = []
if result is not None:
try:
data = json.loads(result)
for d in data['compounds']:
this_smile = d['smiles']
this_chembl = d['chemblId']
# if this_smile == sml:
self.result[sml].append(this_chembl)
except ValueError:
soup = bs4.BeautifulSoup(result)
compounds = soup.find_all('compound')
if compounds is not None:
for compound in compounds:
this_smile = compound.find('smiles').text
this_chembl = compound.find('chemblid').text
# if this_smile == sml:
self.result[sml].append(this_chembl)
prg.step()
prg.terminate()
[docs]
def connectivity_search(
self,
id_list: str | set,
id_type: str | int,
parameters: list[int] = [1, 0, 0, 0, 0, 1, 0]
):
"""
Search for structurally and chemically similar compounds based on
cheminformatics similarity metrics. Read more at
https://www.ebi.ac.uk/unichem/info/widesearchInfo.
Args
id_list:
One or more identifiers to query.
id_type:
Type of the identifiers, either as a string
label or a number as used by UniChem. SMILES is not
available in this type of query.
parameters:
A list of parameters A-H as described in
https://www.ebi.ac.uk/unichem/info/widesearchInfo.
Returns
Returns None, the results are stored in the `result` attribute
of this object.
"""
id_list = common.to_set(id_list)
parameters.append(1) # H parameter must be 1 to process the result
parameters = [str(i) for i in parameters]
self.result = {}
if id_type == 'inchikey':
id_type = ''
method = 'key_search'
elif id_type == 'smiles':
return None
else:
id_type = (
str(id_type)
if type(id_type) is int else
self.name_dict[id_type]
)
id_type = '%s/' % id_type
method = 'cpd_search'
prg = progress.Progress(
total=len(id_list),
name='Connectivity search',
interval=1
)
for i in id_list:
prg.step()
url = self.cpd_search.format(
method,
i,
id_type,
'/'.join(parameters)
)
c = curl.Curl(url, large = False)
result = c.result
self.result[i] = []
if result is not None:
data = json.loads(result)
for k, v in iteritems(data):
for j in xrange(1, len(v)):
self.result[i].append(v[j][0])
self.result[i] = list(set(self.result[i]))
prg.terminate()
