mnowotka

from collections import defaultdict
from itertools import chain
from banyan import SortedDict, OverlappingIntervalsUpdator

class Rectangle(object):

    def __init__(self, left, top, right, bottom):
        self.left = left
        self.bottom = bottom
        self.right = right

mnowotka

# necessary imports first:
from chembl_webresource_client import *

# create resource object:
compounds = CompoundResource()

# before you do anythong else, please check webservices status:
print compounds.status()
True

mnowotka

# our standard invocation:
from chembl_webresource_client import *
targets = TargetResource()
print targets.status()
True

# status returns True so we can proceed:
#first let's get a single target:

t = targets.get('CHEMBL2477')

mnowotka

# first things first:
from chembl_webresource_client import *
assays = AssayResource()
print assays.status()
True

# assays are simple, we can get them by chembl ID:
a = assays.get('CHEMBL1217643')
print a
{u'assayType': u'B', u'chemblId': u'CHEMBL1217643', u'journal': u'Bioorg. Med. Chem. Lett.', 

mnowotka

from chembl_webresource_client import *
compounds = CompoundResource()
cs = compounds.get(['CHEMBL%s' % x for x in range(1,1001)])

mnowotka

from bioservices import *   
s = ChEMBLdb(verbose=False)
res = []
for i in range(1,1001):
    try:
        res.append(s.get_compounds_by_chemblId('CHEMBL%s' % i))
    except:
        res.append(404)

mnowotka

# let's import settings class first:
from chembl_webresource_client.settings import Settings

# we can now decide which protocol to use:
Settings.Instance().WEBSERVICE_PROTOCOL = 'http'

# point our client to our local webservices instance
Settings.Instance().WEBSERVICE_DOMAIN = 'localhost'

# and change their prefix:

mnowotka

mnowotka

{
 "metadata": {
  "name": "",
  "signature": "sha256:f784ff75e0dec53c6fef16fc487214e1f81833324cfa31e787b2ed105592c612"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

mnowotka

import requests
from chembl_webresource_client import *

# For some special SMILES, using GET method against webservices will end up with failure:

res = requests.get('https://www.ebi.ac.uk/chemblws/compounds/smiles/CN1C\C(=C/c2ccc(C)cc2)\C3=C(C1)C(C(=C(N)O3)C#N)c4ccc(C)cc4')
print res.ok
False

print res.status_code