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Python wrapper for the NCI Chemical Identifier Resolver (CIR)

Home Page: https://cirpy.readthedocs.io

License: MIT License

Python 100.00%

cheminformatics chemistry python

cirpy's Introduction

CIRpy

Introduction

CIRpy is a Python interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH.

CIR is a web service that will resolve any chemical identifier to another chemical representation. For example, you can pass it a chemical name and and request the corresponding SMILES string:

>>> import cirpy
>>> cirpy.resolve('Aspirin', 'smiles')
'C1=CC=CC(=C1C(O)=O)OC(C)=O'

CIRpy makes interacting with CIR through Python easy. There's no need to construct url requests and parse XML responses — CIRpy does all this for you.

Installation

Install CIRpy using:

pip install cirpy

Alternatively, try one of the other installation options.

Documentation

Full documentation is available at http://cirpy.readthedocs.org.

Contribute

Feature ideas and bug reports are welcome on the Issue Tracker.
Fork the source code on GitHub, make changes and file a pull request.

Acknowledgements

All of CIRpy's functionality relies on the fantastic CIR web service created by the CADD Group at the NCI/NIH.

License

CIRpy is licensed under the MIT license.

cirpy's People

Contributors

Stargazers

Watchers

cirpy's Issues

API Not responding.

urllib.error.URLError: <urlopen error [WinError 10060] A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond>

Having the above issue while running this command
cirpy.resolve('Aspirin', 'smiles')

Suggestion of code sample: get SMILES of list of molecules

Dear CIRpy developers, I would like to give you a code sample that could be useful for many people and could be provided in some form in the basic documentation (or even integrated as a function). This simple code gets a list of molecule names in a text file and outputs their SMILES in the command prompt.

#!/usr/bin/python
# -*- coding: Latin-1 -*-
# ----- Get SMILES from list of names -----
# 

import cirpy

with open("names.txt") as file:
    data = file.readlines()
    for molecule in data:
        name   = molecule.rstrip("\n\r")
        SMILES = cirpy.resolve(name, 'smiles')
        print name, SMILES

Maintained Alternative to this Repo

Hi All, if anyone is looking for an alternative name resolver we have built another version that uses a local copy of OPSIN here: https://github.com/JacksonBurns/py2opsin

Resolver times out

I just installed CIRpy and tried it out, but got this error, even though my internet is fine:

>>> from cirpy import Molecule
>>> Molecule("water")
Molecule(input='water', resolvers=None, get3d=False, kwargs={})
>>> Molecule("water").formula
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1392, in connect
    super().connect()
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py", line 722, in create_connection
    raise err
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py", line 713, in create_connection
    sock.connect(sa)
TimeoutError: [Errno 60] Operation timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/BenjaminLee/Desktop/Python/Research/flow-chem/env/lib/python3.6/site-packages/cirpy.py", line 296, in fget_memoized
    setattr(self, attr_name, fget(self))
  File "/Users/BenjaminLee/Desktop/Python/Research/flow-chem/env/lib/python3.6/site-packages/cirpy.py", line 384, in formula
    return resolve(self.input, 'formula', self.resolvers, **self.kwargs)
  File "/Users/BenjaminLee/Desktop/Python/Research/flow-chem/env/lib/python3.6/site-packages/cirpy.py", line 192, in resolve
    results = query(input, representation, resolvers, False, get3d, **kwargs)
  File "/Users/BenjaminLee/Desktop/Python/Research/flow-chem/env/lib/python3.6/site-packages/cirpy.py", line 162, in query
    tree = request(input, representation, resolvers, get3d, tautomers, **kwargs)
  File "/Users/BenjaminLee/Desktop/Python/Research/flow-chem/env/lib/python3.6/site-packages/cirpy.py", line 95, in request
    response = urlopen(url)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
    context=self._context, check_hostname=self._check_hostname)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 60] Operation timed out>```

SMILES string full of tungsten

4,4',4''-methanetriyltris(N,N-diethylaniline) (https://pubchem.ncbi.nlm.nih.gov/compound/Leucocrystal-Violet#section=MeSH-Entry-Terms) comes up with the following SMILES:
[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].[W].CCN(CC)c1ccc(cc1)C+c3ccc(cc3)N(CC)CC'

urllib2.URLError: <urlopen error EOF occurred in violation of protocol (_ssl.c:590)>

I recently installed cirpy on mac osx (10.11.1) using pip. I tried the example and got the following:

cirpy.resolve('Aspirin', 'smiles')
Traceback (most recent call last):
File "", line 1, in
File "/Library/Python/2.7/site-packages/cirpy.py", line 192, in resolve
results = query(input, representation, resolvers, False, get3d, *_kwargs)
File "/Library/Python/2.7/site-packages/cirpy.py", line 162, in query
tree = request(input, representation, resolvers, get3d, tautomers, *_kwargs)
File "/Library/Python/2.7/site-packages/cirpy.py", line 95, in request
response = urlopen(url)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen
return opener.open(url, data, timeout)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 431, in open
response = self._open(req, data)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 449, in _open
'_open', req)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 409, in _call_chain
result = func(*args)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1240, in https_open
context=self._context)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1197, in do_open
raise URLError(err)
urllib2.URLError: <urlopen error EOF occurred in violation of protocol (_ssl.c:590)>

get smiles.
smi = cirpy.resolve(query,"smiles",["cir_name","chemspider_name","opsin_name"])
then replace "#"
html_smi = smi.replace("#","%23")
and get image
imageurl = cirpy.Molecule(html_smi, ["smiles"]).image_url

Is that correct way?

Thanks.