OpenBabel not Working in Python 3.6

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OpenBabel not Working in Python 3.6

Muhammad Ali Hashmi

Hi everyone,

I have a problem using Openbabel or Pybel in Python.

I am using Python3.6 and I installed `openbabel-2.4.1-cp36-cp36m-win32` from http://www.lfd.uci.edu/~gohlke/pythonlibs

It says many formats missing. I read a similar thread about this when it was advised not to install openbabel from the above link but instead from Python PiP but the problem is that the Pip only had openbabel-2.4.1-cp35-cp35m-win32 at their website.

If I try to install it with pip, it gives the following error:

C:\>pip install openbabel

Collecting openbabel

  Using cached openbabel-2.4.1.tar.gz

Installing collected packages: openbabel

  Running setup.py install for openbabel ... error

    Complete output from command c:\users\malih\appdata\local\programs\python\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-lkj4qdt1\\openbabel\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\malih\AppData\Local\Temp\pip-tqavb9qy-record\install-record.txt --single-version-externally-managed --compile:

    running install

    running build_ext

    Warning: pkg-config could not be found.

    Guessing Open Babel location:

    - include_dirs: ['c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\include', 'c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\include', '/usr/local/include/openbabel-2.0']

    - library_dirs: ['c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\libs', 'c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\PCbuild\\win32', '/usr/local/lib']

    building '_openbabel' extension

    swigging openbabel-python.i to openbabel-python_wrap.cpp

    swig.exe -python -c++ -small -O -templatereduce -naturalvar -Ic:\users\malih\appdata\local\programs\python\python36-32\include -Ic:\users\malih\appdata\local\programs\python\python36-32\include -I/usr/local/include/openbabel-2.0 -o openbabel-python_wrap.cpp openbabel-python.i

 

    Error: SWIG failed. Is Open Babel installed?

    You may need to manually specify the location of Open Babel include and library directories. For example:

      python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib

      python setup.py install

 

    ----------------------------------------

Command "c:\users\malih\appdata\local\programs\python\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-lkj4qdt1\\openbabel\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\malih\AppData\Local\Temp\pip-tqavb9qy-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\malih\AppData\Local\Temp\pip-build-lkj4qdt1\openbabel\

 

I don’t know how to solve this issue. Please help me here as I need openbabel to work for my research work.

 

Regards,

Muhammad Ali

 

 


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Re: OpenBabel not Working in Python 3.6

Noel O'Boyle
Administrator
I'll make a release for Python 3.6 this week, and let you know.

On 11 Feb 2017 2:54 p.m., "Muhammad Ali Hashmi" <[hidden email]> wrote:

Hi everyone,

I have a problem using Openbabel or Pybel in Python.

I am using Python3.6 and I installed `openbabel-2.4.1-cp36-cp36m-win32` from http://www.lfd.uci.edu/~gohlke/pythonlibs

It says many formats missing. I read a similar thread about this when it was advised not to install openbabel from the above link but instead from Python PiP but the problem is that the Pip only had openbabel-2.4.1-cp35-cp35m-win32 at their website.

If I try to install it with pip, it gives the following error:

C:\>pip install openbabel

Collecting openbabel

  Using cached openbabel-2.4.1.tar.gz

Installing collected packages: openbabel

  Running setup.py install for openbabel ... error

    Complete output from command c:\users\malih\appdata\local\programs\python\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-lkj4qdt1\\openbabel\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\malih\AppData\Local\Temp\pip-tqavb9qy-record\install-record.txt --single-version-externally-managed --compile:

    running install

    running build_ext

    Warning: pkg-config could not be found.

    Guessing Open Babel location:

    - include_dirs: ['c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\include', 'c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\include', '/usr/local/include/openbabel-2.0']

    - library_dirs: ['c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\libs', 'c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\PCbuild\\win32', '/usr/local/lib']

    building '_openbabel' extension

    swigging openbabel-python.i to openbabel-python_wrap.cpp

    swig.exe -python -c++ -small -O -templatereduce -naturalvar -Ic:\users\malih\appdata\local\programs\python\python36-32\include -Ic:\users\malih\appdata\local\programs\python\python36-32\include -I/usr/local/include/openbabel-2.0 -o openbabel-python_wrap.cpp openbabel-python.i

 

    Error: SWIG failed. Is Open Babel installed?

    You may need to manually specify the location of Open Babel include and library directories. For example:

      python setup.py build_ext -I/usr/local/include/openbabel-2.0 -L/usr/local/lib

      python setup.py install

 

    ----------------------------------------

Command "c:\users\malih\appdata\local\programs\python\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-lkj4qdt1\\openbabel\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\malih\AppData\Local\Temp\pip-tqavb9qy-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\malih\AppData\Local\Temp\pip-build-lkj4qdt1\openbabel\

 

I don’t know how to solve this issue. Please help me here as I need openbabel to work for my research work.

 

Regards,

Muhammad Ali

 

 


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Re: OpenBabel not Working in Python 3.6

Noel O'Boyle
Administrator
Ok - just done it. Works for me now on Windows with pip. Assuming you
have the 64-bit Open Babel and Python 3.6 installed then:

C:\> py -3.6 -m pip install openbabel
Collecting openbabel
  Downloading openbabel-2.4.1-cp36-cp36m-win_amd64.whl (729kB)
    100% |████████████████████████████████| 737kB 1.6MB/s
Installing collected packages: openbabel
Successfully installed openbabel
C:\> py -3.6
Python 3.6.0 (v3.6.0:41df79263a11, Dec 23 2016, 08:06:12) [MSC v.1900
64 bit (AMD64)] on win32
>>> import pybel
>>> pybel.readstring("smi", "CC").write("smi")
'CC\t\n'

On 11 February 2017 at 19:06, Noel O'Boyle <[hidden email]> wrote:

> I'll make a release for Python 3.6 this week, and let you know.
>
> On 11 Feb 2017 2:54 p.m., "Muhammad Ali Hashmi" <[hidden email]>
> wrote:
>>
>> Hi everyone,
>>
>> I have a problem using Openbabel or Pybel in Python.
>>
>> I am using Python3.6 and I installed `openbabel-2.4.1-cp36-cp36m-win32`
>> from http://www.lfd.uci.edu/~gohlke/pythonlibs
>>
>> It says many formats missing. I read a similar thread about this when it
>> was advised not to install openbabel from the above link but instead from
>> Python PiP but the problem is that the Pip only had
>> openbabel-2.4.1-cp35-cp35m-win32 at their website.
>>
>> If I try to install it with pip, it gives the following error:
>>
>> C:\>pip install openbabel
>>
>> Collecting openbabel
>>
>>   Using cached openbabel-2.4.1.tar.gz
>>
>> Installing collected packages: openbabel
>>
>>   Running setup.py install for openbabel ... error
>>
>>     Complete output from command
>> c:\users\malih\appdata\local\programs\python\python36-32\python.exe -u -c
>> "import setuptools,
>> tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-lkj4qdt1\\openbabel\\setup.py';f=getattr(tokenize,
>> 'open', open)(__file__);code=f.read().replace('\r\n',
>> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
>> C:\Users\malih\AppData\Local\Temp\pip-tqavb9qy-record\install-record.txt
>> --single-version-externally-managed --compile:
>>
>>     running install
>>
>>     running build_ext
>>
>>     Warning: pkg-config could not be found.
>>
>>     Guessing Open Babel location:
>>
>>     - include_dirs:
>> ['c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\include',
>> 'c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\include',
>> '/usr/local/include/openbabel-2.0']
>>
>>     - library_dirs:
>> ['c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\libs',
>> 'c:\\users\\malih\\appdata\\local\\programs\\python\\python36-32\\PCbuild\\win32',
>> '/usr/local/lib']
>>
>>     building '_openbabel' extension
>>
>>     swigging openbabel-python.i to openbabel-python_wrap.cpp
>>
>>     swig.exe -python -c++ -small -O -templatereduce -naturalvar
>> -Ic:\users\malih\appdata\local\programs\python\python36-32\include
>> -Ic:\users\malih\appdata\local\programs\python\python36-32\include
>> -I/usr/local/include/openbabel-2.0 -o openbabel-python_wrap.cpp
>> openbabel-python.i
>>
>>
>>
>>     Error: SWIG failed. Is Open Babel installed?
>>
>>     You may need to manually specify the location of Open Babel include
>> and library directories. For example:
>>
>>       python setup.py build_ext -I/usr/local/include/openbabel-2.0
>> -L/usr/local/lib
>>
>>       python setup.py install
>>
>>
>>
>>     ----------------------------------------
>>
>> Command
>> "c:\users\malih\appdata\local\programs\python\python36-32\python.exe -u -c
>> "import setuptools,
>> tokenize;__file__='C:\\Users\\malih\\AppData\\Local\\Temp\\pip-build-lkj4qdt1\\openbabel\\setup.py';f=getattr(tokenize,
>> 'open', open)(__file__);code=f.read().replace('\r\n',
>> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
>> C:\Users\malih\AppData\Local\Temp\pip-tqavb9qy-record\install-record.txt
>> --single-version-externally-managed --compile" failed with error code 1 in
>> C:\Users\malih\AppData\Local\Temp\pip-build-lkj4qdt1\openbabel\
>>
>>
>>
>> I don’t know how to solve this issue. Please help me here as I need
>> openbabel to work for my research work.
>>
>>
>>
>> Regards,
>>
>> Muhammad Ali
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>

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