How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

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How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

i4hashmi
I am using Python for making a script to work with some chemical structures in my PhD. I want to install openbabel libraries for python. I tried my best but I could not install it on Windows. I posted a question earlier about installing it on Windows at http://stackoverflow.com/questions/42151301/how-do-i-install-openbabel-for-python-3-6-in-windows-10/42151551?noredirect=1#comment71470260_42151551 but could not find a solution. The solution installed the library but it does not work and could not connect to SWIG.
No I am trying to install it on my office computer which is a mac for past 5 hours but I could not figure what is going on.
I tried to install it from source code of Openbabel and link it with python3 but it is making problem.
If I use the following command:

 `cmake ../ -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON`

It successfully links it to Python 2.7 which I do not want. When I try the following options, it gives the error shown below:

`cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON`

OR

`cmake ../ -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_INCLUDE_DIR=/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -DPYTHON_LIBRARY=/Library/Frameworks/Python.framework/Versions/3.5/lib/libpython3.5m.dylib -DPYTHON_BINDINGS=ON`

It gives the following error at the end after a lot of successful output:

    -- Found PythonInterp: /usr/bin/python3.6 (found version "1.4")
    -- Found SWIG: /usr/local/bin/swig (found version "3.0.12")
    -- Found SWIG: /usr/local/bin/swig (found suitable version "3.0.12", minimum required is "2.0")
    -- Found PythonLibs: /usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/libpython3.6m.dylib (found version "3.6.0")
    -- Python bindings will be compiled
    CMake Error at scripts/CMakeLists.txt:120 (install):
    install TARGETS given no LIBRARY DESTINATION for module target
    "bindings_python".
    CMake Error at scripts/CMakeLists.txt:123 (install):
    install FILES given no DESTINATION!
    CMake Error at scripts/CMakeLists.txt:126 (install):
    install FILES given no DESTINATION!
    -- Configuring incomplete, errors occurred!
    See also "/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeOutput.log".
    See also "/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeError.log".


I am not sure why It detects the Python as v1.4 `-- Found PythonInterp: /usr/bin/python3.6 (found version "1.4") ` instead of finding v.3.5.
I tried all the procedure with python 3.6 as well but the same errors occur. I am also using the openbabel obtained from github which was said to be working with these commands at the following post: http://forums.openbabel.org/OpenBabel-for-Python-3-td4659432.html
But it doesn't work as well.
Please help me as I require this module for my research.
Thanks
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Re: How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

mwojcikowski
Hello,

Python 3.6 support is not there yet. It should be added soon.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
[hidden email]

2017-02-13 5:31 GMT+01:00 i4hashmi <[hidden email]>:
I am using Python for making a script to work with some chemical structures
in my PhD. I want to install openbabel libraries for python. I tried my best
but I could not install it on Windows. I posted a question earlier about
installing it on Windows at
http://stackoverflow.com/questions/42151301/how-do-i-install-openbabel-for-python-3-6-in-windows-10/42151551?noredirect=1#comment71470260_42151551
but could not find a solution. The solution installed the library but it
does not work and could not connect to SWIG.
No I am trying to install it on my office computer which is a mac for past 5
hours but I could not figure what is going on.
I tried to install it from source code of Openbabel and link it with python3
but it is making problem.
If I use the following command:

 `cmake ../ -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON`

It successfully links it to Python 2.7 which I do not want. When I try the
following options, it gives the error shown below:

`cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
-DRUN_SWIG=ON`

OR

`cmake ../ -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3
-DPYTHON_INCLUDE_DIR=/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m
-DPYTHON_LIBRARY=/Library/Frameworks/Python.framework/Versions/3.5/lib/libpython3.5m.dylib
-DPYTHON_BINDINGS=ON`

It gives the following error at the end after a lot of successful output:

    -- Found PythonInterp: /usr/bin/python3.6 (found version "1.4")
    -- Found SWIG: /usr/local/bin/swig (found version "3.0.12")
    -- Found SWIG: /usr/local/bin/swig (found suitable version "3.0.12",
minimum required is "2.0")
    -- Found PythonLibs:
/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/libpython3.6m.dylib
(found version "3.6.0")
    -- Python bindings will be compiled
    CMake Error at scripts/CMakeLists.txt:120 (install):
    install TARGETS given no LIBRARY DESTINATION for module target
    "bindings_python".
    CMake Error at scripts/CMakeLists.txt:123 (install):
    install FILES given no DESTINATION!
    CMake Error at scripts/CMakeLists.txt:126 (install):
    install FILES given no DESTINATION!
    -- Configuring incomplete, errors occurred!
    See also
"/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeOutput.log".
    See also
"/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeError.log".


I am not sure why It detects the Python as v1.4 `-- Found PythonInterp:
/usr/bin/python3.6 (found version "1.4") ` instead of finding v.3.5.
I tried all the procedure with python 3.6 as well but the same errors occur.
I am also using the openbabel obtained from github which was said to be
working with these commands at the following post:
http://forums.openbabel.org/OpenBabel-for-Python-3-td4659432.html
But it doesn't work as well.
Please help me as I require this module for my research.
Thanks



--
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Re: How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

Noel O'Boyle
Administrator
But it should be working with Python 3.5. What version of cmake are you using?

On 13 February 2017 at 09:11, Maciek Wójcikowski <[hidden email]> wrote:

> Hello,
>
> Python 3.6 support is not there yet. It should be added soon.
>
> ----
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> [hidden email]
>
> 2017-02-13 5:31 GMT+01:00 i4hashmi <[hidden email]>:
>>
>> I am using Python for making a script to work with some chemical
>> structures
>> in my PhD. I want to install openbabel libraries for python. I tried my
>> best
>> but I could not install it on Windows. I posted a question earlier about
>> installing it on Windows at
>>
>> http://stackoverflow.com/questions/42151301/how-do-i-install-openbabel-for-python-3-6-in-windows-10/42151551?noredirect=1#comment71470260_42151551
>> but could not find a solution. The solution installed the library but it
>> does not work and could not connect to SWIG.
>> No I am trying to install it on my office computer which is a mac for past
>> 5
>> hours but I could not figure what is going on.
>> I tried to install it from source code of Openbabel and link it with
>> python3
>> but it is making problem.
>> If I use the following command:
>>
>>  `cmake ../ -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON`
>>
>> It successfully links it to Python 2.7 which I do not want. When I try the
>> following options, it gives the error shown below:
>>
>> `cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
>> -DRUN_SWIG=ON`
>>
>> OR
>>
>> `cmake ../ -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3
>>
>> -DPYTHON_INCLUDE_DIR=/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m
>>
>> -DPYTHON_LIBRARY=/Library/Frameworks/Python.framework/Versions/3.5/lib/libpython3.5m.dylib
>> -DPYTHON_BINDINGS=ON`
>>
>> It gives the following error at the end after a lot of successful output:
>>
>>     -- Found PythonInterp: /usr/bin/python3.6 (found version "1.4")
>>     -- Found SWIG: /usr/local/bin/swig (found version "3.0.12")
>>     -- Found SWIG: /usr/local/bin/swig (found suitable version "3.0.12",
>> minimum required is "2.0")
>>     -- Found PythonLibs:
>>
>> /usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/libpython3.6m.dylib
>> (found version "3.6.0")
>>     -- Python bindings will be compiled
>>     CMake Error at scripts/CMakeLists.txt:120 (install):
>>     install TARGETS given no LIBRARY DESTINATION for module target
>>     "bindings_python".
>>     CMake Error at scripts/CMakeLists.txt:123 (install):
>>     install FILES given no DESTINATION!
>>     CMake Error at scripts/CMakeLists.txt:126 (install):
>>     install FILES given no DESTINATION!
>>     -- Configuring incomplete, errors occurred!
>>     See also
>>
>> "/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeOutput.log".
>>     See also
>> "/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeError.log".
>>
>>
>> I am not sure why It detects the Python as v1.4 `-- Found PythonInterp:
>> /usr/bin/python3.6 (found version "1.4") ` instead of finding v.3.5.
>> I tried all the procedure with python 3.6 as well but the same errors
>> occur.
>> I am also using the openbabel obtained from github which was said to be
>> working with these commands at the following post:
>> http://forums.openbabel.org/OpenBabel-for-Python-3-td4659432.html
>> But it doesn't work as well.
>> Please help me as I require this module for my research.
>> Thanks
>>
>>
>>
>> --
>> View this message in context:
>> http://forums.openbabel.org/How-to-Install-openbabel-for-Python-3-6-on-macOS-Sierra-10-12-3-tp4659726.html
>> Sent from the General discussion mailing list archive at Nabble.com.
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

i4hashmi
Hi,

Thanks for the reply. I am using cmake v.3.7.2 on macOS Sierra.
This issue is only with python 3. It compiles fine with default python2.7.
I want to bind it with python3.
Is there any way that I install it for python 2.7 and then edit some environment variable or something to change its binding to Python 3.5???

Regards
Hashmi
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Re: How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

Geoff Hutchison
> Is there any way that I install it for python 2.7 and then edit some
> environment variable or something to change its binding to Python 3.5???

No, because C and C++ libraries such as Open Babel have to link to the appropriate version of libpython.

Noel's question is "why not use Python 3.5" instead of 3.6? Sierra doesn't come with Python 3.6, so why did you install that version?

A new release that will be compatible with Python 3.6 will be released - but in the meantime, I'm using Python 3.5 just fine on my MacBook.

Best regards,
-Geoff
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Re: How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

i4hashmi
In reply to this post by i4hashmi
Hi Geoff,

Thanks for your reply. I am actually using Python 3.5 for quite some time. I discovered Python 3.6 also installed in my system on the day when I was installing openbabel. Then I thought if I can install it for the latest version, then I should use the latest one.
But at least it should work with Python 3.5 as I tried my best to install it for Python 3.5. If I can get a solution for Python 3.5, I'll keep using that. Please help me for that as I cannot understand the problem why it is detecting the correct directory for Python 3.5 but saying that detected v.1.7.

Regards,
Hashmi