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OpenBabel for Python 3?

John Todd
Hello, thank you for your development and publication of the Python
bindings for Open Babel.


I am fairly new at Python, and am trying to stick to the latest version.
Is it possible to install the Open Babel bindings for Python 3? I've
looked at the OpenBabel.org and PyPI website descriptions and can't find
a clear answer, and I haven't been able to puzzle out the answer on my
own. My system is Linux Mint 14-ish. Below is a partial list of the
things I've tried. Is there anything else I can do?


Thanks,

John Todd


$ obabel -V
Open Babel 2.3.2 -- Jan 21 2014 -- 23:20:09                     # Open
Babel is installed on my system
$ sudo apt-get install python-openbabel                       # I can
use apt-get to install it in Python 2
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
   python-openbabel
0 upgraded, 1 newly installed, 0 to remove and 19 not upgraded.

...

Setting up python-openbabel (2.3.2+dfsg-1.1) ...
$ sudo apt-get install python3-openbabel                             #
But not in Python 3
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package python3-openbabel
$ pip3 install openbabel                                         # Using
pip3 gives me an error with SWIG
Downloading/unpacking openbabel
   Downloading openbabel-1.8.4.tar.gz (74kB): 74kB downloaded
   Running setup.py (path:/tmp/pip_build_john/openbabel/setup.py)
egg_info for package openbabel

...


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

----------------------------------------
Cleaning up...
Command /usr/bin/python3 -c "import setuptools,
tokenize;__file__='/tmp/pip_build_john/openbabel/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
'exec'))" install --record /tmp/pip-w5p47a1i-record/install-record.txt
--single-version-externally-managed --compile failed with error code 1
in /tmp/pip_build_john/openbabel
Storing debug log for failure in /home/john/.pip/pip.log


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Re: OpenBabel for Python 3?

Geoff Hutchison
> I am fairly new at Python, and am trying to stick to the latest version.
> Is it possible to install the Open Babel bindings for Python 3?

Yes. I don't know about the pip packages (or Mint ones) but you can do this from source, e.g.:
https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings

Hope that helps,
-Geoff
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Re: OpenBabel for Python 3?

Geoff Hutchison
Please don't reply to me directly. Many other people on the mailing list can answer your question.

Your problem is clear from the WARNING. You want something like -DPYTHON_LIBRARY=/usr/lib/python3.4/libpython.so

You need to link to a *file* not a directory where the file is found.

Hope that helps,
-Geoff

> On Aug 9, 2016, at 9:51 AM, John <[hidden email]> wrote:
>
> Geoff,
>
>
> I downloaded the source and installed all the prerequisites. I can't figure out how to get it to link to the Python 3 bindings, however.
>
> $ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON -DPYTHON_LIBRARY=/usr/lib/python3.4 -DEIGEN3_INCLUDE_DIR=/home/john/eigen/eigen-eigen-dc6cfdf9bcec
>
> <lots of configuration output, most of which looks good>
>
> -- Found PythonInterp: /usr/bin/python (found version "2.7.6")
> -- Found PythonLibs: /usr/lib/python3.4 (found version "2.7.6")
> -- Python bindings will be compiled
> -- Configuring done
> WARNING: Target "bindings_python" requests linking to directory "/usr/lib/python3.4".  Targets may link only to libraries.  CMake is dropping the item.
> -- Generating done
> -- Build files have been written to: /home/john/openbabel/build
>
> As you can see, the configuration has linked to the Python 2 installation, not Python 3. What is the correct setting to get it to link to Python 3 instead?
>
>
> Thanks,
>
> John Todd
>
>
> P.S. A few of the tests seem to have failed, but several Google pages make it sound like it's no big deal. Should I worry about:
>
> -- Looking for conio.h - not found
>
> -- Performing Test SCANDIR_NEEDS_CONST - Failed
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:14
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:31
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:25
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:39
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
> On 08/08/2016 01:27 PM, Geoffrey Hutchison wrote:
>>> I am fairly new at Python, and am trying to stick to the latest version.
>>> Is it possible to install the Open Babel bindings for Python 3?
>> Yes. I don't know about the pip packages (or Mint ones) but you can do this from source, e.g.:
>> https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings
>>
>> Hope that helps,
>> -Geoff
>


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Re: OpenBabel for Python 3?

David Hall
If you use the version of openbabel from git (which I would recommend over for the 2.3.2 release), then you can just specify PYTHON_EXECUTABLE as the python3 and it should find everything correctly.

$ cd openbabel
$ mkdir build
$ cd build
$ cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
...
-- Found PythonInterp: /usr/bin/python3 (found version "3.5.1") 
-- Found PythonLibs: /usr/lib64/libpython3.5m.so (found version "3.5.1") 
...
$ grep '^PYTHON' CMakeCache.txt
...
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3
PYTHON_INCLUDE_DIR:PATH=/usr/include/python3.5m
PYTHON_LIBRARY:FILEPATH=/usr/lib64/libpython3.5m.so
...



-David


On Tue, Aug 9, 2016 at 10:00 AM, Geoffrey Hutchison <[hidden email]> wrote:
Please don't reply to me directly. Many other people on the mailing list can answer your question.

Your problem is clear from the WARNING. You want something like -DPYTHON_LIBRARY=/usr/lib/python3.4/libpython.so

You need to link to a *file* not a directory where the file is found.

Hope that helps,
-Geoff

> On Aug 9, 2016, at 9:51 AM, John <[hidden email]> wrote:
>
> Geoff,
>
>
> I downloaded the source and installed all the prerequisites. I can't figure out how to get it to link to the Python 3 bindings, however.
>
> $ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON -DPYTHON_LIBRARY=/usr/lib/python3.4 -DEIGEN3_INCLUDE_DIR=/home/john/eigen/eigen-eigen-dc6cfdf9bcec
>
> <lots of configuration output, most of which looks good>
>
> -- Found PythonInterp: /usr/bin/python (found version "2.7.6")
> -- Found PythonLibs: /usr/lib/python3.4 (found version "2.7.6")
> -- Python bindings will be compiled
> -- Configuring done
> WARNING: Target "bindings_python" requests linking to directory "/usr/lib/python3.4".  Targets may link only to libraries.  CMake is dropping the item.
> -- Generating done
> -- Build files have been written to: /home/john/openbabel/build
>
> As you can see, the configuration has linked to the Python 2 installation, not Python 3. What is the correct setting to get it to link to Python 3 instead?
>
>
> Thanks,
>
> John Todd
>
>
> P.S. A few of the tests seem to have failed, but several Google pages make it sound like it's no big deal. Should I worry about:
>
> -- Looking for conio.h - not found
>
> -- Performing Test SCANDIR_NEEDS_CONST - Failed
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:14
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:31
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:25
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> CMake Warning (dev) at test/CMakeLists.txt:171 (include):
>  Syntax Warning in cmake code at
>
> /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:39
>
>  Argument not separated from preceding token by whitespace.
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
> On 08/08/2016 01:27 PM, Geoffrey Hutchison wrote:
>>> I am fairly new at Python, and am trying to stick to the latest version.
>>> Is it possible to install the Open Babel bindings for Python 3?
>> Yes. I don't know about the pip packages (or Mint ones) but you can do this from source, e.g.:
>> https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings
>>
>> Hope that helps,
>> -Geoff
>


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Re: OpenBabel for Python 3?

David Hall
do you have python3-dev installed?


On Aug 9, 2016, at 12:57 PM, John <[hidden email]> wrote:

PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7


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Re: OpenBabel for Python 3?

John Todd

I thought I had, but apparently not, because after I installed it everything worked.


Thanks for the help,

John


On 08/09/2016 01:05 PM, David Hall wrote:
do you have python3-dev installed?


On Aug 9, 2016, at 12:57 PM, John <[hidden email]> wrote:

PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7



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Re: OpenBabel for Python 3?

tpsanjan
In reply to this post by David Hall
Hi,

I have been trying install python bindings for openbabel 2.4.1 on Ubunut16.04 with python 3.5.2 (installed via Anaconda) but haven't been able to get it working. Here's what I have tried so far:

Based on David Hall's post in this thread:

$ git clone https://github.com/openbabel/openbabel.git
$ cd openbabel
$ mkdir build
$ cd build
$ cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
$ grep '^PYTHON' CMakeCache.txt

And then followed the steps given on openbabel docs (https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings)

$ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON
$ make
# make install
$ export PYTHONPATH=/usr/local/lib:$PYTHONPATH

All commands seemed to run smoothly (python3-dev is installed). But when I use python shell through terminal:

sgupta78@sgupta78:~$ python
imPython 3.5.2 |Anaconda 4.1.1 (64-bit)| (default, Jul  2 2016, 17:53:06)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import openbabel
>>> mol = openbabel.OBMol()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'openbabel' has no attribute 'OBMol'

import openbabel was successful but none of the functions in openbabel module are being recognized. As shown above it's raising AttributeError. Is there something that I missed during installation steps shown above?

Secondly, when I ran a simple script [just to test OBMol() ] stored in  a sub-folder of home directory, even the import openbabel failed. This possibly means that the environment variables haven't been set. I assumed that cmake and export steps above possibly take care of it.

Any help would be appreciated.

Thanks,
Sanjan



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Re: OpenBabel for Python 3?

mwojcikowski
Hi Sanjan,

Since you've already have (Ana)conda, the easiest solution whould be installing it via conda:

"conda install -c openbabel openbabel"

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

2016-11-30 3:46 GMT+01:00 tpsanjan <[hidden email]>:
Hi,

I have been trying install python bindings for openbabel 2.4.1 on
Ubunut16.04 with python 3.5.2 (installed via Anaconda) but haven't been able
to get it working. Here's what I have tried so far:

Based on David Hall's post in this thread:

$ git clone https://github.com/openbabel/openbabel.git
$ cd openbabel
$ mkdir build
$ cd build
$ cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
-DRUN_SWIG=ON
$ grep '^PYTHON' CMakeCache.txt

And then followed the steps given on openbabel docs
(https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings)

$ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON
$ make
# make install
$ export PYTHONPATH=/usr/local/lib:$PYTHONPATH

All commands seemed to run smoothly (python3-dev is installed). But when I
use python shell through terminal:

sgupta78@sgupta78:~$ python
imPython 3.5.2 |Anaconda 4.1.1 (64-bit)| (default, Jul  2 2016, 17:53:06)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import openbabel
>>> mol = openbabel.OBMol()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'openbabel' has no attribute 'OBMol'

import openbabel was successful *but none of the functions in openbabel
module are being recognized*. As shown above it's raising AttributeError. Is
there something that I missed during installation steps shown above?

Secondly, when I ran a simple script [just to test OBMol() ] stored in  a
sub-folder of home directory, *even the import openbabel failed*. This
possibly means that the environment variables haven't been set. I assumed
that cmake and export steps above possibly take care of it.

Any help would be appreciated.

Thanks,
Sanjan







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Re: OpenBabel for Python 3?

tpsanjan
Thanks ... it worked like a charm. Infact conda was the first thing I had tried, not sure why it didn't work first time.

Best,
Sanjan

On Wed, Nov 30, 2016 at 7:42 AM, mwojcikowski [via Open Babel] <[hidden email]> wrote:
Hi Sanjan,

Since you've already have (Ana)conda, the easiest solution whould be installing it via conda:

"conda install -c openbabel openbabel"

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

2016-11-30 3:46 GMT+01:00 tpsanjan <[hidden email]>:
Hi,

I have been trying install python bindings for openbabel 2.4.1 on
Ubunut16.04 with python 3.5.2 (installed via Anaconda) but haven't been able
to get it working. Here's what I have tried so far:

Based on David Hall's post in this thread:

$ git clone https://github.com/openbabel/openbabel.git
$ cd openbabel
$ mkdir build
$ cd build
$ cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
-DRUN_SWIG=ON
$ grep '^PYTHON' CMakeCache.txt

And then followed the steps given on openbabel docs
(https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings)

$ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON
$ make
# make install
$ export PYTHONPATH=/usr/local/lib:$PYTHONPATH

All commands seemed to run smoothly (python3-dev is installed). But when I
use python shell through terminal:

sgupta78@sgupta78:~$ python
imPython 3.5.2 |Anaconda 4.1.1 (64-bit)| (default, Jul  2 2016, 17:53:06)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import openbabel
>>> mol = openbabel.OBMol()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'openbabel' has no attribute 'OBMol'

import openbabel was successful *but none of the functions in openbabel
module are being recognized*. As shown above it's raising AttributeError. Is
there something that I missed during installation steps shown above?

Secondly, when I ran a simple script [just to test OBMol() ] stored in  a
sub-folder of home directory, *even the import openbabel failed*. This
possibly means that the environment variables haven't been set. I assumed
that cmake and export steps above possibly take care of it.

Any help would be appreciated.

Thanks,
Sanjan







--
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Re: OpenBabel for Python 3?

i4hashmi
In reply to this post by David Hall
Hi David,

Can you please suggest me a solution? I am trying it for the last two weeks but could not find a solution. I even posted a thread at this forum but could not solve the problem.
Now as your directions, I downloaded the openbabel from git:
https://github.com/openbabel/openbabel

And then used the command:
cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON

but the installation gave error at the end. I am appending the whole output below. Please help me here.

c02j2e0bdhjf:build hashmimu$ cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
-- The C compiler identification is AppleClang 8.0.0.8000042
-- The CXX compiler identification is AppleClang 8.0.0.8000042
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Using included inchi library.
-- Found LibXml2: /usr/lib/libxml2.dylib (found version "2.9.4")
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.8")
-- Found wxWidgets: -L/usr/local/lib;;;-framework IOKit;-framework Carbon;-framework Cocoa;-framework AudioToolbox;-framework System;-framework OpenGL;-lwx_baseu-3.0;-lwx_osx_cocoau_core-3.0;-lwx_osx_cocoau_adv-3.0 (found version "3.0.2")
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - not found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Failed
-- Use std::shared_ptr in memory
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0")
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.1")
-- Checking for module 'cairo'
--   Found cairo, version 1.14.8
-- Found Cairo: /usr/local/Cellar/cairo/1.14.8/lib/libcairo.dylib  
-- Cairo found. PNG output will be supported.
-- Looking for getopt
-- Looking for getopt - found
-- GUI will not be built
-- Found PythonInterp: /usr/bin/python3 (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/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/build/CMakeFiles/CMakeOutput.log".
See also "/usr/local/Cellar/obabel/openbabel-master/build/CMakeFiles/CMakeError.log".


I hope it gives you all the information to detect the problem.

Thanks and regards,
Hashmi
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Re: OpenBabel for Python 3?

David Hall
My guess is that your python3 is not at /usr/bin/python3 . Are you sure it isn't at /usr/local/bin/python3 ? Based on your Python.framework information, that would seem to be likely where it is.

On that note, we should consider printing an error if the detected version of python is 1.4 ; that means that FindPythonInterp could not determine the version of python, so it is assuming it is 1.4 (see https://github.com/Kitware/CMake/blob/master/Modules/FindPythonInterp.cmake ). 



On Sun, Feb 19, 2017 at 5:26 PM, i4hashmi <[hidden email]> wrote:
Hi David,

Can you please suggest me a solution? I am trying it for the last two weeks
but could not find a solution. I even posted a thread at this forum but
could not solve the problem.
Now as your directions, I downloaded the openbabel from git:
https://github.com/openbabel/openbabel

And then used the command:
*cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
-DRUN_SWIG=ON*

but the installation gave error at the end. I am appending the whole output
below. Please help me here.

c02j2e0bdhjf:build hashmimu$ cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3
-DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
-- The C compiler identification is AppleClang <a href="tel:8.0.0.8000042" value="+18008000042">8.0.0.8000042
-- The CXX compiler identification is AppleClang <a href="tel:8.0.0.8000042" value="+18008000042">8.0.0.8000042
-- Check for working C compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Using included inchi library.
-- Found LibXml2: /usr/lib/libxml2.dylib (found version "2.9.4")
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.8")
-- Found wxWidgets: -L/usr/local/lib;;;-framework IOKit;-framework
Carbon;-framework Cocoa;-framework AudioToolbox;-framework System;-framework
OpenGL;-lwx_baseu-3.0;-lwx_osx_cocoau_core-3.0;-lwx_osx_cocoau_adv-3.0
(found version "3.0.2")
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - not found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Failed
-- Use std::shared_ptr in memory
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version
"2.91.0")
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.1")
-- Checking for module 'cairo'
--   Found cairo, version 1.14.8
-- Found Cairo: /usr/local/Cellar/cairo/1.14.8/lib/libcairo.dylib
-- Cairo found. PNG output will be supported.
-- Looking for getopt
-- Looking for getopt - found
-- GUI will not be built
-- Found PythonInterp: /usr/bin/python3 (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/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/build/CMakeFiles/CMakeOutput.log".
See also
"/usr/local/Cellar/obabel/openbabel-master/build/CMakeFiles/CMakeError.log".


I hope it gives you all the information to detect the problem.

Thanks and regards,
Hashmi



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Re: OpenBabel for Python 3?

i4hashmi
Thank you so much David for the hint.

Now I checked the path of python3 by "which python3" and it gave me the path "/Library/Frameworks/Python.framework/Versions/3.5/bin/python3"
Then I changed the command to:
cmake ../ -DPYTHON_EXECUTABLE=/Library/Frameworks/Python.framework/Versions/3.5/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON

and it worked. There was one problem that it installed open-babel to the directory:
/usr/local/lib/python3.5/site-packages/

but  my all the other packages are installed to the following directory:
/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages

I never changed any path or anything. But fortunately I copied the files from the installed path to the path of other packages and it is working now.

It would be great if you can suggest me a solution for my Windows laptop as well as I tried but could not install it there. This mac is my office computer! I posted a question here about it:
http://stackoverflow.com/questions/42151301/how-do-i-install-openbabel-for-python-3-6-in-windows-10

The answer given there did not solve the problem. Now the release for python3.6 has been released for windows, i installed using pip and it got installed but it is still not working in python.

Regards,
Hashmi
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