Your INCLUDE_DIR has a ~. This means your home directory. On 8 July 2016 at 16:14, Dan Smith <s...@bellsouth.net> wrote: > Leonardo, thanks for the suggestion. > > I tried the DPYTHON_INCLUDE_DIR option shown below. > > cmake ../openbabel -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON > -DPYTHON_INCLUDE_DIR=~/usr/include/python2.7 > > make failed with the following error. > > /Users/dansmith/Documents/MOLECULAR_MODELING/OpenBabel/openbabel/scripts/python/openbabel-python.cpp:174:11: > fatal error: > 'Python.h' file not found > # include <Python.h> > ^ > 1 error generated. > > In the original build attempt without the DPYTHON_INCLUDE_DIR option. > There were 3 warnings at the same point shown below and several messages. > > I’m not sure why my implementation of your suggestion fails as I verified > that Python.h could be found in /usr/include/python2.7; however, after > closer inspection of the “sudo make install” output I believe I have > discovered part of the problem. I tried the original installation method. > > cmake ../openbabel -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON > make > sudo make install > > The output from “sudo make install” for openbabel.py and pybel.py is shown > below. > > -- Installing: /usr/local/lib/python2.7/site-packages/_openbabel.so > -- Up-to-date: /usr/local/lib/python2.7/site-packages/openbabel.py > -— Up-to-date: /usr/local/lib/python2.7/site-packages/pybel.py > > I set the python path as follows. > > export PYTHONPATH=/usr/local/lib/python2.7/site-packages/:$PYTHONPATH > > Importing pybel and openbabel works now. I tried to work through some of the > examples on the web > (http://openbabel.org/docs/current/UseTheLibrary/Python_Pybel.html). The > examples do not work exactly as written. For instance, I cannot use the > command “read string”, but I can use “pybel.readstring”. > >>>> mymol = readstring("smi", "CCCC") > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > NameError: name 'readstring' is not defined >>>> mymol = pybel.readstring("smi", "CCCC") >>>> print mymol.molwt > 58.1222 > > Is this normal or is there something wrong with my installation? > > Thanks, > > Dan > > > On Jul 7, 2016, at 6:01 PM, Leonardo Lazzaro <llazz...@dc.uba.ar> wrote: > > Hello, > > try to use the options DPYTHON_INCLUDE_DIR, DCMAKE_INSTALL_PREFIX. > for example for anaconda2 I used the following command: > > cmake .. -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON > -DCMAKE_INSTALL_PREFIX=~/anaconda2 > -DPYTHON_INCLUDE_DIR=~/anaconda2/include/python2.7 > -DCMAKE_LIBRARY_PATH=~/anaconda2/lib > -DSWIG_DIR=~/anaconda2/share/swig/3.0.2/ > -DSWIG_EXECUTABLE=~/anaconda2/bin/swig > -DPYTHON_LIBRARY=~/anaconda2/lib/libpython2.7.so > -DCMAKE_BUILD_TYPE=DEBUG > > hope it helps, > Leonardo > > On 2016-07-07 17:23, Dan Smith wrote: > > Hello, > > I am using openbabel on a Mac - El Capitan OS X 10.11.5 operating > system. > > I have installed eigen2. I have python version 2.7.10. > > I have successfully compiled version 2.3.90 using the following > commands in terminal. > > cmake ../openbabel -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON > > make > > sudo make install > export PYTHONPATH=/usr/local/lib:$PYTHONPATH > > When I attempt to import pybel or openbabel in Python I get the > following messages. > > import pybel > > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: No module named pybel > > import openbabel > > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: No module named openbabel > > I have tried to search previous posts but have not found an answer > that will solve my problem. At this point I’m not sure what to do to > diagnose the problem. > > Any help in solving my problem would be appreciated. > > Thanks, > > Dan > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech > luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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