Re: Pybel error

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Re: Pybel error

Geoffrey Hutchison-3
Please don't send e-mail directly to me. There are many users of Open Babel and Pybel that can help you out.

Fundamentally, pybel.py and _openbabel.so, etc. - the Python bindings for Open Babel are not found by the python interpreter. Running "locate pybel.py" might help. I suspect that they're somewhere in ~Tools/openbabel-install

Hope that helps,
-Geoff


On Jun 13, 2016, at 4:22 PM, Pearl Philip <[hidden email]> wrote:

Dear Professor Hutchinson,

I'm a user of your package Pybel and I've encountered this error I don't know how to fix. I installed openbabel and the python bindings on my linux machine. When I run this file  driver.py, which is dependent on pybel, I encounter the following error. 

pphilip@waffle:~/USP-inhibition$ python driver.py
Traceback (most recent call last):
  File "driver.py", line 3, in <module>
    from utils import create_dict, create_dataframe, extract_descriptors
  File "/home/pphilip/USP-inhibition/utils.py", line 13, in <module>
    from pychem.pychem import PyChem2d, PyChem3d
  File "/home/dacb/miniconda2/envs/my-rdkit-env/lib/python2.7/site-packages/pychem/pychem.py", line 34, in <module>
    import cpsa
  File "/home/dacb/miniconda2/envs/my-rdkit-env/lib/python2.7/site-packages/pychem/cpsa.py", line 18, in <module>
    import pybel
ImportError: No module named pybel

This is how I installed the package

mkdir build
cd build
cmake ../openbabel-2.3.2 -DCMAKE_INSTALL_PREFIX=~/Tools/openbabel-install -DPYTHON_BINDINGS=ON
make
make install
export PYTHONPATH=/usr/local/lib/python2.6/site-packages:$PYTHONPATH
 
All these steps worked perfectly. I can't seem to identify the problem. I hope you can help me.

Regards,

Pearl Philip
Graduate Student
Department of Chemical Engineering
University of Washington, Seattle



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Re: Pybel error

Leonardo Lazzaro-2
Pearl Philip,

I think you need to specify at least the PYTHON_INCLUDE_DIR.

Here is an example with anaconda2 installed on the home dir:

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 that helps,
Leonardo

2016-06-14 16:19 GMT-03:00 Geoffrey Hutchison <[hidden email]>:
Please don't send e-mail directly to me. There are many users of Open Babel and Pybel that can help you out.

Fundamentally, pybel.py and _openbabel.so, etc. - the Python bindings for Open Babel are not found by the python interpreter. Running "locate pybel.py" might help. I suspect that they're somewhere in ~Tools/openbabel-install

Hope that helps,
-Geoff


On Jun 13, 2016, at 4:22 PM, Pearl Philip <[hidden email]> wrote:

Dear Professor Hutchinson,

I'm a user of your package Pybel and I've encountered this error I don't know how to fix. I installed openbabel and the python bindings on my linux machine. When I run this file  driver.py, which is dependent on pybel, I encounter the following error. 

pphilip@waffle:~/USP-inhibition$ python driver.py
Traceback (most recent call last):
  File "driver.py", line 3, in <module>
    from utils import create_dict, create_dataframe, extract_descriptors
  File "/home/pphilip/USP-inhibition/utils.py", line 13, in <module>
    from pychem.pychem import PyChem2d, PyChem3d
  File "/home/dacb/miniconda2/envs/my-rdkit-env/lib/python2.7/site-packages/pychem/pychem.py", line 34, in <module>
    import cpsa
  File "/home/dacb/miniconda2/envs/my-rdkit-env/lib/python2.7/site-packages/pychem/cpsa.py", line 18, in <module>
    import pybel
ImportError: No module named pybel

This is how I installed the package

mkdir build
cd build
cmake ../openbabel-2.3.2 -DCMAKE_INSTALL_PREFIX=~/Tools/openbabel-install -DPYTHON_BINDINGS=ON
make
make install
export PYTHONPATH=/usr/local/lib/python2.6/site-packages:$PYTHONPATH
 
All these steps worked perfectly. I can't seem to identify the problem. I hope you can help me.

Regards,

Pearl Philip
Graduate Student
Department of Chemical Engineering
University of Washington, Seattle



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel




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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel