Hello,
I have a couple of questions about building openbabel on mac os catalina. I
cannot install openbabel with pip command and I am using python installed
through pip so I don’t want to install openbabel through conda. For openbabel
installation, I followed the instructions on the webpage. I downloaded
openbabel from sourceforge, the version is 2.0. Then I create build directory
and go in there and run the following commands in order:
cmake ../ -DPYTHON_EXECUTABLE=/usr/local/bin/python3 -DPYTHON_BINDINGS=ON
-DRUN_SWIG=ON
make -j8
make install
Then I have to run export PYTHONPATH=/usr/local/lib:$PYTHONPATH for python to
see openbabel. Unless I run this command I cannot install openbabel.
Question1:
I run the following commands:
import openbabel
from openbabel import pybel
and I get the error:
ImportError: cannot import name 'pybel' from 'openbabel' (unknown location)
I think I am missing some flags in cmake, maybe you can help me with this. My
python packages are in /usr/local/lib/python3.7/site-packages. What needs to be
done to solve this?
Question 2:
I am using pymatgen and I want to use the module molecule_matcher. I get the
following error:
RuntimeError: BabelMolAdaptor requires openbabel to be installed with Python
bindings. Please get it at http://openbabel.org (version >=3.0.0).
Even though openbabel is installed and I can import it, somehow pymatgen fails
to see it. I think this problem is also related to question 1. Again, what do I
need to do?
Thanks in advance,
Beliz
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