The current version of OB is 3.1.1, not 2.0. On Fri, 15 May 2020 at 16:13, Weise, David <dwe...@upenn.edu> wrote:
> Hi, > Try another method listed: > http://openbabel.org/wiki/Category:Macintosh > > I was able to do it on linux with conda. > > --David > > > David Weise > Linux Systems Admin > Penn Medicine Academic Computing Services (PMACS) > Richards Medical Labs > 3700 Hamilton Walk | Philadelphia, PA 19104 > http://www.med.upenn.edu/pmacs/ > > > > ________________________________________ > From: Beliz Sertcan <beliz.sert...@chem.uzh.ch> > Sent: Friday, May 15, 2020 10:13 AM > To: openbabel-discuss@lists.sourceforge.net > Subject: [Open Babel] installing and importing openbabel > > 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 > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
