[Rdkit-discuss] rdkit as python module fragmented

Fri, 28 Feb 2014 07:45:36 -0800 

Hi,

I have been trying to use rdkit in python but cannot seem to get it to import 
properly
RDKit works fine through C++, I have compiled and can run programs but it will 
not import as a python module

from rdkit import Chem
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

I am using Mac OS X 10.8.5 and have home-brewed version of rdkit
I have two versions of Python installed (the Mac default, and a newer version 
in /usr/local/bin/python which I believe is the problem but I can't seem to fix 
it through altering the $PATH variable in the terminal

Here is the error file:



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Attachment: rdkit_error.log
Description: rdkit_error.log



here is the extract from my .bash_profile

#export PATH=/Library/Frameworks/Python.framework/Versions/2.7/bin:$PATH #the directory below contains a symbolic link to the python executable here
export PATH=/usr/local/bin/:$PATH

export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH

#rdkit
export RDBASE=/usr/local/share/RDKit
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$RDBASE/lib

any help would be greatly appreciated,
I have been having this problem for a while now…

Many thanks,
Josh

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