I think that's it. This was subsequently fixed so you should just use the one in git.
Regarding "as it wasn’t installing the python bindings in the right place", ....? Just set PYTHONPATH to the location of openbabel.py and pybel, and Bob should be your uncle - Noel On 5 January 2015 at 16:25, Tim Fallon <tfal...@mit.edu> wrote: > Hi all, > > I’ve run into a strange bug with the Pybel bindings of OpenBabel. I’m using > version OpenBabel 2.3.2 installed from Macports > (https://www.macports.org/ports.php?by=name&substr=openbabel) on Mac OS X > 10.10.1 with Python 2.7.9. I’ve also attempted to compile and install > OpenBabel (with Python bindings) from git myself, which wasn’t quite > successful as it wasn’t installing the python bindings in the right place. I > haven’t been able to rule out that there is some dependency confusion going > on, but I’ve gone through and tried to clean it up so it *should* be using > the Macports compiled versions of everything. > > The bug: I’ve found that whether or not Pybel works seems to be stochastic. > This seems to be an older bug as > this:http://forums.openbabel.org/Pybel-on-Python3-Mavericks-td4657100.html > reports the same problem, but in my case I’m not using Python3. I’m loading > two molecules (one heavy isotope labeled, one not) from a .SDF file. See > attached for both the .sdf file and the python script. The same python > script can work flawlessly, or breaks with an error upon Pybel import, > without any changes on my part. Here is my very simple script: > > ' > import openbabel > import pybel > > print 'Script starting' > molecule_list = > list(pybel.readfile('sdf','/Users/tim/Dropbox/source/Bioinformatics/emzed_developlment/Necine.sdf')) > for molecule in molecule_list: > print 'Formula:',molecule.formula,'Exact mass:',molecule.exactmass > for atom in molecule: > if atom.isotope != 0: > print atom.isotope > print 'Script ending' > > ' > > And the execution, with the first execution working without error and the > second failing stochastically: > > ' > tim:build tim$ python > /Users/tim/Dropbox/source/Bioinformatics/emzed_developlment/parse_sdf.py > Script starting > Formula: C8H15NO Exact mass: 143.115753836 > 13 > 15 > Formula: C8H15NO Exact mass: 141.115364105 > Script ending > tim:build tim$ python > /Users/tim/Dropbox/source/Bioinformatics/emzed_developlment/parse_sdf.py > Traceback (most recent call last): > File > "/Users/tim/Dropbox/source/Bioinformatics/emzed_developlment/parse_sdf.py", > line 2, in <module> > import pybel > File > "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pybel.py", > line 87, in <module> > descs = _getpluginnames("descriptors") > File > "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pybel.py", > line 85, in _getpluginnames > return [x.split()[0] for x in plugins] > IndexError: list index out of range > Midgard:build tim$ > ' > Based on this post: > http://forums.openbabel.org/Pybel-on-Python3-Mavericks-td4657100.html, it > seems like this might be a bug with the C++ library on Mac OS X. Any > thoughts? > > Best, > -Tim > > Timothy R. Fallon > Graduate Student > Laboratory of Jing-Ke Weng > Department of Biology > MIT > > tfal...@mit.edu > 508-274-1995 > > > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming! The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
