Hi Anthony, You're on the right track. "etab" is gone now, as you've found. "ob.GetAtomicNum(element)" is the replacement you're looking for.
Looking through the code, I think it should work now. FYI, if you want to use Python 3 instead of Python 2, you may also need to replace "f.next()" with "next(f)". Regards, - Noel On Fri, 19 Jun 2020 at 17:32, C Anthony Lewis <cale...@plymouth.ac.uk> wrote: > Dear Colleagues, > > > > I hope you are all safe and well at this extraordinary time. > > > > This is a follow-up to messages I sent to the list in late 2013 and early > 2014 regarding an old DOS-based program 'SMOG' (see CCL archives > http://www.ccl.net/cca/software/MS-DOS/SMOG/index.shtml and > http://pubs.acs.org/doi/abs/10.1021/ci950393z) that generates isomers > given a molecular formula and a set of structural constraints. Although the > output is in the form of a connection table it was not understood by other > applications I was aware of and I thought OpenBabel might work. However, at > the time this was not an option and Noel kindly provided me with a Python > script (smog.py – attached as a txt file) that took the SMOG output and > generated SMILES. I believe there was an intention to include this in > future versions of Open Babel but I appreciate there are many calls on time > and I don’t think this has yet happened. > > > > Fast forwarding seven years or so, during which my attention was taken by > other duties, I have now returned to working on the additional SMOG output > I have available and I naively thought I would be able to install current > versions of Open Babel and Python, fire up the script and everything would > work as before. Unfortunately, things didn’t go quite to plan and the > following is what happened. > > > > I Installed Anaconda Powershell and OpenBabel 3.0.0 and, I think, the > bindings ('pip install -U openbabel') correctly. > > > > I ran through the commands given in the ‘Test the installation’ box on > https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html > and obtained a structure in a separate window so it seemed that things were > working okay. I then ran smog.py as attached and got the following: > > > > (base) PS C:\users\anthony\anaconda2> python smog.py myfile.res > myoutputfile.smi > > Traceback (most recent call last): > > File "smog.py", line 5, in <module> > > import pybel > > ImportError: No module named pybel > > > > Having looked at > https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html > again and also the ‘Updating to Open Babel 3.0 from 2.x’ page ( > https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html), > I changed line 5 in smog.py from ‘import pybel’ to ‘from openbabel import > pybel’ and ran smog.py again with the following result: > > > > (base) PS C:\users\anthony\anaconda2> python smog.py myfile.res > myoutputfile.smi > > Traceback (most recent call last): > > File "smog.py", line 60, in <module> > > for mol in readSMOG(options['inputfile']): > > File "smog.py", line 41, in readSMOG > > yield smog2mol(lines) > > File "smog.py", line 16, in smog2mol > > atm.SetAtomicNum(ob.cvar.etab.GetAtomicNum(element)) > > AttributeError: Unknown C global variable 'etab' > > > > At this point I am well beyond my capabilities but I assume there have > been changes since version 2.x'ish that I used in the past and the global > variable 'etab' and is absent. I did find 'etab' defined on line 468 at > https://github.com/openbabel/documentation/blob/master/pybel.py (dated 14 > Oct 2012) but I don't know what to do with this information! > > > > I guess this is a similar issue to one posted to the list at the end of > May and I'm hoping that someone can provide some assistance and, if it's > possible, show me how I can get the smog.py working again. Maybe this is my > chance to learn Python after all the times I’ve said I would… > > > > My apologies for the lengthy post and many thanks for any assistance > received, > > > > Anthony > > > > > > > > C. Anthony Lewis > > Petroleum & Environmental Geochemistry Group & Centre for Chemical > Sciences, > > School of Geography, Earth and Environmental Sciences, > > Plymouth University, > > Plymouth, Devon PL4 8AA, U.K. > > > > tel: +44 (0)1752 584554 > > email: cale...@plymouth.ac.uk > > web: http://www.pegg.org.uk > > http://www.plymouth.ac.uk/chemistry > > > ------------------------------ > <http://www.plymouth.ac.uk/worldclass> > > This email and any files with it are confidential and intended solely for > the use of the recipient to whom it is addressed. If you are not the > intended recipient then copying, distribution or other use of the > information contained is strictly prohibited and you should not rely on it. > If you have received this email in error please let the sender know > immediately and delete it from your system(s). Internet emails are not > necessarily secure. While we take every care, University of Plymouth > accepts no responsibility for viruses and it is your responsibility to scan > emails and their attachments. University of Plymouth does not accept > responsibility for any changes made after it was sent. Nothing in this > email or its attachments constitutes an order for goods or services unless > accompanied by an official order form. > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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