Hi Noel, That's really helpful, many thanks for the Python script. For the moment I don't need to consider double or aromatic bonds but in the longer term this would be useful and I can wait until this is supported in Open Babel.
I am not familiar with Python (although this gives me a chance to learn about it) and I've worked through your instructions and had a look at those at http://openbabel.org/docs/current/UseTheLibrary/PythonInstall.html and then started on testing things as detailed later on that page. Everything seems to be fine until I got to the '>>> import pybel' stage when I obtained: C:\>C:\Python27\python Python 2.7.6 (default, Nov 10 2013, 19:24:18) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import pybel Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Python27\lib\site-packages\pybel.py", line 16, in <module> import openbabel as ob File "C:\Python27\lib\site-packages\openbabel.py", line 28, in <module> _openbabel = swig_import_helper() File "C:\Python27\lib\site-packages\openbabel.py", line 24, in swig_import_helper_mod = imp.load_module('_openbabel', fp, pathname, description) ImportError: DLL load failed: The specified procedure could not be found. >>> import C:\Python27\Lib\site-packages\pybel File "<stdin>", line 1 import C:\Python27\Lib\site-packages\pybel ^ SyntaxError: invalid syntax There are various pybel files in the \Lib\site-packages\ folder so, as you can see, I also tried to use the full directory tree but that didn't work either (also tried with single and double quotes to no avail). Running the script as you suggest gave the following: C:\>C:\Python27\python C:\SMOG\smog.py C6H14.res C6H14_out.smi Traceback (most recent call last): File "C:\SMOG\smog.py", line 5, in <module> import pybel File "C:\Python27\lib\site-packages\pybel.py", line 16, in <module> import openbabel as ob File "C:\Python27\lib\site-packages\openbabel.py", line 28, in <module> _openbabel = swig_import_helper() File "C:\Python27\lib\site-packages\openbabel.py", line 24, in swig_import_helper_mod = imp.load_module('_openbabel', fp, pathname, description) ImportError: DLL load failed: The specified procedure could not be found. C:\> Again, there seems to be an issue with pybel. I'm sure this is straightforward and I'm just being dumb but I'm a bit stumped as to what's wrong so I'm hoping it's easily fixable. Again, many thanks for your help and apologies in advance if I'm doing something obvious daft. Anthony ________________________________________ From: Noel O'Boyle [baoille...@gmail.com] Sent: 08 February 2014 20:23 To: C Anthony Lewis Cc: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] User defined 'mask' for data import (Please cc the list) Well, it hasn't been done, but the goal of the project is to support all chemical file formats. In the meanwhile, I've written a Python script that handles the particular file you sent. If you have more files that exhibit different types of bonds (e.g. aromatic, double) and charges then I can add support for those too. Once the Python prototype is finished, I'll have a go at porting to C++. To run the Python script, install Python 2.7, the Python bindings for Open Babel, and then run the script at the command-line with an inputfile and outputfile, e.g. C:\Python27\python smog.py myfile.res myoutputfile.smi Then, you can convert the file to SVG (for example) and drag-and-drop onto Firefox to see all of the isomers. - Noel On 8 February 2014 16:37, C Anthony Lewis <cale...@plymouth.ac.uk> wrote: > Hi Noel, > > You may remember this thread from late November last year. ... I'm wondering > whether there is an intention to include the SMOG format in Open Babel. I've > had a look at the download page and it doesn't appear there have been any > updates since I first inquired so I'm assuming the format isn't (yet) > included. > ... > > ________________________________ > From: Noel O'Boyle [baoille...@gmail.com] > Sent: 25 November 2013 19:30 > To: C Anthony Lewis > Subject: Re: [Open Babel] User defined 'mask' for data import > > Could you resend and cc the list? Thanks. > > - Noel > > > On 25 November 2013 17:44, C Anthony Lewis > <cale...@plymouth.ac.uk<mailto:cale...@plymouth.ac.uk>> wrote: > Hi Noel, > > Many thanks for the reply... I've attached one of my smaller files, which > contains the data for all constitutional isomers of C8H18 (alkane, 18 > isomers), and a document describing the format of this '*.res' file provided > by the authors. I hope this helps. > > Anthony > > From: Noel O'Boyle [mailto:baoille...@gmail.com<mailto:baoille...@gmail.com>] > Sent: 25 November 2013 13:38 > To: C Anthony Lewis > Cc: > openbabel-discuss@lists.sourceforge.net<mailto:openbabel-discuss@lists.sourceforge.net> > Subject: Re: [Open Babel] User defined 'mask' for data import > > Can you provide an example? (Please cc to the list) > - Noel > > On 25 November 2013 13:20, C Anthony Lewis > <cale...@plymouth.ac.uk<mailto:cale...@plymouth.ac.uk>> wrote: > Dear Open Babelers, > > Is it possible for 'the user' (i.e. me) to define a 'mask' to import data > from a file? I'm not sure if I'm using the appropriate words but by 'mask' I > mean something that will enable me to extract a specific re-occurring (but > varying) portion of a file. > > In particular, I wish to extract the connection tables from output files > generated by '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) and then generate the SMILES > from the table. Unfortunately, I cannot get 'SMOG' to work under Windows 7 > and, anyway, I'm not sure that would help much as the SMILES for each of the > isomers enumerated isn't provided by the application or in the file. Of > course, I could use one or other of the (more current) isomer enumeration > applications to recreate the isomers but I thought I'd first ask about the > files I already have. > > Many thanks for any suggestions, > > Anthony > > > > C. Anthony Lewis > Petroleum & Environmental Geochemistry Group & Centre for Chemical Sciences, > School of Geography, Earth and Environmental Sciences, > University of Plymouth, > Plymouth, Devon PL4 8AA, U.K. > > tel: +44 (0)1752 584554 > email: cale...@plymouth.ac.uk<mailto:cale...@plymouth.ac.uk> > web: http://www.pegg.org.uk<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. 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