Hi Noel, Ah, okay... I see I downloaded and installed the 1.7 Python bindings from openbabel.org so I'll sort that out and see how I get on.
Many thanks, Anthony ________________________________________ From: Noel O'Boyle [baoille...@gmail.com] Sent: 09 February 2014 19:06 To: C Anthony Lewis Cc: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] User defined 'mask' for data import The updated docs were never copied to openbabel.org but you can find them at: http://open-babel.readthedocs.org/en/latest/UseTheLibrary/PythonInstall.html#windows Can you make sure you've installed OB 2.3.2, and separately the 1.8 Python bindings for the version of Python you've installed (note only 32-bit Python is supported). The problem is likely a mismatch. - Noel On 9 February 2014 17:35, C Anthony Lewis <cale...@plymouth.ac.uk> wrote: > 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. 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. 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