(Please cc to the list) When you test Python, start it with the "-v" switch, e.g. "C:\Python27\python -v". Then "import pybel", etc. Is there anything unusual? If not, I'm all out of ideas. Anything strange about your computer?
- Noel On 11 September 2011 17:36, joseph mcdonald <josephjmcdon...@gmail.com> wrote: > Noel, > > Thanks for your response. Following your comments below, running tests > from C:\, I receive the same error (see below). Any guidance would be > appreaciated. > > joe mcdonald > > > c:\>babel -V > Open Babel 2.3.0 -- Nov 25 2010 -- 23:22:17 > > c:\>babel -Hsdf > sdf MDL MOL format > Reads and writes V2000 and V3000 versions > Read Options, e.g. -as > s determine chirality from atom parity flags > This is valid only for 0D information. Atom > parity is always ignored on reading for MOL files > containing 2D or 3D information. > T read title only > P read title and properties only > When filtering an sdf file on title or properties > only, avoid lengthy chemical interpretation by > using the T or P option together with copy format. > > Write Options, e.g. -x3 > 3 output V3000 not V2000 (used for >999 atoms/bonds) > m write no properties > w recalculate wedge and hash bonds(2D structures only) > A output in Alias form, e.g. Ph, if present > > > Specification at: http://www.mdl.com/downloads/public/ctfile/ctfile.jsp > > c:\>dir "%BABEL_DATADIR%"\mr.txt > Volume in drive C is Windows7_OS > Volume Serial Number is D853-7305 > > Directory of C:\Program Files\OpenBabel-2.3.0\data > > 10/26/2010 12:37 PM 4,295 mr.txt > 1 File(s) 4,295 bytes > 0 Dir(s) 45,948,878,848 bytes free > > > c:\>c:\python27\python > Python 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)] on > win > 32 > Type "help", "copyright", "credits" or "license" for more information. >>>> import pybel >>>> mol = pybel.readstring("smi","CC(=O)Br") > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "c:\python27\lib\site-packages\pybel.py", line 119, in readstring > raise ValueError("%s is not a recognised OpenBabel format" % format) > ValueError: smi is not a recognised OpenBabel format > > > > > On Fri, Sep 9, 2011 at 4:58 AM, Noel O'Boyle <baoille...@gmail.com> wrote: >> Something's wrong with your Open Babel installation. >> >> To test your installation, don't run the three tests from C:\Program >> Files\OpenBabel-2.3.0, run them from C:\. >> >> - Noel >> >> On 8 September 2011 20:27, coalmeister <josephjmcdon...@gmail.com> wrote: >>> after following instructions on: >>> http://openbabel.org/docs/2.3.0/UseTheLibrary/PythonInstall.html#windows >>> >>> Receive the following error running testscript. Assistance towards >>> resolution would be greatly appreciated. Would appear that error is >>> encountered in line 119 pybel.py (part of openbabel python bindings). >>> >>> c:\>c:\python25\python >>> Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] >>> on >>> win32 >>> Type "help", "copyright", "credits" or "license" for more information. >>>>>> import pybel >>>>>> mol = pybel.readstring("smi", "CC(=O)Br") >>> Traceback (most recent call last): >>> File "<stdin>", line 1, in <module> >>> File "C:\Python25\Lib\site-packages\pybel.py", line 119, in readstring >>> raise ValueError("%s is not a recognised OpenBabel format" % format) >>> ValueError: smi is not a recognised OpenBabel format >>> >>> I uninstalled 2.5 openbabel bindings, installed 2.7 bindings, ran python2.7, >>> same error. >>> >>> Following previous threads, uninstalled all bindings and openbabel 2.3.0, >>> re-installed openbabel and 2.7 bindings, same error. >>> >>> Previously, users with similar errors have been requested to report details >>> of installation. They are included below (newline whitespaces deleted): >>> >>> c:\Program Files\OpenBabel-2.3.0>babel -V >>> Open Babel 2.3.0 -- Nov 25 2010 -- 23:22:17 >>> >>> c:\Program Files\OpenBabel-2.3.0>babel -Hsdf >>> sdf MDL MOL format >>> Reads and writes V2000 and V3000 versions >>> Read Options, e.g. -as >>> s determine chirality from atom parity flags >>> This is valid only for 0D information. Atom >>> parity is always ignored on reading for MOL files >>> containing 2D or 3D information. >>> T read title only >>> P read title and properties only >>> When filtering an sdf file on title or properties >>> only, avoid lengthy chemical interpretation by >>> using the T or P option together with copy format. >>> Write Options, e.g. -x3 >>> 3 output V3000 not V2000 (used for >999 atoms/bonds) >>> m write no properties >>> w recalculate wedge and hash bonds(2D structures only) >>> A output in Alias form, e.g. Ph, if present >>> Specification at: http://www.mdl.com/downloads/public/ctfile/ctfile.jsp >>> >>> c:\Program Files\OpenBabel-2.3.0>dir "%BABEL_DATADIR%"\mr.txt >>> Volume in drive C is Windows7_OS >>> Volume Serial Number is D853-7305 >>> Directory of C:\Program Files\OpenBabel-2.3.0\data >>> 10/26/2010 12:37 PM 4,295 mr.txt >>> 1 File(s) 4,295 bytes >>> 0 Dir(s) 46,059,106,304 bytes free >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://forums.openbabel.org/problem-with-pybel-on-windows-7-tp3799822p3799822.html >>> Sent from the General discussion mailing list archive at Nabble.com. >>> >>> ------------------------------------------------------------------------------ >>> Why Cloud-Based Security and Archiving Make Sense >>> Osterman Research conducted this study that outlines how and why cloud >>> computing security and archiving is rapidly being adopted across the IT >>> space for its ease of implementation, lower cost, and increased >>> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/ >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >> > ------------------------------------------------------------------------------ Using storage to extend the benefits of virtualization and iSCSI Virtualization increases hardware utilization and delivers a new level of agility. Learn what those decisions are and how to modernize your storage and backup environments for virtualization. http://www.accelacomm.com/jaw/sfnl/114/51434361/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
