Thanks Matt, that is indeed the problem: Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import openbabel Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named openbabel
I have tried recompiling Open Babel with the Python bindings but it fails with (and I realise this is no longer a Pymol problem so I will get on to the Open Babel mailing list): [100%] Building CXX object scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o Linking CXX executable ../bin/test_unitcell [100%] Built target test_unitcell Linking CXX shared module ../lib/_openbabel.so /usr/local/lib/libpython2.7.a(thread.o): In function `_pythread_pthread_set_stacksize': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined reference to `pthread_attr_setstacksize' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined reference to `sem_destroy' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_acquire_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined reference to `sem_trywait' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined reference to `sem_wait' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_start_new_thread': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined reference to `pthread_attr_setstacksize' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined reference to `pthread_create' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined reference to `pthread_detach' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty': /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined reference to `forkpty' /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty': /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined reference to `openpty' collect2: ld returned 1 exit status make[2]: *** [lib/_openbabel.so] Error 1 make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make: *** [all] Error 2 Quoting Matthew Baumgartner <mp...@pitt.edu> on Wed, 12 Nov 2014 08:55:27 -0500: > Hi, > Can you check to see if the python bindings are compiled openbabel? > > On the bash command line, run the command 'python' to get an interactive > shell and then run 'import openbabel'. > > Matt > > On 11/12/2014 07:14 AM, Douglas Houston wrote: >> Hi all, >> >> I installed Optimize.py, now when I start Pymol I see: >> >> "Optimize plug-in needs openbabel to be installed in your system, >> please follow the instructions at >> http://openbabel.org/wiki/Get_Open_Babel"; >> >> If I try to use any optimize commands I get: >> >> "PyMOL>minimize all, nsteps 2 >> Traceback (most recent call last): >> File >> "/usr/people/douglas/programs/pymol-v1.7.2.3/modules/pymol/parser.py", >> line 254, in parse >> self.result=apply(layer.kw[0],layer.args,layer.kw_args) >> File >> "/usr/people/douglas/programs/pymol-v1.7.2.3/modules/pmg_tk/startup/optimize.py", >> line 237, >> in >> minimize >> obconversion = ob.OBConversion() >> NameError: global name 'ob' is not defined >> " >> >> Open Babel IS installed on my system (v2.3.2), do I need to tell >> Pymol where? >> >> cheers, >> Doug >> >> > > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > _____________________________________________________ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
