Re: [OpenBabel-scripting] Python bindings on amd64 Linux

[richard a. <ric...@ya...>]

Hi Marin,

Your suggestion worked perfectly. I changed the first
few lines of openbabel.py to the following:

import sys
if sys.platform.find("linux") != -1:
    #import dl
    sys.setdlopenflags(sys.getdlopenflags() | 0x100)

Doing this I can now import openbabel, create a
working OBConversion, and do a simple smiles->inchi
conversion.

Many thanks!
Rich

--- Martin Vogt <mar...@bi...> wrote:

> Hi,
> 
> there is indeed a simple workaround for this
> problem.
> Note that the dl module is only needed for the
> numerical constant
> 
> dl.RTLD_GLOBAL
> 
> This constant is defined from a system header
> 'dlfcn.h', if i recall 
> correctly. Searching through your system headers you
> might find that 
> this constant is equal to 0x100 (at least on my
> system: Suse 10.1 64bit).
> So you can replace the top lines with:
> 
> if sys.platform.find("linux") != -1:
> 	sys.setdlopenflags(sys.getdlopenflags() | 0x100)
> 
> avoiding the import of the dl module.
> 
> Hth, Martin
> 
> richard apodaca wrote:
> > Has anyone gotten the Python Open Babel interface
> to
> > work on amd64 Linux? I'm using rev 1578 of the svn
> > trunk
> > 
> > When I try to import openbabel, I get the
> following
> > error
> > 
> > 
> >>>>import openbabel
> > 
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File
> > "/usr/lib64/python2.4/site-packages/openbabel.py",
> > line 3, in ?
> >     import dl
> > ImportError: No module named dl
> > 
> > I noticed a similar problem reported here, but no
> > solution:
> > 
> >
>
http://sourceforge.net/mailarchive/message.php?msg_id=37015184
> > 
> > I had no problems either compiling or installing
> > pyopenbabel - just loading it in python.
> > 
> > My system does lack the python dl module, which as
> far
> > as I can tell is supposed to be standard. In
> googling
> > around, I found several references to the python
> dl
> > module being unstable on amd64 - and therefore not
> > available.
> > 
> > So - has anyone found a workaround to this
> problem?
> > 
> > I tried one: comment out the code responsible for
> > loading dl in the first place (openbabel.py):
> > 
> > if sys.platform.find("linux") != -1:
> >     import dl
> >     sys.setdlopenflags(sys.getdlopenflags() |
> > dl.RTLD_GLOBAL)
> > 
> > I can in fact import openbabel after doing this.
> The
> > problem is that when using OBConversion, none of
> the
> > formats are loaded:
> > 
> > 
> >>>>import openbabel
> >>>>c=openbabel.OBConversion()
> > 
> > ==============================
> > *** Open Babel Error  in LoadFormatFiles
> >   /usr/local/lib/openbabel/cmlreactlformat.so did
> not
> > load properly
> > ==============================
> > 
> > ... and dozens more load errors after this one ...
> > 
> > thanks,
> > Rich
> > 
> > 
> > 
> > 
> > ____________________________
> > Richard Apodaca
> > Blog: http://depth-first.com
> > 
> > 
> >  
> >
>
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> 
> 
> -- 
> Martin Vogt
> Vorgebirgsstr. 14, D-53111 Bonn
> Email: mo...@t-...              Tel.: +49
> (0)228 634376
> 


____________________________
Richard Apodaca
Blog: http://depth-first.com


 
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