VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 18 2005 - 12:05:51 CST

Guys,
  I didn't get a chance to sort all of this out for you before leaving for
vacation, but I'm posting a raw copy of the Python library used to compile
VMD on the web site so you guys can install it on your machine and set
the PYTHONHOME variable to make VMD use it. It should cure your problems,
it worked fine when I tested it on my own machines.
If this doesn't solve your problems, I'll help you when I return on March 28.

I've posted the binary Python libraries and sample install instructions here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 14, 2005 at 01:47:10PM +0100, Florian Haberl wrote:
> Hi,
> >
> > I am trying to get the python scripting functionality, in addition to
> > the Numeric module working with VMD 1.8.3 on Mac OS X 10.3.8. I have
> > installed python 2.2.3 with fink, and Numeric 22.0 from its source
> > using the python 2.2.3 from fink.
>
> I think you need Numpy not Numeric.
>
> http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351
>
> >
> > 1. I am able to execute from a python interactive shell:
> > >>> import _numpy
> > >>> dir(_numpy)
> >
> > ['_ARRAY_API', '_UFUNC_API', '__doc__', '__file__', '__name__']
> >
> > >>> import _tkinter
> > >>> dir(_tkinter)
> >
> > ['ALL_EVENTS', 'DONT_WAIT', 'EXCEPTION', 'FILE_EVENTS', 'IDLE_EVENTS',
> > 'READABLE', 'TCL_VERSION', 'TIMER_EVENTS', 'TK_VERSION', 'TclError',
> > 'TkappType', 'TkttType', 'WINDOW_EVENTS', 'WRITABLE', '__doc__',
> > '__file__', '__name__', '_flatten', 'create', 'createfilehandler',
> > 'createtimerhandler', 'deletefilehandler', 'dooneevent', 'mainloop',
> > 'quit']
> >
> > so it appears that this is "working." ( I think that Tkinter might
> > actually come from the Tkinter.py in the VMD directory. )
> >
> >
> > 2. Based on the manual, I modified my .vmdrc file to have:
> >
> > set env(PYTHONHOME) /sw
> > set env(PYTHONPATH) /sw
> > gopython
> >
> > because in fink, the python libraries are in /sw/lib/python2.2.
> > Incidentally, I am using the bash shell.
> >
> > 3. Checking the python executable,
> >
> > $ which python
> > /sw/bin/python
> >
> > $ ls -l /sw/bin/python
> > lrwxr-xr-x 1 root admin 9 Mar 14 11:30 /sw/bin/python
> > -> python2.2
> >
> > so it looks ok, and is the one that I built numeric with.
> >
> > 4. Now, I start VMD 1.8.3, and I get in the console window:
> >
> > /sw
> > /sw
> > Info) Starting Python...
> > Numeric Python module _numpy not found; vmdnumpy module not available.
> > ImportError: Failure linking new module
> > Info) Text interpreter now Python
> > Traceback (most recent call last):
> > File "<string>", line 1, in ?
> > File "/sw/lib/python2.2/lib-tk/Tkinter.py", line 33, in ?
> > import _tkinter # If this fails your Python may not be configured
> > for Tk
> > ImportError: Failure linking new module
> >
> >
> > I am uncertain as to why this is happening! Any help would be most
> > appreciated.
> >
> > Best regards,
> >
> > Eric
>
> Greetings,
>
> Florian
>
> --
> -------------------------------------------------------------------------------
> Florian Haberl Universitaet Erlangen/
> Computer-Chemie-Centrum Nuernberg
> Naegelsbachstr. 25
> D-91052 Erlangen
> Mailto: florian.haberl AT chemie.uni-erlangen.de
> ------------------------------------------------------------------------------- 

-- 
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