Re: [PyMOL] using package Scientific from within pymol on OS X-X11 hybrid

[<hi...@ll...>]

On Oct 13, 2004, at 19:47, gilleain torrance wrote:

> however, it turns out that if you copy the entire (python) source tree=20=

> of Scientific - IE:
>
> "ScientificPython<version>/Scientific/"
>
> into
>
> "/Applications/PyMolX11blahHybridetc/py23/lib/python2.3/site-packages"

Apparently you are using the X11 hybrid version for MacOS. This comes=20
with its own Python installation, but there doesn't seem to be a way to=20=

use its Python interpreter separately, outside of PyMOL, so the=20
standard installation script for Scientific Python (or any other=20
package) cannot be used.

There are three solutions:

1) The one you used. Its main disadvantage is that you don't get the C=20=

modules of Scientific Python, i.e. the netCDF interface.

2) Install Scientific Python with another Python 2.3 installation (i.e.=20=

the one that comes with MacOS 10.3, or the one from fink) and copy=20
site-packages/Scientific from that installation to the the place you=20
already discovered.

3) [Hypothetical, I did not test this]. Modify the setup.py in such a=20
way that it does the buiild and install steps without requiring command=20=

line parameters, then run it using the "run" command from inside PyMOL.

I used solution 1).

> hopefully! Anyway, there might be a better way, but this works. One=20
> tiny glitch is the change from Numeric to numarray. This can be=20
> 'fixed' ('hacked') by using *cough*perl*cough*:
>
> perl -i -p -e 's/Numeric/numarray/g' *.py */*.py
>
> which should substitiute all instances of 'Numeric' with 'numarray'.
>
But the PyMOL hybrid distribution comes with Numeric, not numarray. Or=20=

has this changed recently? Mine is 0.95.

For daily use, I prefer to build PyMOL from source under the Python=20
that comes with fink. In that way, I have all my python packages=20
available for PyMOL scripts. In fact, I had almost forgotten that I=20
still had the X11 hybrid on my machine.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------