Robert Kern wrote:
<div class="moz-text-flowed" style="font-family: -moz-fixed">Jeremiah
H. Savage wrote:
To use pymol and numpy together, I now do the following:
To ~/.bashrc add:
PYMOL_PATH=/usr/lib/pymodules/python2.5/pymol
export PYMOL_PATH
Then I can do the following in python:
import numpy
numpy.save('123',numpy.array([1,2,3]))
numpy.load('123.npy')
array([1, 2, 3])
import sys
sys.path.append( "/usr/lib/pymodules/python2.5/pymol")
import pymol
pymol.finish_launching()
pymol.importing.load("/path/to/file.pdb")
No, do not do this. Add /usr/lib/pymodules/python2.5/ to your
$PYTHONPATH, *not* /usr/lib/pymodules/python2.5/pymol/. You will
continue to run into problems if you do it this way. You are not
supposed to put the directory *of* the package onto sys.path but
rather the directory that *contains* the package directory.
As I said before, I don't know pymol. But if that is the package name,
then Robert is certainly right. You need to read the docs on pymol to
see what they require. For example, it's surprising they require a
separate PYMOL_PATH environment variable, since they can find their own
directory path with the __file__ attribute of one of the modules.
Anyway, one more generic comment. Rather than having that directory in
both the bashrc file AND in your python source, I'd consider deriving
the latter from the environment variable, once you determine that it's
actually necessary. And of course you could strip the last node from
the path in the environment variable before appending it to sys.path, if
that's what's appropriate.
DaveA
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