pymol vs numpy conflict

["Jeremiah H. Savage" <jeremiahsavage@gmail.com>]

Hello,

I'm fairly new to python (2.5.4-2), and am writing a program which
uses both pymol (1.2r1-3) and numpy (1:1.3.0-3) from unstable.

The situation is that I have a large numpy array which takes an hour
to generate. Therefore, I'd like to use numpy.save() and then
numpy.load() so I could just generate the first time the program runs,
and then load it later as needed.

I've successfully tested the use of numpy.save() and numpy.load() with
a small example:

    >>> import numpy
    >>> numpy.save('123',numpy.array([1,2,3]))
    >>> numpy.load('123.npy')
    array([1, 2, 3])


However, a problem arises when I attempt to use pymol in the same
program. First, to use the pymol api, I add the following to
~/.bashrc:

    PYMOL_PATH=/usr/lib/pymodules/python2.5/pymol
    export PYMOL_PATH
    PYTHONPATH=$PYMOL_PATH
    export PYTHONPATH

But once this is done, numpy.load() no longer works correctly:

    >>> numpy.load('123.npy')
    Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File "/usr/lib/python2.5/site-packages/numpy/lib/io.py", line 195, in load
        return format.read_array(fid)
      File "/usr/lib/python2.5/site-packages/numpy/lib/format.py",
line 353, in read_array
        shape, fortran_order, dtype = read_array_header_1_0(fp)
      File "/usr/lib/python2.5/site-packages/numpy/lib/format.py",
line 250, in read_array_header_1_0
        d = safe_eval(header)
      File "/usr/lib/python2.5/site-packages/numpy/lib/utils.py", line
840, in safe_eval
        ast = compiler.parse(source, "eval")
      File "/usr/lib/python2.5/compiler/transformer.py", line 54, in parse
        return Transformer().parseexpr(buf)
      File "/usr/lib/python2.5/compiler/transformer.py", line 133, in parseexpr
        return self.transform(parser.expr(text))
    AttributeError: 'module' object has no attribute 'expr'


I've seen where someone else has had a similar problem
http://groups.google.com/group/genshi/browse_thread/thread/05ae0216b01dced8
and the listed cause is a file "parser.py"

There is a file /usr/lib/pymodules/python2.5/pymol/parser.py so this
is probably the cause.

How should I deal with this? Should I rename .../pymol/parser.py and
all references to it?

Thanks,
Jeremiah