Jeremiah wrote:
Hello,
I'm fairly new to python (version 2.5.4), and am writing a program
which uses both pymol (version 1.2r1) and numpy (version 1.3.0) from
debian.
It appears that when I add pymol to $PYTHONPATH, that parser.expr() is
no longer available, and so I am unable to use numpy.load(). I have
looked for where parser.expr() is defined in the python system so I
could place that directory first in $PYTHONPATH, but I have not been
able to find the file that defines expr().
My reason for using numpy.load() is that I have a numpy array which
takes an hour to generate. Therefore, I'd like to use numpy.save() so
I could generate the array one time, and then load it later as needed
with numpy.load().
I've successfully tested the use of numpy.save() and numpy.load() with
a small example when the pymol path is not defined in $PYTHONPATH :
>>> import numpy
>>> numpy.save('123',numpy.array([1,2,3]))
>>> numpy.load('123.npy')
array([1, 2, 3])
However, a problem arises once $PYTHONPATH includes the pymol
directory. To use the pymol api, I add the following to ~/.bashrc:
PYMOL_PATH=/usr/lib/pymodules/python2.5/pymol
export PYMOL_PATH
PYTHONPATH=$PYMOL_PATH
export PYTHONPATH
Once this is done, numpy.load() no longer works correctly, as pymol
contains a file named parser.py ( /usr/lib/pymodules/python2.5/pymol/
parser.py ), which apparently prevents python from using its native
parser.
>>> 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'
If I understand the problem correctly, can anyone tell me where
python.expr() is defined, or suggest a better method to fix this
problem?
Thanks,
Jeremiah
Generic answers, I have no experience with pymol
If pymol really needs that parser.py, you have a problem, as there can
only be one module by that name in the application. But assuming it's
needed for some obscure feature that you don't need, you could try the
following sequence.
1) temporarily rename the pymol's parser.py file to something else,
like pymolparser.py, and see what runs.
2) rather than changing the PYTHONPATH, fix up sys.path during your
script initialization.
In particular, do an import parser near the beginning of the
script. This gets it loaded, even though you might not need to use it
from this module.
After that import, then add the following line (which could be
generalized later)
sys.path.append( "/usr/lib/pymodules/python2.5/pymol")
If this works, then you can experiment a bit more, perhaps you don't
need the extra import parser, just putting the pymol directory at the
end of the sys.path rather than the beginning may be good enough.
If the parser.py in the pymol is actually needed, you might need to
rename its internal references to some other name, like pymolparser.
HTH,
DaveA
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