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python parser overridden by pymol

 
 
Jeremiah
Guest
Posts: n/a
 
      11-12-2009
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
 
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Robert Kern
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Posts: n/a
 
      11-12-2009
Jeremiah wrote:

> 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


Don't change your PYTHONPATH like that. You want to put
/usr/lib/pymodules/python2.5 onto your PYTHONPATH and import PyMOL's stuff from
the pymol package. I.e., instead of

import api

Do

from pymol import api

pymol is a package for precisely this reason.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

 
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Steven D'Aprano
Guest
Posts: n/a
 
      11-12-2009
On Wed, 11 Nov 2009 17:41:07 -0800, 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().



>>> import parser
>>> parser.__file__

'/usr/lib/python2.5/lib-dynload/parsermodule.so'
>>> parser.expr

<built-in function expr>



[...]
> 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



Change that to

PYMOL_PATH=/usr/lib/pymodules/python2.5


and it should work, assuming pymol uses a package, as it should. If it
doesn't, if it's just a hodge-podge of loose modules in a directory, then
they should be slapped with a wet fish for shadowing a standard library
module.



--
Steven
 
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Dave Angel
Guest
Posts: n/a
 
      11-12-2009


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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Jeremiah H. Savage
Guest
Posts: n/a
 
      11-13-2009
On Wed, Nov 11, 2009 at 7:48 PM, Dave Angel <(E-Mail Removed)> wrote:
>
>
> 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)Thank you. That really helped.


To use pymol and numpy to
>> * * 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
>
>


Thank you. Your second suggestion really helped.

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")

Thanks,
Jeremiah
 
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Robert Kern
Guest
Posts: n/a
 
      11-13-2009
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.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

 
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Dave Angel
Guest
Posts: n/a
 
      11-13-2009


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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