python parser overridden by pymol
in [Python]
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From: Jeremiah on 11 Nov 2009 20:41 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
From: Robert Kern on 11 Nov 2009 22:12 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
From: Steven D'Aprano on 11 Nov 2009 22:16 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
From: Dave Angel on 11 Nov 2009 22:48 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
From: Jeremiah H. Savage on 12 Nov 2009 20:38
On Wed, Nov 11, 2009 at 7:48 PM, Dave Angel <davea(a)ieee.org> 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 |