[Chimera-users] error: from DockPrep import prep

wascm wascm at 126.com
Tue Mar 15 05:37:27 PDT 2011


Dear sir:

Thanks for the detailed reply!

When the following code was added to the start of sciprt:

import chimeraInit
chimeraInit.init(nogui=True, silent=True)

The interpreter print the following confused error:

---------------------------------------------
Traceback (most recent call last):
 File "./xx.py", line 5, in <module>
 chimeraInit.init(nogui=True, silent=True)
TypeError: init() takes at least 1 argument (2 given)
-----------------------------------------------

it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module.

For example, when i run some command like this:

chimera –nogui test.py -t test

test.py
###################
#!/usr/bin/python

t=None

try:
    opts, args = getopt.getopt(sys.argv[1:], "t:")
except getopt.GetoptError, err:
    pass
finally:
    for arg_k, arg_v in opts:
        if (arg_k =="-t"): t=arg_v
####################################

This will raise running exception!

is there a way for me to add the coustom option to python script and run the script with chimera?

the exception message as follow:

-------------------------------------------------
Executing test.py...

Traceback (most recent call last):
  File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open
    models = func(filename, *args, **kw)
  File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython
    loadFunc(sandboxName, fileName, f)
  File "test.py", line 10, in <module>
    for arg_k, arg_v in opts:
NameError: name 'opts' is not defined
Error while processing test.py:
NameError: name 'opts' is not defined

  File "test.py", line 10, in <module>
    for arg_k, arg_v in opts:

See reply log for Python traceback.

Traceback (most recent call last):
  File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open
    raise ValueError, "Unknown model type"
ValueError: Unknown model type
Error while processing -t:
ValueError: Unknown model type

  File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open
    raise ValueError, "Unknown model type"

See reply log for Python traceback.

Traceback (most recent call last):
  File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open
    raise ValueError, "Unknown model type"
ValueError: Unknown model type
Error while processing test:
ValueError: Unknown model type

  File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open
    raise ValueError, "Unknown model type"

See reply log for Python traceback.
----------------------------------------------------------


At 2011-03-15 09:02:09,"Greg Couch" <gregc at cgl.ucsf.edu> wrote:
(This is really achimera-dev at cgl.ucsf.edu mailing list question.)

My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up.  So in the beginning of your Python script, add:

    import chimeraInit
    chimeraInit.init(nogui=True, silent=True)

before using chimera's modules.

But, in general, you would be better off running those python scripts with chimera.  For example:

    % chimera --nogui --silent script.py

That would set up the the appropriate environment for chimera, execute the python script, and exit.  And you would be protected against any future changes in how chimera is initialized.

If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera).

If you want to install other Python packages into chimera's Python that have a setup.py file, use:

    % chimera --nogui --silent setup.py install

It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details).  Right now, chimera is using Python 2.7.

    HTH,

    Greg
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