[Chimera-users] [chimera-dev] error: from DockPrep import prep

[Greg Couch]

See the Chimera Programmer's FAQ, question #3, 
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3, for 
how to write a shell script wrapper around a chimera script to hide the 
fact that chimera is running the script instead of python and use getopt 
everywhere.

     -- Greg

On 03/15/2011 02:12 PM, Eric Pettersen wrote:
> On Mar 15, 2011, at 5:37 AM, wascm wrote:
>
>> 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)/
>
> There was an oversight in the code Greg provided:  chimeraInit.init 
> takes a mandatory "argv" argument, which is exactly like sys.argv.
>
>> -----------------------------------------------
>>
>> 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?
>
> Yes.  Use a --script argument, like this:
>
> chimera --nogui --script "test.py -t test"
>
> --Eric
>
>
>
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