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

[Eric Pettersen]

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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