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.
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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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