Re: [Chimera-users] error: from DockPrep import prep
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"
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
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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participants (3)
-
Eric Pettersen -
Greg Couch -
wascm