Re: [task #3838] Splitting up and redesigning the 'pdb()' user function. -- October 19, 2006

I think I have fixed up all the problems with the 'pdb.vectors()' user
function for reading in different atom names for different residues
(1.3 line).  Alex, could I ask another favour of you?  Would you be
able to re-test this function and see if this now works with your RNA
data?

Thanks,

Edward

On 10/14/06, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:

On 10/14/06, Alexandar Hansen <viochemist@xxxxxxxxx> wrote:
> That's my bad ... I forgot to use pdb.read(....) instead of pdb( .... ).
>
> However, Now I'm getting this traceback error for diffusion models not
> local_tm:
>
> Traceback (most recent call last):
>   File "relax", line 458, in ?
>     Relax()
>   File "relax", line 170, in __init__
>     self.interpreter.run()
>   File "/local/home/viochem/relax/prompt/interpreter.py",
> line 213, in run
>     run_script(intro=self.relax.intro_string , local=self.local,
> script_file=self.relax.script_file, quit=1)
>   File "/local/home/viochem/relax/prompt/interpreter.py",
> line 388, in run_script
>     console.interact(intro, local, script_file, quit)
>   File "/local/home/viochem/relax/prompt/interpreter.py",
> line 340, in interact_script
>     execfile(script_file, local)
>   File "full_analysis-sphere.py", line 437, in ?
>     Main()
>   File "full_analysis-sphere.py", line 194, in __init__
>     pdb.vectors(name, heteronuc=self.alex_het1 , proton=self.alex_hyd1,
> res_name=self.alex_res1)
>   File "/local/home/viochem/relax/prompt/pdb.py", line 202,
> in vectors
>     self.__relax__.generic.pdb.vectors(run=run,
> heteronuc=heteronuc, proton=proton, res_num=res_num, res_name=res_name)
> TypeError: vectors() got an unexpected keyword argument 'run'

Damn.  Looks like I forgot the run argument.  It's going to be good to
eliminate these things.  Actually, I won't have commit access for a
while.  Would you be able to replace the line:

    def vectors(self, heteronuc=None, proton=None, res_num=None, 
res_name=None):

with:

    def vectors(self, run=None, heteronuc=None, proton=None,
res_num=None, res_name=None):

in your copy (1.3) and retest it?  Thanks.  Oh the file is
'generic_fns/pdb.py' and the function is near the end.

Edward

Re: [task #3838] Splitting up and redesigning the 'pdb()' user function.

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