First, I tried the test-suite again, and it failed (new failures this time though :) )
#############################
# Results of the test suite #
#############################
Updated to revision 2654:
The model-free tests:
Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} ....... [ Failed ]
Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} ....... [ Failed ]
Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149} [ Failed ]
Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149
} [ Failed ]
then I tried running my data through each of the models. Sphere and higher produces the error:
RelaxError: The residue name argument 'G' is not valid regular _expression_.
There's no other error information to go off of. Sorry ...
Alex
On 10/19/06, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
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.