Hi Carl,
I'm sorry about the delayed response. I have just moved from
Australia to Germany to start a postdoc and have been too busy to
reply to any email until now. Thank you for the bug report. I've
tried replicating the bug you have identified using your attached
files but unfortunately I have recently upgraded my system and
realised that relax doesn't function using Python 2.5. The relax
error system is completely broken. I'll fix that then try to fix your
problem.
Cheers,
Edward
On 4/25/07, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
>
> URL:
> <http://gna.org/bugs/?8996>
>
> Summary: Bugs in palmer.py
> Project: relax
> Submitted by: None
> Submitted on: Wednesday 04/25/2007 at 12:32 CEST
> Category: relax's source code
> Severity: 3 - Normal
> Priority: 5 - Normal
> Status: None
> Privacy: Public
> Assigned to: None
> Originator Name: Carl Diehl
> Originator Email: carl.diehl@xxxxxxxxx
> Open/Closed: Open
> Discussion Lock: Any
> Release: 1.2.10
> Operating System: GNU/Linux
>
> _______________________________________________________
>
> Details:
>
> The following bug were encountered while running the palmer.py script with
> stage=2, stage=1 worked fine with the original data.
>
>
> relax> run.create(run='aic', run_type='mf')
>
> relax> model_selection(method='AIC', modsel_run='aic', runs=None)
> AIC model selection.
>
> Instance 0.
>
> Run Num_params_(k) Num_data_sets_(n) Chi2
> Criterion
>
> The model from the run None has been selected.
>
> Instance 1.
>
> Run Num_params_(k) Num_data_sets_(n) Chi2
> Criterion
> m1 1 6 4.17590
> 6.17590
> m2 2 6 3.77440
> 7.77440
> m3 2 6 4.17590
> 8.17590
> m4 3 6 3.77440
> 9.77440
> m5 3 6 6.09960
> 12.09960
>
> The model from the run 'm1' has been selected.
>
> relax> results.write(run='aic', file='results', dir='aic', force=1,
> format='columnar', compress_type=1)
> Opening the file 'aic/results.bz2' for writing.
> Traceback (most recent call last):
> File "/home/matsl/carl/apps/relax-1.2.10/relax", line 454, in ?
> Relax()
> File "/home/matsl/carl/apps/relax-1.2.10/relax", line 166, in __init__
> self.interpreter.run()
> File "/home/matsl/carl/apps/relax-1.2.10/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 "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py", line 388,
> in run_script
> console.interact(intro, local, script_file, quit)
> File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py", line 340,
> in interact_script
> execfile(script_file, local)
> File "palmer.py", line 132, in ?
> exec_stage_2(runs)
> File "palmer.py", line 85, in exec_stage_2
> results.write(run=name, file='results', force=1)
> File "/home/matsl/carl/apps/relax-1.2.10/prompt/results.py", line 201, in
> write
> self.__relax__.generic.results.write(run=run, file=file, directory=dir,
> force=force, format=format, compress_type=compress_type)
> File "/home/matsl/carl/apps/relax-1.2.10/generic_fns/results.py", line
166,
> in write
> self.write_function(results_file, run)
> File "/home/matsl/carl/apps/relax-1.2.10/specific_fns/model_free.py", line
> 4980, in write_columnar_results
> self.write_columnar_line(file=file, num=data.num, name=data.name,
> select=data.select, data_set='error', nucleus=nucleus, model=model,
> equation=equation, params=params, param_set=self.param_set, s2=s2, s2f=s2f,
> s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa,
> diff_type=diff_type, diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
> pdb_heteronuc=data.heteronuc, pdb_proton=data.proton, xh_vect=xh_vect,
> ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels,
frq=frq,
> ri=ri, ri_error=ri_error)
> AttributeError: Element instance has no attribute 'heteronuc'
>
>
>
>
> _______________________________________________________
>
> File Attachments:
>
>
> -------------------------------------------------------
> Date: Wednesday 04/25/2007 at 12:32 CEST Name: palmer.py Size: 4kB By:
> None
>
> <http://gna.org/bugs/download.php?file_id=2268>
> -------------------------------------------------------
> Date: Wednesday 04/25/2007 at 12:32 CEST Name: stage1.save.bz2 Size: 3kB
> By: None
>
> <http://gna.org/bugs/download.php?file_id=2269>
>
> _______________________________________________________
>
> Reply to this item at:
>
> <http://gna.org/bugs/?8996>
>
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> http://gna.org/
>
>
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Re: [bug #8996] Bugs in palmer.py