Re: [bug #8996] Bugs in palmer.py -- May 07, 2007

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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Re: [bug #8996] Bugs in palmer.py

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