[bug #11483] Parsing problem in ModelFree4 gets relax crash when using "palmer.py" -- April 13, 2008 - 01:44

URL:
  <http://gna.org/bugs/?11483>

                 Summary: Parsing problem in ModelFree4 gets relax crash when
using "palmer.py"
                 Project: relax
            Submitted by: semor
            Submitted on: Saturday 04/12/2008 at 19:44
                Category: relax's source code
                Severity: 3 - Normal
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: bugman
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: Repository: 1.2 line
        Operating System: GNU/Linux

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Details:

Hi,

I am using the script "palmer.py" to extract dynamic information by AIC model
selection using ModelFree4 as an optimization tool.

I get an error message when trying to extract parameters for model "m5"
during stage 2.

=========================
relax> palmer.extract(run='m5', dir=None)
Traceback (most recent call last):
 File "/home/semor/packages/relax-1.2/relax", line 454, in ?
   Relax()
 File "/home/semor/packages/relax-1.2/relax", line 166, in __init__
   self.interpreter.run()
 File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 216, in
run
   run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
 File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 391, in
run_script
   console.interact(intro, local, script_file, quit)
 File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 343, in
interact_script
   execfile(script_file, local)
 File "./palmer__stage_2.py", line 142, in ?
   exec_stage_2(runs)
 File "./palmer__stage_2.py", line 76, in exec_stage_2
   palmer.extract(run=name)
 File "/home/semor/packages/relax-1.2/prompt/palmer.py", line 263, in
extract
   self.__relax__.generic.palmer.extract(run=run, dir=dir)
 File "/home/semor/packages/relax-1.2/generic_fns/palmer.py", line 562, in
extract
   data.ts = data.ts / 1e12
TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'
=========================


I had a look at the "te" parameter and one line is badly formatted with an
absent separating field (no space between fields for value and error) :

=========================
246      10000.00019682363392.000    1          0.000          0.000         
0.000          0.000
=========================


This line should be :

=========================
246      10000.000 19682363392.000    1          0.000          0.000        
 0.000          0.000
=========================


This issue is caused by the ModelFree4 parser...

However, it could be catched by relax and re-formatted so that relax doesn't
crash ?

Thanks !




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