Re: Error message with the script "palmer.py"Re: Error message with the script "palmer.py"|
Hi again, The bug report is made. Ciao ! Séb Edward d'Auvergne wrote: This discussion overflows into the thread starting at: https://mail.gna.org/public/relax-devel/2008-04/msg00062.html (Message-id: <7f080ed10804121415r2032989fka786b656c6ab3b83@xxxxxxxxxxxxxx>). An import description is given at: https://mail.gna.org/public/relax-devel/2008-04/msg00066.html (# Message-id: <7f080ed10804121614u4d5b16f5rb58bfdf28f214392@xxxxxxxxxxxxxx>). Seb, would you be able to make a bug report for this issue? I can see the exact position in the get_mf_data() method to catch this. Cheers, Edward On Wed, Apr 9, 2008 at 10:12 AM, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:Hi, This problem is a hard one to handle. There is already a bit of code in relax's parser of Modelfree's mfout STAR formatted file which handles corrupted mfout files (the problem was with fused columns with many *****). But catching this one is much harder. The easy fix here it to put an upper limit on te when running Modelfree, or to get the print statements in Modelfree to have a single space between column format strings (like when relax uses "%s %s %8.3f" rather than "%s%s%8.3f). This problem, I'm pretty sure, is not handled by the STAR format itself and is simply a Modelfree output formatting bug. But despite this, relax could be modified to handle this type of corruption in the mfout file. Right now though, I can't think of a robust algorithm to handle this. It will have to be a check in the parser, but relying on there being exactly 3 decimal places in all floating point numbers in the mfout file is dangerous. The algorithm should handle column fusions anywhere in the mfout file where 2 floating point numbers are located side by side. I'll have to think about this one some more. Cheers, Edward On Tue, Apr 8, 2008 at 5:19 PM, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote: > Hi, > > I am using the script "palmer.py" to extract dynamic information using > AIC model selection, but ModelFree4 as an optimization tool. > > I tried the script several times before with a good success, however, I > now 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 (sometimes called "ts" in relax, but > always "te" in ModelFree4) and the values and errors are sometimes > extremely high... For example : > > ========================= > ... > 41 0.000 1279767296.000 1 0.000 > 0.000 0.000 0.000 > ... > 59 10000.000 215564320.000 1 0.000 > 0.000 0.000 0.000 > 60 10000.000 3750023168.000 1 0.000 > 0.000 0.000 0.000 > 61 10000.000 11655.404 1 0.000 > 0.000 0.000 0.000 > ... > ========================= > > > Also, on line is badly formatted with an absent separating field : > > ========================= > 246 10000.00019682363392.000 1 0.000 > 0.000 0.000 0.000 > ========================= > > > I modified the "mfout" file so this line is now : > > ========================= > 246 10000.00 19682363392.000 1 0.000 > 0.000 0.000 0.000 > ========================= > > > and the script now passes without any problem... > > This issue is probably caused by the ModelFree4 parser... However, do > you think it could be catched by relax and re-formatted so that relax > doesn't crash ? > > Thanks ! > Cheers, > > > Séb :) > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > relax-users@xxxxxxx > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users > |