Thanks. I've now written all the code required to handle the two Modelfree4 mfout column fusion bugs (the '*' characters fusing 2 columns and the 15.3f column widths with no empty spacing between not being enough (https://gna.org/bugs/?11483)). However, unlike bug #11476 (https://gna.org/bugs/?11476), I'm unable to test this new code. Seb, would you be able to either check this with your mfout file, or maybe attach the mfout file to the bug report https://gna.org/bugs/?11483 so I can test this. I would like to get this tested and the bug confirmed as being fixed before releasing a new version of relax.
Cheers, Edward On Sun, Apr 13, 2008 at 1:42 AM, Sébastien Morin <[EMAIL PROTECTED]> wrote: > > 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: <[EMAIL PROTECTED]>). > > An import description is given at: > > https://mail.gna.org/public/relax-devel/2008-04/msg00066.html (# > Message-id: <[EMAIL PROTECTED]>). > > 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 > <[EMAIL PROTECTED]> 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 > <[EMAIL PROTECTED]> 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 > > [email protected] > > > > 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 > > > > > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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
