Re: r8138 - /1.3/generic_fns/spectrum.py -- December 04, 2008 - 21:18

Hi,

It's not urgent to get this implemented as no one is currently waiting
for the code, and it doesn't effect the rest of the program.  I was
just offering a way out as even I would struggle with this job.  So
feel free to keep running with this (and I'll continue to drop many
hints).  As for relaxation dispersion analysis, I have recently
silently added some data to the test suite for this ;)  You can see it
in test_suite/shared_data/peak_lists/700mhz-263k-1m-*, though
obviously not complete.  The script
test_suite/system_tests/scripts/1UBQ_relax_fit.py uses this data, but
rather than doing relaxation dispersion, it is doing exponential
curve-fitting.  This can be copied and modified later for the new
'relax_disp' data pipe type.  And the S2 prediction would be a welcome
addition too.

Cheers,

Edward


On Thu, Dec 4, 2008 at 9:08 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
> Hi again Edward,
>
> Thanks for proposing some help !
>
> If this is not urgent, I would like to continue trying to make my way
> within this problem which allows me to progress quite fast in code
> development... However, if this is urgent, go ahead and take over right
> now as I will have plenty of other occasions to contribute (consistency
> tests improvements, jw mapping using multiple field data at once,
> relaxation dispersion analysis, S2 prediction using the contact model of
> Zhang & Bruschweiler, etc)...
>
> Regards,
>
>
> Séb  :)
>
>
>
> Edward d'Auvergne wrote:
> > Sorry, this task of the generic formatted file is far more complicated
> > than I thought.  It's structure should be modelled after the
> > generic_fns.value.read() function, as this takes a similarly formatted
> > file.  Flexibility here is key - any int arguments for the
> > mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col
> > should be acceptable.  I.e. you can put this information at the end of
> > the file if you are crazy enough.  But most of the code in
> > generic_fns.value.read() can be used.  It just needs to be shifted
> > into functions of generic_fns.spectrum such as
> > number_of_header_lines() and intensity_generic().
> >
> > In the future I might write some functions in generic_fns.mol_res_spin
> > to parse any spin specific but generically formatted file.  But for
> > now, the generic_fns.value.read() function needs to be mimicked.  This
> > is an insanely complex task, considering the additional flexibility I
> > talked about in
> > https://mail.gna.org/public/relax-devel/2008-12/msg00016.html
> > especially the automatic reading with the spin specific columns being
> > allowed to be anywhere.  So if you think this is too much, I can take
> > over at any point.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On Thu, Dec 4, 2008 at 7:30 PM,  <sebastien.morin.1@xxxxxxxxx> wrote:
> >
> > > Author: semor
> > > Date: Thu Dec  4 19:30:11 2008
> > > New Revision: 8138
> > >
> > > URL: http://svn.gna.org/viewcvs/relax?rev=8138&view=rev
> > > Log:
> > > Modified the autodetection code for the generic format.
> > >
> > > This now recognizes the most generic format as in
> > > 'test_suite/shared_data/peak_lists/generic_intensity2.txt'.
> > >
> > >
> > > Modified:
> > >    1.3/generic_fns/spectrum.py
> > >
> > > Modified: 1.3/generic_fns/spectrum.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=8138&r1=8137&r2=8138&view=diff
> > > ==============================================================================
> > > --- 1.3/generic_fns/spectrum.py (original)
> > > +++ 1.3/generic_fns/spectrum.py Thu Dec  4 19:30:11 2008
> > > @@ -254,7 +254,7 @@
> > >             break
> > >
> > >     # Generic format.
> > > -    if line[0] in ['mol_name', 'res_num', 'res_name', 'spin_num', 
> > > 'spin_name']:
> > > +    if line[0] in ['mol_name', 'res_num', 'res_name', 'spin_num', 
> > > 'spin_name'] or line[0] in ['Num', 'Name']:
> > >         return 'generic'
> > >
> > >     # Sparky format.
> > >
> > >
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