Hi Edward.
Yep, the placement of the "nesting functions" in variables.py was not
the best place.
But I could not figure out where to do it better.
So model.py sound good.
Unit tests are implemented, and function fine.
One should note, that this nesting is breaking away from the method
described in the paper:
Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S.,
Tollinger, M., Teilum, K., Gagné, S., Marion, D., Griesinger, C.,
Blackledge, M., and d'Auvergne, E. J. (2014). relax: the analysis of
biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics.
http://dx.doi.org/10.1093/bioinformatics/btu166
It will not always nest from CR72 for example.
But it depends on which earlier models have already been analysed.
Order is:
Numerical, analytical
Same parameter / partial parameters
Best
Troels
2014-08-18 15:41 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
A table might be the best way to document this. It should include all
models and the table can be added to the manual (as a new section or
an expansion of the current nested parameter description). I would
highly recommend that unit tests are created, one for each model, to
make sure that the nesting occurs correctly and as expected for all
models.
Cheers,
Edward
On 18 August 2014 15:36, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi Troels,
This change requires a bit of work. Firstly the functions would be
better in their own module, as in the case of the
specific_analyses.model_free.model module. Secondly could you
document the parameter nesting you implemented in the nesting_model()
function? Is this different to the nesting() method of the Relax_disp
auto-analysis? What is its purpose? There are many ways to nest test
dispersion models, but here I am confused as to what is happening and
why.
Cheers,
Edward
On 12 August 2014 10:54, <tlinnet@xxxxxxxxxxxxx> wrote:
Author: tlinnet
Date: Tue Aug 12 10:54:39 2014
New Revision: 24984
URL: http://svn.gna.org/viewcvs/relax?rev=24984&view=rev
Log:
Implemented nesting function, which will determine which model to nest
from.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1
relaxation rate for the off-resonance R1rho relaxation dispersion models.
Modified:
branches/R1_fitting/specific_analyses/relax_disp/variables.py
branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/variables.py?rev=24984&r1=24983&r2=24984&view=diff
Modified:
branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py?rev=24984&r1=24983&r2=24984&view=diff
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Re: r24984 - in /branches/R1_fitting: specific_analyses/relax_disp/ test_suite/unit_tests/_specific_analyses/_relax_disp/