Hi Edward.
I have already implemented this:
model_NEST = filter(partial(ne, self.model), model_NEST)
self.nest_list = model_NEST
Best
Troels
2014-08-19 14:34 GMT+02:00 Edward d'Auvergne <[email protected]>:
> I've looked at that bug. It's probably the case of just choosing the
> wrong relaxation time from the list for exponential curves - maybe the
> longest time would be best (actually any time should be fine as long
> as it is not 0). As this is just a bug, then using the 'NS R1rho
> 2-site' model for this purpose should be ok as, when the bug is
> solved, then this will be a non-issue.
>
> As for overriding the __setitem__() method, here it is for the
> diffusion tensor object:
>
> http://www.nmr-relax.com/api/3.2/data_store.diff_tensor.DiffTensorSimList-class.html#__setitem__
> http://www.nmr-relax.com/api/3.2/data_store.diff_tensor-pysrc.html#DiffTensorSimList.__setitem__
>
> Here it is used to prevent values being set. But the method can be
> made to check the input, that it's a list, and remove the model from
> the list that corresponds to the model being set. What do you think
> of this approach for filtering the model list? Here is a simple and
> functional code example:
>
> -----
> class A(dict):
> def __setitem__(self, key, val):
> if val == None:
> raise NameError("The value of None is not supported.")
> print("Setting the key '%s' to %s." % (key, val))
> dict.__setitem__(self, key, val)
>
> a = A()
> print(a)
> a['x'] = 10
> print(a)
> a['y'] = 'test'
> print(a)
> a['z'] = None
> print(a)
> -----
>
> As you can see, this is quite easy to set up. And creating a special
> method to pick the single model to use for nesting would also be easy,
>
> Regards,
>
> Edward
>
>
> On 19 August 2014 13:17, Troels Emtekær Linnet <[email protected]> wrote:
>> Hi Edward.
>>
>> I agree with your list, and aim for this,
>>
>> I though see a little error:
>> TP02 <- NS R1RHO 2-site, MP05, TAP03
>>
>> The analytical R1rho off resonance can't learn from NS R1RHO 2-site,
>> since there is a bug in this model.
>> bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has
>> extremely high chi2 value in systemtest
>> Relax_disp.test_r1rho_kjaergaard_missing_r1
>>
>>
>> Best
>> Troels
>>
>> 2014-08-19 12:23 GMT+02:00 Edward d'Auvergne <[email protected]>:
>>> Hi,
>>>
>>> Could these be turned into the MODEL_NEST dictionary? I.e. as you
>>> have done with the MODEL_DESC, MODEL_PARAMS, MODEL_YEAR,
>>> MODEL_EXP_TYPE, etc. I have expanded your table to the following.
>>> This is for the manual, which I am adding at the moment.
>>>
>>> R2EFF <- None
>>> NOREX <- None
>>> LM63 <- None
>>> LM63 3-site <- LM63
>>> CR72 <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site
>>> expanded, B14, CR72, NS CPMG 2-site 3D full, NS CPMG 2-site star full,
>>> B14 full, CR72 full
>>> CR72 full <- NS CPMG 2-site 3D full, NS CPMG 2-site star full, B14
>>> full, CR72 full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG
>>> 2-site expanded, B14, CR72
>>> IT99 <- None
>>> TSMFK01 <- None
>>> B14 <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site
>>> expanded, B14, CR72, NS CPMG 2-site 3D full, NS CPMG 2-site star full,
>>> B14 full, CR72 full
>>> B14 full <- NS CPMG 2-site 3D full, NS CPMG 2-site star full, B14
>>> full, CR72 full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG
>>> 2-site expanded, B14, CR72
>>> M61 <- None
>>> M61B <- None
>>> DPL94 <- None
>>> DPL94 R1 fit <- None
>>> TP02 <- MP05, TAP03, TP02
>>> TP02 R1 fit <- MP05 R1 fit, TAP03 R1 fit, TP02 R1 fit
>>> TAP03 <- MP05, TAP03, TP02
>>> TAP03 R1 fit <- MP05 R1 fit, TAP03 R1 fit, TP02 R1 fit
>>> MP05 <- MP05, TAP03, TP02
>>> MP05 R1 fit <- MP05 R1 fit, TAP03 R1 fit, TP02 R1 fit
>>> NS CPMG 2-site 3D <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG
>>> 2-site expanded, B14, CR72, NS CPMG 2-site 3D full, NS CPMG 2-site
>>> star full, B14 full, CR72 full
>>> NS CPMG 2-site 3D full <- NS CPMG 2-site 3D full, NS CPMG 2-site star
>>> full, B14 full, CR72 full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS
>>> CPMG 2-site expanded, B14, CR72
>>> NS CPMG 2-site star <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG
>>> 2-site expanded, B14, CR72, NS CPMG 2-site 3D full, NS CPMG 2-site
>>> star full, B14 full, CR72 full
>>> NS CPMG 2-site star full <- NS CPMG 2-site 3D full, NS CPMG 2-site
>>> star full, B14 full, CR72 full, NS CPMG 2-site 3D, NS CPMG 2-site
>>> star, NS CPMG 2-site expanded, B14, CR72
>>> NS CPMG 2-site expanded <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS
>>> CPMG 2-site expanded, B14, CR72, NS CPMG 2-site 3D full, NS CPMG
>>> 2-site star full, B14 full, CR72 full
>>> NS R1RHO 2-site <- MP05, TAP03, TP02
>>> NS R1RHO 2-site R1 fit <- MP05 R1 fit, TAP03 R1 fit, TP02 R1 fit
>>> NS R1RHO 3-site <- NS R1RHO 3-site linear, NS R1RHO 2-site, MP05, TAP03,
>>> TP02
>>> NS R1RHO 3-site linear <- NS R1RHO 3-site linear, NS R1RHO 2-site,
>>> MP05, TAP03, TP02
>>> MMQ CR72 <- NS MMQ 2-site, MMQ CR72, CR72
>>> NS MMQ 2-site <- NS MMQ 2-site, MMQ CR72, CR72
>>> NS MMQ 3-site <- NS MMQ 3-site linear, NS MMQ 2-site, MMQ CR72, CR72
>>> NS MMQ 3-site linear <- NS MMQ 2-site, MMQ CR72, CR72
>>>
>>> There are some issues here:
>>>
>>> 1) Because of model instability, we should exclude some of these
>>> combinations. For example:
>>>
>>> CR72 <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site
>>> expanded, B14, CR72, NS CPMG 2-site 3D full, NS CPMG 2-site star full,
>>> B14 full, CR72 full
>>>
>>> The model instability is in the '* full' models. No one really uses
>>> these in publications, other than theoretical ones, as they are rarely
>>> usable in practice. The separation of R20A != R20B introduces huge
>>> instabilities and possibly multiple minima in the space. The results
>>> from these models almost always terrible. For these models to be
>>> useful, some NMR spectroscopist needs to publish a comprehensive study
>>> of their optimisation properties. This is similar to to the 3-site
>>> model instability problems. Both problems are open-ended and not yet
>>> solved by the dispersion field.
>>>
>>> 2) Another problem is with the MMQ models. CR72 cannot be used for
>>> these, as CR72 does not support all of the MMQ experiment types and
>>> hence cannot be optimised.
>>>
>>> 3) There is model duplication. CR72 is listed as a nested model for
>>> CR72, etc. A special MODEL_NEST dictionary object where the
>>> set_deps() or __setitem__() method removes the 'self' model before
>>> storing the list would be useful for this purpose (see
>>> http://thread.gmane.org/gmane.science.nmr.relax.devel/6684/focus=6685
>>> and
>>> http://www.diveintopython.net/object_oriented_framework/special_class_methods.html).
>>>
>>> 4) The 'NS R1rho 2-site' model is not used for the analytic R1rho
>>> models, as the 'NS CPMG *' models are for the analytic CPMG models.
>>>
>>> Therefore a better table eliminated or fixing these problems would be:
>>>
>>> R2EFF <- None
>>> NOREX <- None
>>> LM63 <- None
>>> LM63 3-site <- LM63
>>> CR72 <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site expanded, B14
>>> CR72 full <- NS CPMG 2-site 3D full, NS CPMG 2-site star full, B14
>>> full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site expanded,
>>> B14, CR72
>>> IT99 <- None
>>> TSMFK01 <- None
>>> B14 <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site expanded, CR72
>>> B14 full <- NS CPMG 2-site 3D full, NS CPMG 2-site star full, CR72
>>> full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site expanded,
>>> B14, CR72
>>> NS CPMG 2-site expanded <- NS CPMG 2-site 3D, NS CPMG 2-site star, NS
>>> CPMG 2-site expanded, B14, CR72
>>> NS CPMG 2-site 3D <- NS CPMG 2-site star, NS CPMG 2-site expanded, B14, CR72
>>> NS CPMG 2-site 3D full <- NS CPMG 2-site star full, B14 full, CR72
>>> full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site expanded,
>>> B14, CR72
>>> NS CPMG 2-site star <- NS CPMG 2-site 3D, NS CPMG 2-site expanded, B14, CR72
>>> NS CPMG 2-site star full <- NS CPMG 2-site 3D full, B14 full, CR72
>>> full, NS CPMG 2-site 3D, NS CPMG 2-site star, NS CPMG 2-site expanded,
>>> B14, CR72
>>> M61 <- None
>>> M61B <- None
>>> DPL94 <- None
>>> DPL94 R1 fit <- None
>>> TP02 <- NS R1RHO 2-site, MP05, TAP03
>>> TP02 R1 fit <- MP05 R1 fit, TAP03 R1 fit
>>> TAP03 <- NS R1RHO 2-site, MP05, TP02
>>> TAP03 R1 fit <- MP05 R1 fit, TP02 R1 fit
>>> MP05 <- NS R1RHO 2-site, TAP03, TP02
>>> MP05 R1 fit <- TAP03 R1 fit, TP02 R1 fit
>>> NS R1RHO 2-site <- MP05, TAP03, TP02
>>> NS R1RHO 2-site R1 fit <- MP05 R1 fit, TAP03 R1 fit, TP02 R1 fit
>>> NS R1RHO 3-site linear <- NS R1RHO 2-site, MP05, TAP03, TP02
>>> NS R1RHO 3-site <- NS R1RHO 3-site linear, NS R1RHO 2-site, MP05, TAP03,
>>> TP02
>>> MMQ CR72 <- NS MMQ 2-site
>>> NS MMQ 2-site <- MMQ CR72
>>> NS MMQ 3-site linear <- NS MMQ 2-site, MMQ CR72
>>> NS MMQ 3-site <- NS MMQ 3-site linear, NS MMQ 2-site, MMQ CR72
>>>
>>> What do you think? I will add this version to the manual.
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>> P. S. Note that CR72 should always be optimised before the numerical
>>> models! A grid search for the numerical models is pretty much
>>> impossible - it takes far too long. As the CR72 model will always be
>>> optimised before the numeric models in the auto-analysis (I can add
>>> the ordering function, if required), then having the NS models in the
>>> list is not needed. This is really a massively important part of the
>>> paper (http://dx.doi.org/10.1093/bioinformatics/btu166). The CR72
>>> model is very stable and is in the most number of cases the best
>>> approximation for the numerical solution. Of course, now we have B14
>>> which is better. But CR72 is really fast and using it as a starting
>>> point for the other CPMG models really massively speeds up an analysis
>>> with the NS models.
>>>
>>> On 19 August 2014 10:50, Troels Emtekær Linnet <[email protected]>
>>> wrote:
>>>> Hi Edward.
>>>>
>>>> After having sleeping on it, I will now change to a hard-coded version.
>>>>
>>>> You will see, that I have some differences from you.
>>>>
>>>> I will also accept, that CR72 can learn from the other similar models.
>>>>
>>>> I cannot see the argument, why this should not be the case?
>>>>
>>>>
>>>> It looks like this:
>>>> ------------
>>>>
>>>> # Define recurring lists.
>>>> ## For CPMG.
>>>> MODEL_NEST_LIST_CPMG = [MODEL_NS_CPMG_2SITE_3D,
>>>> MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_B14,
>>>> MODEL_CR72]
>>>> MODEL_NEST_LIST_CPMG_R20B = [MODEL_NS_CPMG_2SITE_3D_FULL,
>>>> MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_B14_FULL, MODEL_CR72_FULL]
>>>> ## For R1rho.
>>>> MODEL_NEST_LIST_R1RHO_2SITE = [MODEL_MP05, MODEL_TAP03, MODEL_TP02]
>>>> MODEL_NEST_LIST_R1RHO_2SITE_FIT_R1 = [MODEL_MP05_FIT_R1,
>>>> MODEL_TAP03_FIT_R1, MODEL_TP02_FIT_R1]
>>>> MODEL_NEST_LIST_R1RHO_3SITE = [MODEL_NS_R1RHO_3SITE_LINEAR,
>>>> MODEL_NS_R1RHO_2SITE]
>>>> ## For CPMG MMQ.
>>>> MODEL_NEST_LIST_MMQ_2SITE = [MODEL_NS_MMQ_2SITE, MODEL_MMQ_CR72,
>>>> MODEL_CR72]
>>>> MODEL_NEST_LIST_MMQ_3SITE = [MODEL_NS_MMQ_3SITE_LINEAR]
>>>>
>>>> # Define order of nesting models for each model.
>>>> MODEL_NEST_R2EFF = None
>>>> MODEL_NEST_NOREX = None
>>>> MODEL_NEST_NOREX_R1RHO = None
>>>> MODEL_NEST_NOREX_R1RHO_FIT_R1 = None
>>>> MODEL_NEST_LM63 = None
>>>> MODEL_NEST_LM63_3SITE = [MODEL_LM63]
>>>> MODEL_NEST_CR72 = MODEL_NEST_LIST_CPMG + MODEL_NEST_LIST_CPMG_R20B
>>>> MODEL_NEST_CR72_FULL = MODEL_NEST_LIST_CPMG_R20B + MODEL_NEST_LIST_CPMG
>>>> MODEL_NEST_IT99 = None
>>>> MODEL_NEST_TSMFK01 = None
>>>> MODEL_NEST_B14 = MODEL_NEST_LIST_CPMG + MODEL_NEST_LIST_CPMG_R20B
>>>> MODEL_NEST_B14_FULL = MODEL_NEST_LIST_CPMG_R20B + MODEL_NEST_LIST_CPMG
>>>> MODEL_NEST_M61 = None
>>>> MODEL_NEST_M61B = None
>>>> MODEL_NEST_DPL94 = None
>>>> MODEL_NEST_DPL94_FIT_R1 = None
>>>> MODEL_NEST_TP02 = MODEL_NEST_LIST_R1RHO_2SITE
>>>> MODEL_NEST_TP02_FIT_R1 = MODEL_NEST_LIST_R1RHO_2SITE_FIT_R1
>>>> MODEL_NEST_TAP03 = MODEL_NEST_LIST_R1RHO_2SITE
>>>> MODEL_NEST_TAP03_FIT_R1 = MODEL_NEST_LIST_R1RHO_2SITE_FIT_R1
>>>> MODEL_NEST_MP05 = MODEL_NEST_LIST_R1RHO_2SITE
>>>> MODEL_NEST_MP05_FIT_R1 = MODEL_NEST_LIST_R1RHO_2SITE_FIT_R1
>>>> MODEL_NEST_NS_CPMG_2SITE_3D = MODEL_NEST_LIST_CPMG +
>>>> MODEL_NEST_LIST_CPMG_R20B
>>>> MODEL_NEST_NS_CPMG_2SITE_3D_FULL = MODEL_NEST_LIST_CPMG_R20B +
>>>> MODEL_NEST_LIST_CPMG
>>>> MODEL_NEST_NS_CPMG_2SITE_STAR = MODEL_NEST_LIST_CPMG +
>>>> MODEL_NEST_LIST_CPMG_R20B
>>>> MODEL_NEST_NS_CPMG_2SITE_STAR_FULL = MODEL_NEST_LIST_CPMG_R20B +
>>>> MODEL_NEST_LIST_CPMG
>>>> MODEL_NEST_NS_CPMG_2SITE_EXPANDED = MODEL_NEST_LIST_CPMG +
>>>> MODEL_NEST_LIST_CPMG_R20B
>>>> MODEL_NEST_NS_R1RHO_2SITE = MODEL_NEST_LIST_R1RHO_2SITE
>>>> MODEL_NEST_NS_R1RHO_2SITE_FIT_R1 = MODEL_NEST_LIST_R1RHO_2SITE_FIT_R1
>>>> MODEL_NEST_NS_R1RHO_3SITE = MODEL_NEST_LIST_R1RHO_3SITE +
>>>> MODEL_NEST_LIST_R1RHO_2SITE
>>>> MODEL_NEST_NS_R1RHO_3SITE_LINEAR = MODEL_NEST_LIST_R1RHO_3SITE +
>>>> MODEL_NEST_LIST_R1RHO_2SITE
>>>> MODEL_NEST_MMQ_CR72 = MODEL_NEST_LIST_MMQ_2SITE
>>>> MODEL_NEST_NS_MMQ_2SITE = MODEL_NEST_LIST_MMQ_2SITE
>>>> MODEL_NEST_NS_MMQ_3SITE = MODEL_NEST_LIST_MMQ_3SITE +
>>>> MODEL_NEST_LIST_MMQ_2SITE
>>>> MODEL_NEST_NS_MMQ_3SITE_LINEAR = MODEL_NEST_LIST_MMQ_2SITE
>>>>
>>>> 2014-08-19 10:21 GMT+02:00 Edward d'Auvergne <[email protected]>:
>>>>> Hi,
>>>>>
>>>>> Here is a mini-proposal for a special Python dictionary object to help
>>>>> with dispersion model nesting:
>>>>>
>>>>> -----
>>>>> class Model_nesting(dict):
>>>>> """Special object for handling model nesting for avoiding the grid
>>>>> search."""
>>>>>
>>>>> def get_deps(self, model):
>>>>> """Return the dependency list for the given model."""
>>>>>
>>>>> return self[model]
>>>>>
>>>>>
>>>>> def set_deps(self, model, deps=None):
>>>>> """Set the model dependency list for the given model."""
>>>>>
>>>>> self[model] = deps
>>>>>
>>>>>
>>>>> MODEL_NESTING = Model_nesting()
>>>>> MODEL_NESTING['B14 full'] = ['CR72 full', 'B14', 'CR72']
>>>>> -----
>>>>>
>>>>> The class would be in the specific_analyses.relax_disp.models module
>>>>> and the MODEL_NESTING instantiation in the
>>>>> specific_analyses.relax_disp.variables module. This can have error
>>>>> checking added and additional methods for manipulating the data added.
>>>>> The get_deps() and set_deps() methods are optional for the power user.
>>>>> They may be useful if the __getattr__(), __getitem__(), __setattr__(),
>>>>> and __setitem__() methods are overridden to allow for better object
>>>>> control (see the objects in the data_store package for how this is
>>>>> done). A get_dep() method could be added which accepts the model and
>>>>> a list of the currently optimised models and then returns the nested
>>>>> model to be used or None, i.e. to implement the model preference.
>>>>>
>>>>> Or, this could just be a normal Python dictionary rather than a
>>>>> special dictionary object. Such an object could be used by relax
>>>>> power users, via scripting, to implement their own relaxation
>>>>> dispersion analysis protocol. But this is just an idea and many
>>>>> alternatives exist.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Edward
>>>>>
>>>>>
>>>>> On 19 August 2014 10:07, Edward d'Auvergne <[email protected]> wrote:
>>>>>> Hi Troels,
>>>>>>
>>>>>> This continues from
>>>>>> http://thread.gmane.org/gmane.science.nmr.relax.scm/22733/, and all
>>>>>> the related threads. For the change of r25060
>>>>>> (http://article.gmane.org/gmane.science.nmr.relax.scm/22810), could
>>>>>> you please document all cases? I.e. model x takes its parameters from
>>>>>> model y, and then do this for all models. See the table below for how
>>>>>> to document this. This algorithm really worries me and I strongly
>>>>>> think that this development is in the wrong direction. All models are
>>>>>> special cases! You can't just take any model as the starting point
>>>>>> for another. The following ordering is not a good idea:
>>>>>>
>>>>>> 1) EQ_NUMERIC, EQ_SILICO, EQ_ANALYTIC.
>>>>>> 2) Year (from newest).
>>>>>> 3) Number of sites.
>>>>>>
>>>>>> Models should be rather classified in the following groups:
>>>>>>
>>>>>> 1) Parameter nesting (related to 2). The models should ideally have
>>>>>> identical parameter sets.
>>>>>> 2) Fast exchange, slow exchange, very slow exchange, vs. all exchange
>>>>>> regimes. These are mutually exclusive (apart from the last).
>>>>>> 3) The pA >> pB limit - this can never be mixed with the normal pA >
>>>>>> pB condition.
>>>>>> 4) Model stability (i.e. stable vs. unstable).
>>>>>> 5) Model accuracy.
>>>>>> 6) Analytic vs. numeric.
>>>>>>
>>>>>> This is in order of importance. Part 2) here excludes most
>>>>>> combinations of the new algorithm - you cannot mix the models for
>>>>>> different mutually exclusive exchange regimes.
>>>>>>
>>>>>> The one and only aim is for speed by avoiding the grid search,
>>>>>> therefore the nested model from which the parameters are copied from
>>>>>> must be a good estimate for the solution of the target model. I would
>>>>>> then propose the following table mapping models to nested models for
>>>>>> avoiding the grid search. The order is also the order of
>>>>>> optimisation, as you will see from the nested model dependencies. The
>>>>>> proposal is:
>>>>>>
>>>>>> R2eff <- None
>>>>>> No Rex <- None
>>>>>>
>>>>>> LM63 <- None
>>>>>> LM63 3-site <- LM63
>>>>>> CR72 <- None
>>>>>> CR72 full <- CR72
>>>>>> IT99 <- None
>>>>>> TSMFK01 <- None
>>>>>> B14 <- CR72
>>>>>> B14 full <- CR72 full, B14, CR72
>>>>>> NS CPMG 2-site expanded <- B14, CR72
>>>>>> NS CPMG 2-site 3D <- NS CPMG 2-site expanded, B14, CR72
>>>>>> NS CPMG 2-site 3D full <- B14 full, CR72 full, NS CPMG 2-site
>>>>>> expanded, B14, CR72
>>>>>> NS CPMG 2-site star <- NS CPMG 2-site expanded, B14, CR72
>>>>>> NS CPMG 2-site star full <- B14 full, CR72 full, NS CPMG 2-site
>>>>>> expanded, B14, CR72
>>>>>>
>>>>>> M61 <- None
>>>>>> M61 skew <- None
>>>>>> DPL94 <- None
>>>>>> DPL94 R1 fit <- DPL94
>>>>>> TP02 <- None
>>>>>> TP02 R1 fit <- TP02
>>>>>> TAP03 <- None
>>>>>> TAP03 R1 fit <- TAP03
>>>>>> MP05 <- TAP03, TP02
>>>>>> MP05 R1 fit <- MP05, TAP03, TP02
>>>>>> NS R1rho 2-site <- MP05, TAP03, TP02
>>>>>> NS R1rho 2-site R1 fit <- NS R1rho 2-site, MP05, TAP03, TP02
>>>>>> NS R1rho 3-site linear <- NS R1rho 2-site, MP05, TAP03, TP02
>>>>>> NS R1rho 3-site <- NS R1rho 3-site linear, NS R1rho 2-site,
>>>>>> MP05, TAP03, TP02
>>>>>>
>>>>>> MMQ CR72 <- None
>>>>>> NS MMQ 2-site <- MMQ CR72
>>>>>> NS MMQ 3-site linear <- NS MMQ 2-site, MMQ CR72
>>>>>> NS MMQ 3-site <- NS MMQ 3-site linear, NS MMQ 2-site, MMQ CR72
>>>>>>
>>>>>> In the second column, the list of models indicate importance. For
>>>>>> example for the 'B14 full' model, the 'CR72 full' model is the first
>>>>>> preference. If that model has not been optimised, then B14 is used.
>>>>>> And if B14 is missing, the fall back is to CR72. If none of these
>>>>>> models have been optimised, the grid search will be performed. In
>>>>>> this case, 'CR72 full' is preferred as it has perfect parameter
>>>>>> nesting - all parameters of 'B14 full' are found in 'CR72 full'. The
>>>>>> B14 and CR72 are fallbacks - here R20A and R20B are copied from R20 so
>>>>>> they start optimisation as R20A == R20B. Hence 'CR72 full' whereby
>>>>>> R20A != R20B is a much better starting point as R20A and R20B have
>>>>>> been optimised to different values. But the large model instability
>>>>>> in 'CR72 full' might make the user want to start with 'B14'.
>>>>>>
>>>>>> For the '* R1 fit' models, this nesting is of little interest in
>>>>>> experimental cases, as you either measure R1 data or not (measuring it
>>>>>> is always preferable for model stability). Some people who have
>>>>>> measured R1 data might still be interested in what will if R1 is
>>>>>> nevertheless optimised, so that nesting could be of use.
>>>>>>
>>>>>> This nesting table is complete as far as I can tell. Some of this
>>>>>> nesting could be still argued to be wrong, for example TP02 with pA <<
>>>>>> pB as a starting point. I would not use any other nesting for fear of
>>>>>> creating a very bad optimisation starting position. The table is very
>>>>>> easy to extend for new models as well. But because of model
>>>>>> instability, the user may wish to change this nesting.
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Edward
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 18 August 2014 18:11, Edward d'Auvergne <[email protected]> wrote:
>>>>>>> Hi Troels,
>>>>>>>
>>>>>>> I will continue from your last post in the triplet thread at
>>>>>>> http://thread.gmane.org/gmane.science.nmr.relax.scm/22737. I have
>>>>>>> copied and pasted your message below:
>>>>>>>
>>>>>>> On 18 August 2014 17:17, Troels Emtekær Linnet <[email protected]>
>>>>>>> wrote:
>>>>>>>> I will remove the nesting of IT99, since it also worried me.
>>>>>>>
>>>>>>> I would also suggest removing TSMFK01, TAP03, M61, M61 skew, and DPL94.
>>>>>>>
>>>>>>>
>>>>>>>> But do you really intent to stay on the argument that nesting should
>>>>>>>> always be from CR72?
>>>>>>>
>>>>>>> No, we need a 3rd solution for this.
>>>>>>>
>>>>>>>
>>>>>>>> What if the model pipe for B14 is available.
>>>>>>>> Or from NS CPMG 2-site expanded ?
>>>>>>>
>>>>>>> We could, for example, have a list of nested models. For example for
>>>>>>> the NS CPMG 2-site expanded model, the list would be [MODEL_B41,
>>>>>>> MODEL_CR72]. It used B14 first, but switches to CR72 if B14 is not
>>>>>>> available. This is easy to hardcode in a dictionary (or special
>>>>>>> Python dictionary object) and hardcode into a table in the manual.
>>>>>>>
>>>>>>> For all of the numeric CPMG models, which should be optimised after
>>>>>>> the analytic models in all cases so that model nesting can be useful
>>>>>>> for speed, I would suggest using B14 and then CR72. But if you have
>>>>>>> fast exchange, then the LM63 model is far better for these models than
>>>>>>> B14 or CR72, however the parameters are not nested. There are
>>>>>>> infinite parameter combinations of the numeric models which give the
>>>>>>> same parameter values as LM63.
>>>>>>>
>>>>>>> For the R1rho models, a similar logic would be used. MP05 replaces
>>>>>>> B14, and TP02 replaces CR72. The BK13 model will also need to be
>>>>>>> considered in the future (https://gna.org/support/?3155). DPL94
>>>>>>> replaces LM63 for the fast vs. slow exchange problem, but then you
>>>>>>> also have the infinite parameter combination problem.
>>>>>>>
>>>>>>> Note that the infinite parameter combination problem is actually a
>>>>>>> major issue affecting the optimisation of all numeric models when the
>>>>>>> exchange is fast, but that no one talks about this!
>>>>>>>
>>>>>>>
>>>>>>>> Is this issue rather related how to sort the models first?
>>>>>>>
>>>>>>> This is an important issue which requires knowledge of the nesting, as
>>>>>>> I mentioned previously. Our understanding of the models themselves
>>>>>>> and our logic based on experiment is far more useful for determining
>>>>>>> model nesting and the order in which they should be optimised. This
>>>>>>> is why a hardcoded solution is very powerful.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Edward
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 12 August 2014 10:54, <[email protected]> wrote:
>>>>>>>> Author: tlinnet
>>>>>>>> Date: Tue Aug 12 10:54:36 2014
>>>>>>>> New Revision: 24983
>>>>>>>>
>>>>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=24983&view=rev
>>>>>>>> Log:
>>>>>>>> Added meta information about equation type.
>>>>>>>>
>>>>>>>> The models are dividided into: analytic, silico or numeric.
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>> 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=24983&r1=24982&r2=24983&view=diff
>>>>>>>> ==============================================================================
>>>>>>>> --- branches/R1_fitting/specific_analyses/relax_disp/variables.py
>>>>>>>> (original)
>>>>>>>> +++ branches/R1_fitting/specific_analyses/relax_disp/variables.py
>>>>>>>> Tue Aug 12 10:54:36 2014
>>>>>>>> @@ -59,6 +59,12 @@
>>>>>>>> """The list of all dispersion experiment types."""
>>>>>>>>
>>>>>>>>
>>>>>>>> +# Model equation types. Either analytic, silico or numeric.
>>>>>>>> +EQ_ANALYTIC = 'analytic'
>>>>>>>> +EQ_NUMERIC = 'numeric'
>>>>>>>> +EQ_SILICO = 'silico'
>>>>>>>> +
>>>>>>>> +
>>>>>>>> # The model names, parameters, and descriptions.
>>>>>>>> MODEL_R2EFF = 'R2eff'
>>>>>>>> MODEL_DESC_R2EFF = "The model for determining the R2eff/R1rho values
>>>>>>>> from peak intensities."
>>>>>>>> @@ -67,6 +73,7 @@
>>>>>>>> MODEL_YEAR_R2EFF = 1950
>>>>>>>> MODEL_EXP_TYPE_R2EFF = EXP_TYPE_R2EFF
>>>>>>>> MODEL_SITES_R2EFF = None
>>>>>>>> +MODEL_EQ_R2EFF = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_NOREX = 'No Rex'
>>>>>>>> MODEL_DESC_NOREX = "The model for no chemical exchange relaxation."
>>>>>>>> @@ -75,6 +82,7 @@
>>>>>>>> MODEL_YEAR_NOREX = 1951
>>>>>>>> MODEL_EXP_TYPE_NOREX = EXP_TYPE_NOREX
>>>>>>>> MODEL_SITES_NOREX = 1
>>>>>>>> +MODEL_EQ_NOREX = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_NOREX_R1RHO = "No_Rex_R1rho_off_res"
>>>>>>>> MODEL_DESC_NOREX_R1RHO = "The model for no chemical exchange
>>>>>>>> relaxation, for R1rho off resonance models."
>>>>>>>> @@ -83,6 +91,7 @@
>>>>>>>> MODEL_YEAR_NOREX_R1RHO = 1952
>>>>>>>> MODEL_EXP_TYPE_NOREX_R1RHO = EXP_TYPE_NOREX_R1RHO
>>>>>>>> MODEL_SITES_NOREX_R1RHO = 1
>>>>>>>> +MODEL_EQ_NOREX_R1RHO = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_NOREX_R1RHO_FIT_R1 = "%s_fit_r1"%MODEL_NOREX_R1RHO
>>>>>>>> MODEL_DESC_NOREX_R1RHO_FIT_R1 = "The model for no chemical exchange
>>>>>>>> relaxation, for R1rho off resonance models, where R1 is fitted."
>>>>>>>> @@ -91,6 +100,7 @@
>>>>>>>> MODEL_YEAR_NOREX_R1RHO_FIT_R1 = 1953
>>>>>>>> MODEL_EXP_TYPE_NOREX_R1RHO_FIT_R1 = EXP_TYPE_NOREX_R1RHO
>>>>>>>> MODEL_SITES_NOREX_R1RHO_FIT_R1 = 1
>>>>>>>> +MODEL_EQ_NOREX_R1RHO_FIT_R1 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_LM63 = 'LM63'
>>>>>>>> MODEL_DESC_LM63 = "The Luz and Meiboom (1963) 2-site fast exchange
>>>>>>>> model for SQ-CPMG experiments."
>>>>>>>> @@ -98,6 +108,7 @@
>>>>>>>> MODEL_YEAR_LM63 = 1963
>>>>>>>> MODEL_EXP_TYPE_LM63 = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_LM63 = 2
>>>>>>>> +MODEL_EQ_LM63 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_LM63_3SITE = 'LM63 3-site'
>>>>>>>> MODEL_DESC_LM63_3SITE = "The Luz and Meiboom (1963) 3-site fast
>>>>>>>> exchange model for SQ-CPMG experiments."
>>>>>>>> @@ -105,6 +116,7 @@
>>>>>>>> MODEL_YEAR_LM63_3SITE = 1963
>>>>>>>> MODEL_EXP_TYPE_LM63_3SITE = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_LM63_3SITE = 3
>>>>>>>> +MODEL_EQ_LM63_3SITE = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_CR72 = 'CR72'
>>>>>>>> MODEL_DESC_CR72 = "The reduced Carver and Richards (1972) 2-site
>>>>>>>> model for all time scales for SQ-CPMG experiments, whereby the
>>>>>>>> simplification R20A = R20B is assumed."
>>>>>>>> @@ -112,6 +124,7 @@
>>>>>>>> MODEL_YEAR_CR72 = 1972
>>>>>>>> MODEL_EXP_TYPE_CR72 = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_CR72 = 2
>>>>>>>> +MODEL_EQ_CR72 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_CR72_FULL = 'CR72 full'
>>>>>>>> MODEL_DESC_CR72_FULL = "The full Carver and Richards (1972) 2-site
>>>>>>>> model for all time scales for SQ-CPMG experiments."
>>>>>>>> @@ -119,6 +132,7 @@
>>>>>>>> MODEL_YEAR_CR72_FULL = 1972
>>>>>>>> MODEL_EXP_TYPE_CR72_FULL = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_CR72_FULL = 2
>>>>>>>> +MODEL_EQ_CR72_FULL = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_IT99 = 'IT99'
>>>>>>>> MODEL_DESC_IT99 = "The Ishima and Torchia (1999) 2-site CPMG model
>>>>>>>> for all time scales for SQ-CPMG experiments, with skewed populations
>>>>>>>> (pA >> pB)."
>>>>>>>> @@ -126,6 +140,7 @@
>>>>>>>> MODEL_YEAR_IT99 = 1999
>>>>>>>> MODEL_EXP_TYPE_IT99 = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_IT99 = 2
>>>>>>>> +MODEL_EQ_IT99 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_TSMFK01 = 'TSMFK01'
>>>>>>>> MODEL_DESC_TSMFK01 = "The Tollinger et al. (2001) 2-site very-slow
>>>>>>>> exchange model for SQ-CPMG experiments."
>>>>>>>> @@ -133,6 +148,7 @@
>>>>>>>> MODEL_YEAR_TSMFK01 = 2001
>>>>>>>> MODEL_EXP_TYPE_TSMFK01 = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_TSMFK01 = 2
>>>>>>>> +MODEL_EQ_TSMFK01 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_B14 = 'B14'
>>>>>>>> MODEL_DESC_B14 = "The Baldwin (2014) 2-site CPMG exact solution model
>>>>>>>> for all time scales for SQ-CPMG experiments, whereby the
>>>>>>>> simplification R20A = R20B is assumed."
>>>>>>>> @@ -140,6 +156,7 @@
>>>>>>>> MODEL_YEAR_B14 = 2014
>>>>>>>> MODEL_EXP_TYPE_B14 = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_B14 = 2
>>>>>>>> +MODEL_EQ_B14 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_B14_FULL = 'B14 full'
>>>>>>>> MODEL_DESC_B14_FULL = "The Baldwin (2014) 2-site CPMG exact solution
>>>>>>>> model for all time scales for SQ-CPMG experiments."
>>>>>>>> @@ -147,6 +164,7 @@
>>>>>>>> MODEL_YEAR_B14_FULL = 2014
>>>>>>>> MODEL_EXP_TYPE_B14_FULL = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_B14_FULL = 2
>>>>>>>> +MODEL_EQ_B14_FULL = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_M61 = 'M61'
>>>>>>>> MODEL_DESC_M61 = "The Meiboom (1961) on-resonance 2-site fast
>>>>>>>> exchange model for R1rho-type experiments."
>>>>>>>> @@ -154,6 +172,7 @@
>>>>>>>> MODEL_YEAR_M61 = 1961
>>>>>>>> MODEL_EXP_TYPE_M61 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_M61 = 2
>>>>>>>> +MODEL_EQ_M61 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_M61B = 'M61 skew'
>>>>>>>> MODEL_DESC_M61B = "The Meiboom (1961) on-resonance 2-site model for
>>>>>>>> R1rho-type experiments, with skewed populations (pA >> pB)."
>>>>>>>> @@ -161,6 +180,7 @@
>>>>>>>> MODEL_YEAR_M61B = 1961
>>>>>>>> MODEL_EXP_TYPE_M61B = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_M61B = 2
>>>>>>>> +MODEL_EQ_M61B = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_DPL94 = 'DPL94'
>>>>>>>> """The R1rho 2-site fast exchange model of Davis, Perlman and London
>>>>>>>> (1994)."""
>>>>>>>> @@ -169,6 +189,7 @@
>>>>>>>> MODEL_YEAR_DPL94 = 1994
>>>>>>>> MODEL_EXP_TYPE_DPL94 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_DPL94 = 2
>>>>>>>> +MODEL_EQ_DPL94 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_DPL94_FIT_R1 = "%s_fit_r1"%MODEL_DPL94
>>>>>>>> """The R1rho 2-site fast exchange model of Davis, Perlman and London
>>>>>>>> (1994), where R1 is fitted."""
>>>>>>>> @@ -177,6 +198,7 @@
>>>>>>>> MODEL_YEAR_DPL94_FIT_R1 = 1994
>>>>>>>> MODEL_EXP_TYPE_DPL94_FIT_R1 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_DPL94_FIT_R1 = 2
>>>>>>>> +MODEL_EQ_DPL94_FIT_R1 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_TP02 = 'TP02'
>>>>>>>> MODEL_DESC_TP02 = "The Trott and Palmer (2002) off-resonance 2-site
>>>>>>>> model for R1rho-type experiments."
>>>>>>>> @@ -184,6 +206,7 @@
>>>>>>>> MODEL_YEAR_TP02 = 2002
>>>>>>>> MODEL_EXP_TYPE_TP02 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_TP02 = 2
>>>>>>>> +MODEL_EQ_TP02 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_TP02_FIT_R1 = "%s_fit_r1"%MODEL_TP02
>>>>>>>> MODEL_DESC_TP02_FIT_R1 = "The Trott and Palmer (2002) off-resonance
>>>>>>>> 2-site model for R1rho-type experiments, where R1 is fitted."
>>>>>>>> @@ -191,6 +214,7 @@
>>>>>>>> MODEL_YEAR_TP02_FIT_R1 = 2002
>>>>>>>> MODEL_EXP_TYPE_TP02_FIT_R1 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_TP02_FIT_R1 = 2
>>>>>>>> +MODEL_EQ_TP02_FIT_R1 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_TAP03 = 'TAP03'
>>>>>>>> MODEL_DESC_TAP03 = "The Trott, Abergel and Palmer (2003)
>>>>>>>> off-resonance 2-site model for R1rho-type experiments."
>>>>>>>> @@ -198,6 +222,7 @@
>>>>>>>> MODEL_YEAR_TAP03 = 2003
>>>>>>>> MODEL_EXP_TYPE_TAP03 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_TAP03 = 2
>>>>>>>> +MODEL_EQ_TAP03 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_TAP03_FIT_R1 = "%s_fit_r1"%MODEL_TAP03
>>>>>>>> MODEL_DESC_TAP03_FIT_R1 = "The Trott, Abergel and Palmer (2003)
>>>>>>>> off-resonance 2-site model for R1rho-type experiments, where R1 is
>>>>>>>> fitted."
>>>>>>>> @@ -205,6 +230,7 @@
>>>>>>>> MODEL_YEAR_TAP03_FIT_R1 = 2003
>>>>>>>> MODEL_EXP_TYPE_TAP03_FIT_R1 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_TAP03_FIT_R1 = 2
>>>>>>>> +MODEL_EQ_TAP03_FIT_R1 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_MP05 = 'MP05'
>>>>>>>> """The R1rho 2-site off-resonance exchange model of Miloushev and
>>>>>>>> Palmer (2005)."""
>>>>>>>> @@ -213,6 +239,7 @@
>>>>>>>> MODEL_YEAR_MP05 = 2005
>>>>>>>> MODEL_EXP_TYPE_MP05 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_MP05 = 2
>>>>>>>> +MODEL_EQ_MP05 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_MP05_FIT_R1 = "%s_fit_r1"%MODEL_MP05
>>>>>>>> """The R1rho 2-site off-resonance exchange model of Miloushev and
>>>>>>>> Palmer (2005)."""
>>>>>>>> @@ -221,6 +248,7 @@
>>>>>>>> MODEL_YEAR_MP05_FIT_R1 = 2005
>>>>>>>> MODEL_EXP_TYPE_MP05_FIT_R1 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_MP05_FIT_R1 = 2
>>>>>>>> +MODEL_EQ_MP05_FIT_R1 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>>
>>>>>>>> # The Numerical model names.
>>>>>>>> @@ -230,6 +258,7 @@
>>>>>>>> MODEL_YEAR_NS_CPMG_2SITE_3D = 2004
>>>>>>>> MODEL_EXP_TYPE_NS_CPMG_2SITE_3D = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_NS_CPMG_2SITE_3D = 2
>>>>>>>> +MODEL_EQ_NS_CPMG_2SITE_3D = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_CPMG_2SITE_3D_FULL = 'NS CPMG 2-site 3D full'
>>>>>>>> MODEL_DESC_NS_CPMG_2SITE_3D_FULL = "The full numerical solution for
>>>>>>>> the 2-site Bloch-McConnell equations using 3D magnetisation vectors
>>>>>>>> for SQ CPMG experiments."
>>>>>>>> @@ -237,6 +266,7 @@
>>>>>>>> MODEL_YEAR_NS_CPMG_2SITE_3D_FULL = 2004
>>>>>>>> MODEL_EXP_TYPE_NS_CPMG_2SITE_3D_FULL = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_NS_CPMG_2SITE_3D_FULL = 2
>>>>>>>> +MODEL_EQ_NS_CPMG_2SITE_3D_FULL = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_CPMG_2SITE_STAR = 'NS CPMG 2-site star'
>>>>>>>> MODEL_DESC_NS_CPMG_2SITE_STAR = "The numerical reduced solution for
>>>>>>>> the 2-site Bloch-McConnell equations using complex conjugate matrices
>>>>>>>> for SQ CPMG experiments, whereby the simplification R20A = R20B is
>>>>>>>> assumed."
>>>>>>>> @@ -244,6 +274,7 @@
>>>>>>>> MODEL_YEAR_NS_CPMG_2SITE_STAR = 2004
>>>>>>>> MODEL_EXP_TYPE_NS_CPMG_2SITE_STAR = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_NS_CPMG_2SITE_STAR = 2
>>>>>>>> +MODEL_EQ_NS_CPMG_2SITE_STAR = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_CPMG_2SITE_STAR_FULL = 'NS CPMG 2-site star full'
>>>>>>>> MODEL_DESC_NS_CPMG_2SITE_STAR_FULL = "The full numerical solution for
>>>>>>>> the 2-site Bloch-McConnell equations using complex conjugate matrices
>>>>>>>> for SQ CPMG experiments."
>>>>>>>> @@ -251,6 +282,7 @@
>>>>>>>> MODEL_YEAR_NS_CPMG_2SITE_STAR_FULL = 2004
>>>>>>>> MODEL_EXP_TYPE_NS_CPMG_2SITE_STAR_FULL = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_NS_CPMG_2SITE_STAR_FULL = 2
>>>>>>>> +MODEL_EQ_NS_CPMG_2SITE_STAR_FULL = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_CPMG_2SITE_EXPANDED = 'NS CPMG 2-site expanded'
>>>>>>>> MODEL_DESC_NS_CPMG_2SITE_EXPANDED = "The numerical solution for the
>>>>>>>> 2-site Bloch-McConnell equations for SQ CPMG experiments, expanded
>>>>>>>> using Maple by Nikolai Skrynnikov."
>>>>>>>> @@ -258,6 +290,7 @@
>>>>>>>> MODEL_YEAR_NS_CPMG_2SITE_EXPANDED = 2001
>>>>>>>> MODEL_EXP_TYPE_NS_CPMG_2SITE_EXPANDED = EXP_TYPE_CPMG_SQ
>>>>>>>> MODEL_SITES_NS_CPMG_2SITE_EXPANDED = 2
>>>>>>>> +MODEL_EQ_NS_CPMG_2SITE_EXPANDED = EQ_SILICO
>>>>>>>>
>>>>>>>> MODEL_NS_R1RHO_2SITE = 'NS R1rho 2-site'
>>>>>>>> MODEL_DESC_NS_R1RHO_2SITE = "The reduced numerical solution for the
>>>>>>>> 2-site Bloch-McConnell equations using 3D magnetisation vectors for
>>>>>>>> R1rho-type experiments, whereby the simplification R20A = R20B is
>>>>>>>> assumed."
>>>>>>>> @@ -265,6 +298,7 @@
>>>>>>>> MODEL_YEAR_NS_R1RHO_2SITE = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_R1RHO_2SITE = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_NS_R1RHO_2SITE = 2
>>>>>>>> +MODEL_EQ_NS_R1RHO_2SITE = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_R1RHO_2SITE_FIT_R1 = "%s_fit_r1"%MODEL_NS_R1RHO_2SITE
>>>>>>>> MODEL_DESC_NS_R1RHO_2SITE_FIT_R1 = "The reduced numerical solution
>>>>>>>> for the 2-site Bloch-McConnell equations using 3D magnetisation
>>>>>>>> vectors for R1rho-type experiments, whereby the simplification R20A =
>>>>>>>> R20B is assumed, and where R1 is fitted."
>>>>>>>> @@ -272,6 +306,7 @@
>>>>>>>> MODEL_YEAR_NS_R1RHO_2SITE_FIT_R1 = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_R1RHO_2SITE_FIT_R1 = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_NS_R1RHO_2SITE_FIT_R1 = 2
>>>>>>>> +MODEL_EQ_NS_R1RHO_2SITE_FIT_R1 = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_R1RHO_3SITE = 'NS R1rho 3-site'
>>>>>>>> MODEL_DESC_NS_R1RHO_3SITE = "The numerical solution for the 3-site
>>>>>>>> Bloch-McConnell equations using 3D magnetisation vectors for
>>>>>>>> R1rho-type experiments, whereby the simplification R20A = R20B = R20C
>>>>>>>> is assumed."
>>>>>>>> @@ -279,6 +314,7 @@
>>>>>>>> MODEL_YEAR_NS_R1RHO_3SITE = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_R1RHO_3SITE = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_NS_R1RHO_3SITE = 3
>>>>>>>> +MODEL_EQ_NS_R1RHO_3SITE = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_R1RHO_3SITE_LINEAR = 'NS R1rho 3-site linear'
>>>>>>>> MODEL_DESC_NS_R1RHO_3SITE_LINEAR = "The numerical solution for the
>>>>>>>> 3-site Bloch-McConnell equations using 3D magnetisation vectors for
>>>>>>>> R1rho-type experiments, linearised with kAC = kCA = 0 and whereby the
>>>>>>>> simplification R20A = R20B = R20C is assumed."
>>>>>>>> @@ -286,6 +322,7 @@
>>>>>>>> MODEL_YEAR_NS_R1RHO_3SITE_LINEAR = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_R1RHO_3SITE_LINEAR = EXP_TYPE_R1RHO
>>>>>>>> MODEL_SITES_NS_R1RHO_3SITE_LINEAR = 3
>>>>>>>> +MODEL_EQ_NS_R1RHO_3SITE_LINEAR = EQ_NUMERIC
>>>>>>>>
>>>>>>>> # The multi-quantum data model names.
>>>>>>>> MODEL_MMQ_CR72 = 'MMQ CR72'
>>>>>>>> @@ -294,6 +331,7 @@
>>>>>>>> MODEL_YEAR_MMQ_CR72 = 2004
>>>>>>>> MODEL_EXP_TYPE_MMQ_CR72 = EXP_TYPE_CPMG_MMQ
>>>>>>>> MODEL_SITES_MMQ_CR72 = 2
>>>>>>>> +MODEL_EQ_MMQ_CR72 = EQ_ANALYTIC
>>>>>>>>
>>>>>>>> MODEL_NS_MMQ_2SITE = 'NS MMQ 2-site'
>>>>>>>> MODEL_DESC_NS_MMQ_2SITE = "The reduced numerical solution for the
>>>>>>>> 2-site Bloch-McConnell equations for MMQ CPMG experiments, whereby the
>>>>>>>> simplification R20A = R20B is assumed."
>>>>>>>> @@ -301,6 +339,7 @@
>>>>>>>> MODEL_YEAR_NS_MMQ_2SITE = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_MMQ_2SITE = EXP_TYPE_CPMG_MMQ
>>>>>>>> MODEL_SITES_NS_MMQ_2SITE = 2
>>>>>>>> +MODEL_EQ_NS_MMQ_2SITE = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_MMQ_3SITE = 'NS MMQ 3-site'
>>>>>>>> MODEL_DESC_NS_MMQ_3SITE = "The numerical solution for the 3-site
>>>>>>>> Bloch-McConnell equations for MMQ CPMG experiments, whereby the
>>>>>>>> simplification R20A = R20B = R20C is assumed."
>>>>>>>> @@ -308,6 +347,7 @@
>>>>>>>> MODEL_YEAR_NS_MMQ_3SITE = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_MMQ_3SITE = EXP_TYPE_CPMG_MMQ
>>>>>>>> MODEL_SITES_NS_MMQ_3SITE = 3
>>>>>>>> +MODEL_EQ_NS_MMQ_3SITE = EQ_NUMERIC
>>>>>>>>
>>>>>>>> MODEL_NS_MMQ_3SITE_LINEAR = 'NS MMQ 3-site linear'
>>>>>>>> MODEL_DESC_NS_MMQ_3SITE_LINEAR = "The numerical solution for the
>>>>>>>> 3-site Bloch-McConnell equations for MMQ CPMG experiments, linearised
>>>>>>>> with kAC = kCA = 0 and whereby the simplification R20A = R20B = R20C
>>>>>>>> is assumed."
>>>>>>>> @@ -315,6 +355,7 @@
>>>>>>>> MODEL_YEAR_NS_MMQ_3SITE_LINEAR = 2005
>>>>>>>> MODEL_EXP_TYPE_NS_MMQ_3SITE_LINEAR = EXP_TYPE_CPMG_MMQ
>>>>>>>> MODEL_SITES_NS_MMQ_3SITE_LINEAR = 3
>>>>>>>> +MODEL_EQ_NS_MMQ_3SITE_LINEAR = EQ_NUMERIC
>>>>>>>>
>>>>>>>> # The parameters.
>>>>>>>> PARAMS_R20 = ['r2', 'r2a', 'r2b']
>>>>>>>> @@ -650,4 +691,43 @@
>>>>>>>> MODEL_NS_MMQ_2SITE: MODEL_SITES_NS_MMQ_2SITE,
>>>>>>>> MODEL_NS_MMQ_3SITE: MODEL_SITES_NS_MMQ_3SITE,
>>>>>>>> MODEL_NS_MMQ_3SITE_LINEAR: MODEL_SITES_NS_MMQ_3SITE_LINEAR
>>>>>>>> +}
>>>>>>>> +
>>>>>>>> +# Full list of equation type.
>>>>>>>> +MODEL_EQ = {
>>>>>>>> + MODEL_R2EFF: MODEL_EQ_R2EFF,
>>>>>>>> + MODEL_NOREX: MODEL_EQ_NOREX,
>>>>>>>> + MODEL_NOREX_R1RHO: MODEL_EQ_NOREX_R1RHO,
>>>>>>>> + MODEL_NOREX_R1RHO_FIT_R1: MODEL_EQ_NOREX_R1RHO_FIT_R1,
>>>>>>>> + MODEL_LM63: MODEL_EQ_LM63,
>>>>>>>> + MODEL_LM63_3SITE: MODEL_EQ_LM63_3SITE,
>>>>>>>> + MODEL_CR72: MODEL_EQ_CR72,
>>>>>>>> + MODEL_CR72_FULL: MODEL_EQ_CR72_FULL,
>>>>>>>> + MODEL_IT99: MODEL_EQ_IT99,
>>>>>>>> + MODEL_TSMFK01: MODEL_EQ_TSMFK01,
>>>>>>>> + MODEL_B14: MODEL_EQ_B14,
>>>>>>>> + MODEL_B14_FULL: MODEL_EQ_B14_FULL,
>>>>>>>> + MODEL_M61: MODEL_EQ_M61,
>>>>>>>> + MODEL_M61B: MODEL_EQ_M61B,
>>>>>>>> + MODEL_DPL94: MODEL_EQ_DPL94,
>>>>>>>> + MODEL_DPL94_FIT_R1: MODEL_EQ_DPL94_FIT_R1,
>>>>>>>> + MODEL_TP02: MODEL_EQ_TP02,
>>>>>>>> + MODEL_TP02_FIT_R1: MODEL_EQ_TP02_FIT_R1,
>>>>>>>> + MODEL_TAP03: MODEL_EQ_TAP03,
>>>>>>>> + MODEL_TAP03_FIT_R1: MODEL_EQ_TAP03_FIT_R1,
>>>>>>>> + MODEL_MP05: MODEL_EQ_MP05,
>>>>>>>> + MODEL_MP05_FIT_R1: MODEL_EQ_MP05_FIT_R1,
>>>>>>>> + MODEL_NS_CPMG_2SITE_3D: MODEL_EQ_NS_CPMG_2SITE_3D,
>>>>>>>> + MODEL_NS_CPMG_2SITE_3D_FULL: MODEL_EQ_NS_CPMG_2SITE_3D_FULL,
>>>>>>>> + MODEL_NS_CPMG_2SITE_STAR: MODEL_EQ_NS_CPMG_2SITE_STAR,
>>>>>>>> + MODEL_NS_CPMG_2SITE_STAR_FULL: MODEL_EQ_NS_CPMG_2SITE_STAR_FULL,
>>>>>>>> + MODEL_NS_CPMG_2SITE_EXPANDED: MODEL_EQ_NS_CPMG_2SITE_EXPANDED,
>>>>>>>> + MODEL_NS_R1RHO_2SITE: MODEL_EQ_NS_R1RHO_2SITE,
>>>>>>>> + MODEL_NS_R1RHO_2SITE_FIT_R1: MODEL_EQ_NS_R1RHO_2SITE_FIT_R1,
>>>>>>>> + MODEL_NS_R1RHO_3SITE: MODEL_EQ_NS_R1RHO_3SITE,
>>>>>>>> + MODEL_NS_R1RHO_3SITE_LINEAR: MODEL_EQ_NS_R1RHO_3SITE_LINEAR,
>>>>>>>> + MODEL_MMQ_CR72: MODEL_EQ_MMQ_CR72,
>>>>>>>> + MODEL_NS_MMQ_2SITE: MODEL_EQ_NS_MMQ_2SITE,
>>>>>>>> + MODEL_NS_MMQ_3SITE: MODEL_EQ_NS_MMQ_3SITE,
>>>>>>>> + MODEL_NS_MMQ_3SITE_LINEAR: MODEL_EQ_NS_MMQ_3SITE_LINEAR
>>>>>>>> }
>>>>>>>>
>>>>>>>> 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=24983&r1=24982&r2=24983&view=diff
>>>>>>>> ==============================================================================
>>>>>>>> ---
>>>>>>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
>>>>>>>> (original)
>>>>>>>> +++
>>>>>>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py
>>>>>>>> Tue Aug 12 10:54:36 2014
>>>>>>>> @@ -20,8 +20,8 @@
>>>>>>>>
>>>>>>>> ###############################################################################
>>>>>>>>
>>>>>>>> # relax module imports.
>>>>>>>> -from specific_analyses.relax_disp.variables import MODEL_CR72,
>>>>>>>> MODEL_MMQ_CR72, MODEL_NS_R1RHO_3SITE
>>>>>>>> -from specific_analyses.relax_disp.variables import MODEL_EXP_TYPE,
>>>>>>>> MODEL_PARAMS, MODEL_SITES, MODEL_YEAR
>>>>>>>> +from specific_analyses.relax_disp.variables import MODEL_CR72,
>>>>>>>> MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_3SITE
>>>>>>>> +from specific_analyses.relax_disp.variables import MODEL_EXP_TYPE,
>>>>>>>> MODEL_EQ, MODEL_PARAMS, MODEL_SITES, MODEL_YEAR
>>>>>>>> from test_suite.unit_tests.base_classes import UnitTestCase
>>>>>>>>
>>>>>>>>
>>>>>>>> @@ -67,3 +67,13 @@
>>>>>>>>
>>>>>>>> # Test the return.
>>>>>>>> self.assertEqual(model_sites, 3)
>>>>>>>> +
>>>>>>>> +
>>>>>>>> + def test_MODEL_EQ(self):
>>>>>>>> + """Unit test of the MODEL_EQ dictionary."""
>>>>>>>> +
>>>>>>>> + # Test model equation type return from model equation
>>>>>>>> dictionary.
>>>>>>>> + model_eq = MODEL_EQ[MODEL_NS_CPMG_2SITE_EXPANDED]
>>>>>>>> +
>>>>>>>> + # Test the return.
>>>>>>>> + self.assertEqual(model_eq, 'silico')
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> relax (http://www.nmr-relax.com)
>>>>>>>>
>>>>>>>> This is the relax-commits 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-commits
>>>>>
>>>>> _______________________________________________
>>>>> relax (http://www.nmr-relax.com)
>>>>>
>>>>> This is the relax-devel mailing list
>>>>> [email protected]
>>>>>
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>>>>> reminder, or change your subscription options,
>>>>> visit the list information page at
>>>>> https://mail.gna.org/listinfo/relax-devel
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