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 <tlin...@nmr-relax.com> 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 <edw...@nmr-relax.com>: >> 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 <tlin...@nmr-relax.com> 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 <edw...@nmr-relax.com>: >>>> 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 <edw...@nmr-relax.com> 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 <edw...@nmr-relax.com> 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 <tlin...@nmr-relax.com> >>>>>> 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, <tlin...@nmr-relax.com> 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 >>>>>>> relax-comm...@gna.org >>>>>>> >>>>>>> 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 >>>> relax-devel@gna.org >>>> >>>> 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-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org 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-devel
