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
