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] > > 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 [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-devel
