Author: tlinnet
Date: Wed Aug 20 13:56:54 2014
New Revision: 25091
URL: http://svn.gna.org/viewcvs/relax?rev=25091&view=rev
Log:
Implemented function that determine if any model in the list of all models
should be replaced or inserted as the correct 'No Rex' model.
It also translate the R1rho off-resonance model to the corresponding 'R1 fit'
models, if R1 is not loaded.
Modified:
trunk/specific_analyses/relax_disp/model.py
Modified: trunk/specific_analyses/relax_disp/model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/model.py?rev=25091&r1=25090&r2=25091&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/model.py (original)
+++ trunk/specific_analyses/relax_disp/model.py Wed Aug 20 13:56:54 2014
@@ -28,7 +28,9 @@
from operator import attrgetter, ne
# relax module imports.
-from specific_analyses.relax_disp.variables import EQ_ANALYTIC, EQ_NUMERIC,
EQ_SILICO, EXP_TYPE_CPMG_MMQ, EXP_TYPE_R1RHO, EXP_TYPE_CPMG_SQ,
EXP_TYPE_NOREX, EXP_TYPE_NOREX_R1RHO, EXP_TYPE_R2EFF, MODEL_DESC, MODEL_EQ,
MODEL_EXP_TYPE, MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_NUMERIC_CPMG,
MODEL_LIST_R1RHO_FIT_R1_ONLY, MODEL_LIST_R1RHO_W_R1_ONLY, MODEL_CR72,
MODEL_DPL94, MODEL_DPL94_FIT_R1, MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_MMQ_CR72, MODEL_NEST, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_PARAMS_LM63,
MODEL_PARAMS_LM63_3SITE, MODEL_SITES, MODEL_YEAR, PARAMS_R20
+from lib.errors import RelaxError
+from specific_analyses.relax_disp.checks import check_missing_r1
+from specific_analyses.relax_disp.variables import EQ_ANALYTIC, EQ_NUMERIC,
EQ_SILICO, EXP_TYPE_CPMG_MMQ, EXP_TYPE_R1RHO, EXP_TYPE_CPMG_SQ,
EXP_TYPE_NOREX, EXP_TYPE_NOREX_R1RHO, EXP_TYPE_R2EFF, MODEL_DESC, MODEL_EQ,
MODEL_EXP_TYPE, MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_NUMERIC_CPMG,
MODEL_LIST_R1RHO_FIT_R1_ONLY, MODEL_LIST_R1RHO_W_R1_ONLY, MODEL_CR72,
MODEL_DPL94, MODEL_DPL94_FIT_R1, MODEL_FIT_R1, MODEL_IT99, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_MMQ_CR72, MODEL_NEST, MODEL_NOREX, MODEL_NOREX_R1RHO,
MODEL_NOREX_R1RHO_FIT_R1, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_PARAMS_LM63,
MODEL_PARAMS_LM63_3SITE, MODEL_LIST_R1RHO_FIT_R1_ONLY,
MODEL_LIST_R1RHO_W_R1_ONLY, MODEL_R2EFF, MODEL_SITES, MODEL_YEAR, PARAMS_R20
# Define class for describing the model.
@@ -99,6 +101,78 @@
# Make a readable presentation of the class object. Here a tuple.
def __repr__(self):
return repr((self.model, self.desc, self.exp_type, self.eq,
self.sites, self.year, self.params, self.params_nr))
+
+
+# Define function, to convert/insert 'No Rex' for R1rho off-resonance
models, and translates models which miss R1.
+def convert_no_rex_fit_r1(self_models=None):
+ """Determine if any model in the list of all models should be replaced
or inserted as the correct 'No Rex' model and also translate the R1rho
off-resonance model to the corresponding 'R1 fit' models, if R1 is not loaded.
+
+ @keyword self_models: The list of all models analysed.
+ @type self_models: list of str
+ @return: The corrected all models list.
+ @rtype: list of str
+ """
+
+ # First check if 'No Rex' model should be converted to 'No Rex R1rho off
res' for R1rho off-resonance.
+ # First remove 'R2eff' model from the list.
+ self_models_rem_r2eff = filter(partial(ne, MODEL_R2EFF), self_models)
+
+ # Then remove all 'No Rex' model.
+ self_models_rem_r2eff_norex = filter(partial(ne, MODEL_NOREX),
self_models_rem_r2eff)
+ self_models_rem_r2eff_norex = filter(partial(ne, MODEL_NOREX_R1RHO),
self_models_rem_r2eff_norex)
+ self_models_rem_r2eff_norex = filter(partial(ne,
MODEL_NOREX_R1RHO_FIT_R1), self_models_rem_r2eff_norex)
+
+ # Then test if all or any models analysed is R1rho off-resonance models.
+ all_r1rho_off_res = True
+ any_r1rho_off_res = False
+
+ # Define the model list which is R1rho off-resonance.
+ model_list_r1rho_off_res = MODEL_LIST_R1RHO_FIT_R1_ONLY +
MODEL_LIST_R1RHO_W_R1_ONLY
+
+ # Loop through models.
+ for i, model in enumerate(self_models_rem_r2eff_norex):
+ if model in model_list_r1rho_off_res:
+ any_r1rho_off_res = True
+
+ else:
+ all_r1rho_off_res = False
+
+ # Now either replace or insert MODEL_NOREX_R1RHO.
+ # If all models is R1rho off resonance.
+ if all_r1rho_off_res:
+ # Then test if 'No Rex' is the only 'No Rex' model.
+ if MODEL_NOREX in self_models and MODEL_NOREX_R1RHO not in
self_models and MODEL_NOREX_R1RHO_FIT_R1 not in self_models:
+ # Then replace 'No Rex' with 'No Rex R1rho off res'
+ no_rex_index = self_models.index(MODEL_NOREX)
+ self_models[no_rex_index] = MODEL_NOREX_R1RHO
+
+ # If some of the models are R1rho off-resonance, and MODEL_NOREX is
present but MODEL_NOREX_R1RHO is not present.
+ elif any_r1rho_off_res:
+ # Then test if 'No Rex' is the only 'No Rex' model.
+ if MODEL_NOREX in self_models and MODEL_NOREX_R1RHO not in
self_models and MODEL_NOREX_R1RHO_FIT_R1 not in self_models:
+ # Then insert 'No Rex R1rho off res' after 'No Rex'.
+ no_rex_index = self_models.index(MODEL_NOREX)
+ self_models.insert(no_rex_index + 1, MODEL_NOREX_R1RHO)
+
+ # Loop through all models, to replace with 'R1 fit' model, if R1 is
missing.
+ for i, model in enumerate(self_models):
+ # Check if R1 is missing.
+ is_missing = check_missing_r1(model=model)
+
+ # If R1 is missing, convert the model.
+ if is_missing:
+ try:
+ translated_model = MODEL_FIT_R1[model]
+
+ # If there exist no conversion model, then raise an RelaxError.
+ except KeyError:
+ raise RelaxError("The current data pipe has no R1 data
loaded, and the selected model '%s' cannot not be analysed without this." %
(model))
+
+ # Replace the model.
+ self_models[i] = translated_model
+
+ # Return the model.
+ return self_models
# Define function, to return model info.
r25091 - /trunk/specific_analyses/relax_disp/model.py