Author: bugman
Date: Thu Aug 21 14:52:29 2014
New Revision: 25168
URL: http://svn.gna.org/viewcvs/relax?rev=25168&view=rev
Log:
Removed all references to the 'No Rex R1rho off res' model in the system tests.
In addition, the Relax_disp.test_convert_no_rex system test has been deleted as
it no longer has a
purpose. For the Relax_disp.test_model_nesting_and_param system test, to allow
this to work the
cdp.exp_type_list list is set to EXP_TYPE_LIST.
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25168&r1=25167&r2=25168&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Thu Aug 21 14:52:29 2014
@@ -37,8 +37,8 @@
from specific_analyses.relax_disp.checks import check_missing_r1
from specific_analyses.relax_disp.data import generate_r20_key,
get_curve_type, has_r1rho_exp_type, loop_exp_frq, loop_exp_frq_offset_point,
return_grace_file_name_ini, return_param_key_from_data
from specific_analyses.relax_disp.data import INTERPOLATE_DISP,
INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, Y_AXIS_R2_R1RHO,
Y_AXIS_R2_EFF
-from specific_analyses.relax_disp.model import convert_no_rex, models_info,
nesting_param
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_B14_FULL, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC_CPMG,
MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG, MODEL_LM63, MODEL_M61, MODEL_M61B,
MODEL_MP05, MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR,
MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03
+from specific_analyses.relax_disp.model import models_info, nesting_param
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST, EXP_TYPE_R1RHO,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99,
MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG, MODEL_LM63,
MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR,
MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -1389,183 +1389,6 @@
# Check R1.
check_missing_r1_return = check_missing_r1(model=MODEL_DPL94)
self.assertEqual(check_missing_r1_return, False)
-
-
- def test_convert_no_rex(self):
- """Test of specific_analyses.relax_disp.model.convert_no_rex()
function."""
-
- # Set up some spins.
- self.setup_missing_r1_spins()
-
- # Set variables.
- exp_type = 'R1rho'
- frq = 800.1 * 1E6
-
- spectrum_id='test'
-
- # Set an experiment type to the pipe.
- self.interpreter.relax_disp.exp_type(spectrum_id=spectrum_id,
exp_type=exp_type)
-
- # Set a frequency to loop through.
- self.interpreter.spectrometer.frequency(id=spectrum_id, frq=frq,
units='Hz')
-
- ##### Test the translations, if R1 is not present.
-
- # First check that CPMG models are not converted.
-
- ## First check analytic.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_ANALYTIC_CPMG
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, self_models)
-
- ## First check numeric.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_NUMERIC_CPMG
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, self_models)
-
- # Then check the R1ho models which is available through the GUI.
-
- ## Check for a normal 2 site setup.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE])
-
- ## Check for a 2 site setup, where both MODEL_NOREX and
MODEL_NOREX_R1RHO are sent to auto_analyses.
- ## This should not be possible through the GUI, but could be wished to
do through scripting.
- ## This should just make a conversion to the 'R1 fit' models, and keep
MODEL_NOREX.
-
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
MODEL_NS_R1RHO_2SITE])
-
- ## Check again with MODEL_NOREX_R1RHO.
-
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
MODEL_NS_R1RHO_2SITE])
-
- ## Now check if there is a mix of On-resonance and Off-resonance
models.
- ## This should insert 'MODEL_NOREX_R1RHO', if it is not present.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_DPL94,
MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_M61, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
MODEL_NS_R1RHO_2SITE])
-
- ##### Test the translations, if R1 is present.
-
- ## The path to the data files.
- data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
-
- ## Now load some R1 data.
- self.interpreter.relax_data.read(ri_id='R1', ri_type='R1',
frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path,
mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5,
data_col=6, error_col=7)
-
- # First check that CPMG models are not converted.
-
- ## First check analytic.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_ANALYTIC_CPMG
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, self_models)
-
- ## First check numeric.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX] + MODEL_LIST_NUMERIC_CPMG
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, self_models)
-
- # Then check the R1ho models which is available through the GUI.
-
- ## Check for a normal 2 site setup.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE])
-
- ## Check for a 2 site setup, including a 3 site.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE,
MODEL_NS_R1RHO_3SITE_LINEAR])
-
- ## Check for a 2 site setup, where both MODEL_NOREX and
MODEL_NOREX_R1RHO are sent to auto_analyses.
- ## This should not be possible through the GUI, but could be wished to
do through scripting.
- ## This should just make a conversion to the 'R1 fit' models, and keep
MODEL_NOREX.
-
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
MODEL_NS_R1RHO_2SITE])
-
- ## Check again with MODEL_NOREX_R1RHO.
-
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
MODEL_NS_R1RHO_2SITE])
-
- ## Now check if there is a mix of On-resonance and Off-resonance
models.
- ## This should insert 'MODEL_NOREX_R1RHO', if it is not present.
- ### Setup the models, which is available through the GUI.
- self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_DPL94,
MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
-
- ### Get the return after the conversion.
- self_models_return = convert_no_rex(self_models=self_models)[0]
-
- ### Check that the models have been translated correctly.
- self.assertEqual(self_models_return, [MODEL_R2EFF, MODEL_NOREX,
MODEL_NOREX_R1RHO, MODEL_M61, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
MODEL_NS_R1RHO_2SITE])
def test_cpmg_synthetic_b14_to_ns3d_cluster(self):
@@ -5028,6 +4851,9 @@
def test_model_nesting_and_param(self):
"""Test that all models which can nest, have all their parameters
converted."""
+ # Set the experiment type.
+ cdp.exp_type_list = EXP_TYPE_LIST
+
# Get info for all models.
all_models_info = models_info(models=MODEL_LIST_FULL)
@@ -5232,7 +5058,7 @@
self.assert_(hasattr(cdp.mol[0].res[42].spin[0], 'ri_data'))
# The dispersion models.
- MODELS = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
+ MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
# The grid search size (the number of increments per dimension).
GRID_INC = 4
@@ -5497,7 +5323,7 @@
self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False)
# The dispersion models.
- MODELS = [MODEL_R2EFF, MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
+ MODELS = [MODEL_R2EFF, MODEL_NOREX, MODEL_DPL94, MODEL_TP02,
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE]
# The grid search size (the number of increments per dimension).
GRID_INC = None
@@ -5578,7 +5404,7 @@
# Compare values.
if spin_id == ':52@N':
if param == 'r1':
- if model == MODEL_NOREX_R1RHO:
+ if model == MODEL_NOREX:
self.assertAlmostEqual(value,
1.46328102)
elif model == MODEL_DPL94:
self.assertAlmostEqual(value,
1.45019848)
@@ -5592,7 +5418,7 @@
self.assertAlmostEqual(value,
1.54354372)
elif param == 'r2':
- if model == MODEL_NOREX_R1RHO:
+ if model == MODEL_NOREX:
self.assertAlmostEqual(value,
11.48040934)
elif model == MODEL_DPL94:
self.assertAlmostEqual(value,
10.16304887, 6)
@@ -5652,7 +5478,7 @@
self.assertAlmostEqual(value,
4909.88110195, 3)
elif param == 'chi2':
- if model == MODEL_NOREX_R1RHO:
+ if model == MODEL_NOREX:
self.assertAlmostEqual(value,
3363.95829122)
elif model == MODEL_DPL94:
self.assertAlmostEqual(value, 710.24767560)
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