Author: tlinnet
Date: Wed Aug 13 21:29:57 2014
New Revision: 25011
URL: http://svn.gna.org/viewcvs/relax?rev=25011&view=rev
Log:
Deleted systemtest test_r1rho_kjaergaard_man, since it was no necessary.
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/test_suite/system_tests/relax_disp.py
Modified: branches/R1_fitting/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/system_tests/relax_disp.py?rev=25011&r1=25010&r2=25011&view=diff
==============================================================================
--- branches/R1_fitting/test_suite/system_tests/relax_disp.py (original)
+++ branches/R1_fitting/test_suite/system_tests/relax_disp.py Wed Aug 13
21:29:57 2014
@@ -5100,199 +5100,6 @@
self.assertAlmostEqual(float(y_prod),
float(y_comp))
- def test_r1rho_kjaergaard_man(self):
- """Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
-
- This uses the data from Kjaergaard's paper at U{DOI:
10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}.
-
- This uses the manual analysis.
-
- """
-
- # Cluster residues
- cluster_ids = [
- ":13@N",
- ":15@N",
- ":16@N",
- ":25@N",
- ":26@N",
- ":28@N",
- ":39@N",
- ":40@N",
- ":41@N",
- ":43@N",
- ":44@N",
- ":45@N",
- ":49@N",
- ":52@N",
- ":53@N"]
-
-
- # Load the data.
- self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids)
-
- # The grid search size (the number of increments per dimension).
- GRID_INC = 4
-
- # The number of Monte Carlo simulations to be used for error
analysis at the end of the analysis.
- MC_NUM = 3
-
- # Execute the auto-analysis (fast).
- # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
- OPT_FUNC_TOL = 1e-1
- OPT_MAX_ITERATIONS = 1000
-
- result_dir_name = ds.tmpdir
-
- # Make all spins free, and select a subset.
- for curspin in cluster_ids:
- self.interpreter.relax_disp.cluster('free spins', curspin)
- # Shut them down
- self.interpreter.deselect.spin(spin_id=curspin, change_all=False)
-
- self.interpreter.select.spin(spin_id=':52@N', change_all=False)
- #self.interpreter.relax_disp.cluster('model_cluster', ':52@N')
-
- # Do the analysis manual
- self.interpreter.spectrum.error_analysis(subset=['46_0_35_0',
'48_0_35_4', '47_0_35_10', '49_0_35_20', '36_0_39_0', '39_0_39_4',
'37_0_39_10', '40_0_39_20', '38_0_39_40', '41_0_41_0', '44_0_41_4',
'42_0_41_10', '45_0_41_20', '43_0_41_40', '31_0_43_0', '34_0_43_4',
'32_0_43_10', '35_0_43_20', '33_0_43_40', '1_0_46_0', '4_0_46_4',
'2_0_46_10', '5_0_46_20', '3_0_46_40', '60_0_48_0', '63_0_48_4',
'61_0_48_10', '62_0_48_14', '64_0_48_20', '11_500_46_0', '14_500_46_4',
'12_500_46_10', '15_500_46_20', '13_500_46_40', '50_1000_41_0',
'53_1000_41_4', '51_1000_41_10', '54_1000_41_20', '52_1000_41_40',
'21_1000_46_0', '24_1000_46_4', '22_1000_46_10', '25_1000_46_20',
'23_1000_46_40', '65_1000_48_0', '68_1000_48_4', '66_1000_48_10',
'67_1000_48_14', '69_1000_48_20', '55_2000_41_0', '58_2000_41_4',
'56_2000_41_10', '59_2000_41_20', '57_2000_41_40', '6_2000_46_0',
'9_2000_46_4', '7_2000_46_10', '10_2000_46_20', '8_2000_46_40',
'16_5000_46_0', '19_5000_46_4', '17_5000_46_10', '20_5000_46_20',
'18_5000_46_40', '26_10000_46_0', '29_10000_46_4', '27_10000_46_10',
'30_10000_46_20', '28_10000_46_40'])
-
- ##- The 'R2eff' model -
- self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='R2eff -
relax_disp', bundle_to='relax_disp')
- self.interpreter.pipe.switch(pipe_name='R2eff - relax_disp')
- self.interpreter.relax_disp.select_model(model='R2eff')
- self.interpreter.minimise.grid_search(lower=None, upper=None,
inc=GRID_INC, constraints=True, verbosity=1)
-
- self.interpreter.minimise.execute(min_algor='simplex',
line_search=None, hessian_mod=None, hessian_type=None, func_tol=OPT_FUNC_TOL,
grad_tol=None, max_iter=OPT_MAX_ITERATIONS, constraints=True, scaling=True,
verbosity=1)
- self.interpreter.eliminate(function=None, args=None)
- self.interpreter.monte_carlo.setup(number=MC_NUM)
- self.interpreter.monte_carlo.create_data(method='back_calc')
- self.interpreter.monte_carlo.initial_values()
-
- self.interpreter.minimise.execute(min_algor='simplex',
line_search=None, hessian_mod=None, hessian_type=None, func_tol=OPT_FUNC_TOL,
grad_tol=None, max_iter=OPT_MAX_ITERATIONS, constraints=True, scaling=True,
verbosity=1)
- self.interpreter.eliminate(function=None, args=None)
- self.interpreter.monte_carlo.error_analysis()
-
- # Write results
- #self.interpreter.relax_disp.plot_exp_curves(file='intensities.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
-
#self.interpreter.relax_disp.plot_exp_curves(file='intensities_norm.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=True)
-
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'R2eff',
num_points=1000, extend=500.0, force=True)
-
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'R2eff',
force=True)
- #self.interpreter.value.write(param='r2eff', file='r2eff.out',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2eff', spin_id=None, plot_data='value', file='r2eff.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
- #self.interpreter.value.write(param='i0', file='i0.out',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='i0', spin_id=None, plot_data='value', file='i0.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
- #self.interpreter.value.write(param='chi2', file='chi2.out',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
-
- ## Save results as state
- #self.interpreter.results.write(file='results',
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', compress_type=1, force=True)
-
- ##- The 'No Rex' model -
- self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='No Rex -
relax_disp', bundle_to='relax_disp')
- self.interpreter.pipe.switch(pipe_name='No Rex - relax_disp')
- self.interpreter.relax_disp.select_model(model='No Rex')
- self.interpreter.value.copy(pipe_from='R2eff - relax_disp',
pipe_to='No Rex - relax_disp', param='r2eff')
- self.interpreter.minimise.grid_search(lower=None, upper=None,
inc=GRID_INC, constraints=True, verbosity=1)
-
- self.interpreter.minimise.execute(min_algor='simplex',
line_search=None, hessian_mod=None, hessian_type=None, func_tol=OPT_FUNC_TOL,
grad_tol=None, max_iter=OPT_MAX_ITERATIONS, constraints=True, scaling=True,
verbosity=1)
- self.interpreter.eliminate(function=None, args=None)
-
- ## Write results
-
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'No
Rex', num_points=1000, extend=500.0, force=True)
-
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'No
Rex', force=True)
- #self.interpreter.value.write(param='chi2', file='chi2.out',
dir=result_dir_name+sep+'resultsR1'+sep+'No Rex', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'No Rex', force=True, norm=False)
-
- ## Save results as state
- self.interpreter.results.write(file='results',
dir=result_dir_name+sep+'resultsR1'+sep+'No Rex', compress_type=1, force=True)
-
- ##- The 'DPL94' model -
- self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='DPL94 -
relax_disp', bundle_to='relax_disp')
- self.interpreter.pipe.switch(pipe_name='DPL94 - relax_disp')
- self.interpreter.relax_disp.select_model(model='DPL94')
- self.interpreter.value.copy(pipe_from='R2eff - relax_disp',
pipe_to='DPL94 - relax_disp', param='r2eff')
- self.interpreter.relax_disp.insignificance(level=1.0)
- self.interpreter.minimise.grid_search(lower=None, upper=None,
inc=GRID_INC, constraints=True, verbosity=1)
-
- self.interpreter.minimise.execute(min_algor='simplex',
line_search=None, hessian_mod=None, hessian_type=None, func_tol=OPT_FUNC_TOL,
grad_tol=None, max_iter=OPT_MAX_ITERATIONS, constraints=True, scaling=True,
verbosity=1)
- self.interpreter.eliminate(function=None, args=None)
-
- ## Write results
-
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'DPL94',
num_points=1000, extend=500.0, force=True)
-
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'DPL94',
force=True)
- #self.interpreter.value.write(param='phi_ex', file='phi_ex.out',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='phi_ex', spin_id=None, plot_data='value', file='phi_ex.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
- #self.interpreter.value.write(param='k_AB', file='k_AB.out',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='kex', file='kex.out',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='tex', file='tex.out',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='k_AB', spin_id=None, plot_data='value', file='k_AB.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='kex', spin_id=None, plot_data='value', file='kex.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='tex', spin_id=None, plot_data='value', file='tex.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
- #self.interpreter.value.write(param='chi2', file='chi2.out',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
-
- ## Save results as state
- #self.interpreter.results.write(file='results',
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', compress_type=1, force=True)
-
- ##- The 'final' model -
- self.interpreter.model_selection(method='AIC', modsel_pipe='final -
relax_disp', bundle='relax_disp', pipes=['No Rex - relax_disp', 'DPL94 -
relax_disp'])
- self.interpreter.monte_carlo.setup(number=MC_NUM)
- self.interpreter.monte_carlo.create_data(method='back_calc')
- self.interpreter.monte_carlo.initial_values()
-
- self.interpreter.minimise.execute(min_algor='simplex',
line_search=None, hessian_mod=None, hessian_type=None, func_tol=OPT_FUNC_TOL,
grad_tol=None, max_iter=OPT_MAX_ITERATIONS, constraints=True, scaling=True,
verbosity=1)
- self.interpreter.eliminate(function=None, args=None)
- self.interpreter.monte_carlo.error_analysis()
-
- ## Write results
-
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'final',
num_points=1000, extend=500.0, force=True)
-
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'final',
force=True)
- #self.interpreter.value.write(param='model', file='model.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='pA', file='pA.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='pB', file='pB.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='pA', spin_id=None, plot_data='value', file='pA.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='pB', spin_id=None, plot_data='value', file='pB.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- self.interpreter.value.write(param='phi_ex', file='phi_ex.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='phi_ex', spin_id=None, plot_data='value', file='phi_ex.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='phi_ex_B', file='phi_ex_B.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='phi_ex_C', file='phi_ex_C.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='phi_ex_B', spin_id=None, plot_data='value', file='phi_ex_B.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='phi_ex_C', spin_id=None, plot_data='value', file='phi_ex_C.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='dw', file='dw.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='dw', spin_id=None, plot_data='value', file='dw.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='dwH', file='dwH.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='dwH', spin_id=None, plot_data='value', file='dwH.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='k_AB', file='k_AB.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- self.interpreter.value.write(param='kex', file='kex.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='tex', file='tex.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='k_AB', spin_id=None, plot_data='value', file='k_AB.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='kex', spin_id=None, plot_data='value', file='kex.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='tex', spin_id=None, plot_data='value', file='tex.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='k_AB', file='k_AB.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='k_AB', spin_id=None, plot_data='value', file='k_AB.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='kB', file='kB.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='kC', file='kC.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='kB', spin_id=None, plot_data='value', file='kB.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='kC', spin_id=None, plot_data='value', file='kC.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
- #self.interpreter.value.write(param='chi2', file='chi2.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.grace.write(x_data_type='res_num',
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr',
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-
- # Test of new parameters to write out.
- self.interpreter.value.write(param='theta', file='theta.out',
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, comment=None,
bc=False, force=True)
- #self.interpreter.value.write(param='theta', file='theta.out',
dir='~', scaling=1.0, comment=None, bc=False, force=True)
- #self.assert_(hasattr(cdp.mol[0].res[7].spin[0], 'theta'))
-
- ## Save results as state
- #self.interpreter.results.write(file='results',
dir=result_dir_name+sep+'resultsR1'+sep+'final', compress_type=1, force=True)
- ## Save all results in all pipes in state
- #self.interpreter.state.save(state='final_state',
dir=result_dir_name+sep+'resultsR1', compress_type=1, force=True)
-
- # Assert the file existence of the written value files
-
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'phi_ex.out',
F_OK))
-
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'kex.out',
F_OK))
-
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'theta.out',
F_OK))
-
-
def test_r1rho_kjaergaard_missing_r1(self):
"""Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
r25011 - /branches/R1_fitting/test_suite/system_tests/relax_disp.py