Author: tlinnet
Date: Wed Aug 27 21:55:19 2014
New Revision: 25358
URL: http://svn.gna.org/viewcvs/relax?rev=25358&view=rev
Log:
Added systemtest, Relax_disp.test_estimate_r2eff_err_auto and extended
functionality to the auto analyses protocol.
If "exp_mc_sim_num" is set to "-1" and sent to the auto analyses, the errors
of R2eff will be estimated from the Co-Variance matrix.
These errors is HIGHLY likely to be wrong, but can be used in an initial test
fase, to rapidly produce data for plotting data.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
Modified:
trunk/auto_analyses/relax_disp.py
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=25358&r1=25357&r2=25358&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp.py (original)
+++ trunk/auto_analyses/relax_disp.py Wed Aug 27 21:55:19 2014
@@ -497,18 +497,31 @@
# The minimisation algorithm to use. If the Jacobian and Hessian
matrix have not been specified for fitting, 'simplex' should be used.
min_algor = 'simplex'
- # Do Monte Carlo simulations.
+ # Error estimation by Monte Carlo simulations.
if do_monte_carlo:
+ # Set the number of Monte-Carlo simulations.
+ monte_carlo_sim = self.mc_sim_num
+
+ # If the number for exponential curve fitting has been set.
if model == MODEL_R2EFF and self.exp_mc_sim_num != None:
-
self.interpreter.monte_carlo.setup(number=self.exp_mc_sim_num)
+ monte_carlo_sim = self.exp_mc_sim_num
+
+ # When set to minus 1, estimation of the errors will be
extracted from the covariance matrix.
+ # This is HIGHLY likely to be wrong, but can be used in an
initial test fase.
+ if model == MODEL_R2EFF and self.exp_mc_sim_num == -1:
+ # Print
+ subsection(file=sys.stdout, text="Estimating errors from
Covariance matrix", prespace=1)
+
+ # Estimate errors
+ self.interpreter.relax_disp.r2eff_err_estimate()
else:
- self.interpreter.monte_carlo.setup(number=self.mc_sim_num)
- self.interpreter.monte_carlo.create_data()
- self.interpreter.monte_carlo.initial_values()
- self.interpreter.minimise.execute(min_algor=min_algor,
func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations,
constraints=constraints)
- if self.eliminate:
- self.interpreter.eliminate()
- self.interpreter.monte_carlo.error_analysis()
+ self.interpreter.monte_carlo.setup(number=monte_carlo_sim)
+ self.interpreter.monte_carlo.create_data()
+ self.interpreter.monte_carlo.initial_values()
+ self.interpreter.minimise.execute(min_algor=min_algor,
func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations,
constraints=constraints)
+ if self.eliminate:
+ self.interpreter.eliminate()
+ self.interpreter.monte_carlo.error_analysis()
def pre_run_parameters(self, model=None, model_path=None):
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=25358&r1=25357&r2=25358&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Wed Aug 27 21:55:19 2014
@@ -63,6 +63,7 @@
to_skip = [
"test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp",
"test_estimate_r2eff_err",
+ "test_estimate_r2eff_err_auto",
"test_estimate_r2eff_err_methods"
"test_exp_fit",
"test_m61_exp_data_to_m61",
@@ -2746,6 +2747,86 @@
# Run the analysis.
relax_disp.Relax_disp(pipe_name=ds.pipe_name,
pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS,
grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL)
+
+ # Verify the data.
+ self.verify_r1rho_kjaergaard_missing_r1(models=MODELS,
result_dir_name=result_dir_name, do_assert=False)
+
+
+ def test_estimate_r2eff_err_auto(self):
+ """Test the user function for estimating R2eff errors from
exponential curve fitting, via the auto_analyses menu.
+
+ This follows Task 7822.
+ U{task #7822<https://gna.org/task/index.php?7822>}: Implement user
function to estimate R2eff and associated errors for exponential curve
fitting.
+
+ This uses the data from Kjaergaard's paper at U{DOI:
10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}.
+ Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
+ """
+
+ # 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, read_R1=False)
+
+ # The dispersion models.
+ MODELS = [MODEL_R2EFF, MODEL_NOREX]
+
+ # The grid search size (the number of increments per dimension).
+ GRID_INC = None
+
+ # The number of Monte Carlo simulations to be used for error
analysis for exponential curve fitting of R2eff.
+ # When set to minus 1, estimation of the errors will be extracted
from the covariance matrix.
+ # This is HIGHLY likely to be wrong, but can be used in an initial
test fase.
+ EXP_MC_NUM = -1
+
+ # The number of Monte Carlo simulations to be used for error
analysis at the end of the analysis.
+ MC_NUM = 3
+
+ # Model selection technique.
+ MODSEL = 'AIC'
+
+ # Execute the auto-analysis (fast).
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
+ OPT_FUNC_TOL = 1e-25
+ relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
+ OPT_MAX_ITERATIONS = 10000000
+ relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS
+
+ result_dir_name = ds.tmpdir
+
+ # Make all spins free
+ 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)
+
+ # Select only a subset of spins for global fitting
+ #self.interpreter.select.spin(spin_id=':41@N', change_all=False)
+ #self.interpreter.relax_disp.cluster('model_cluster', ':41@N')
+
+ #self.interpreter.select.spin(spin_id=':40@N', change_all=False)
+ #self.interpreter.relax_disp.cluster('model_cluster', ':40@N')
+
+ self.interpreter.select.spin(spin_id=':52@N', change_all=False)
+ #self.interpreter.relax_disp.cluster('model_cluster', ':52@N')
+
+ # Run the analysis.
+ relax_disp.Relax_disp(pipe_name=ds.pipe_name,
pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS,
grid_inc=GRID_INC, mc_sim_num=MC_NUM, exp_mc_sim_num=EXP_MC_NUM,
modsel=MODSEL)
# Verify the data.
self.verify_r1rho_kjaergaard_missing_r1(models=MODELS,
result_dir_name=result_dir_name, do_assert=False)
r25358 - in /trunk: auto_analyses/relax_disp.py test_suite/system_tests/relax_disp.py