Author: bugman
Date: Mon Oct 28 16:05:05 2013
New Revision: 21284
URL: http://svn.gna.org/viewcvs/relax?rev=21284&view=rev
Log:
The relaxation dispersion auto-analysis now accepts the 'insignificance'
argument.
This is then used in the relax_disp.insignificance user function prior to the
optimisation of each
model, so that spins with insignificant dispersion curves are not optimised.
The 'R2eff' and
'No Rex' models are skipped for obvious reasons.
Modified:
branches/relax_disp/auto_analyses/relax_disp.py
Modified: branches/relax_disp/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/relax_disp.py?rev=21284&r1=21283&r2=21284&view=diff
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (original)
+++ branches/relax_disp/auto_analyses/relax_disp.py Mon Oct 28 16:05:05 2013
@@ -47,7 +47,7 @@
opt_func_tol = 1e-25
opt_max_iterations = int(1e7)
- def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
models=[MODEL_R2EFF], grid_inc=11, mc_sim_num=500, modsel='AIC',
pre_run_dir=None, numeric_only=False, mc_sim_all_models=False):
+ def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
models=[MODEL_R2EFF], grid_inc=11, mc_sim_num=500, modsel='AIC',
pre_run_dir=None, insignificance=0.0, numeric_only=False,
mc_sim_all_models=False):
"""Perform a full relaxation dispersion analysis for the given list
of models.
@keyword pipe_name: The name of the data pipe containing all
of the data for the analysis.
@@ -66,6 +66,8 @@
@type modsel: str
@keyword pre_run_dir: The optional directory containing the
dispersion auto-analysis results from a previous run. The optimised
parameters from these previous results will be used as the starting point for
optimisation rather than performing a grid search. This is essential for
when large spin clusters are specified, as a grid search becomes
prohibitively expensive with clusters of three or more spins. At some point
a RelaxError will occur because the grid search is impossibly large. For the
cluster specific parameters, i.e. the populations of the states and the
exchange parameters, an average value will be used as the starting point.
For all other parameters, the R20 values for each spin and magnetic field, as
well as the parameters related to the chemical shift difference dw, the
optimised values of the previous run will be directly copied.
@type pre_run_dir: None or str
+ @keyword insignificance: The R2eff/R1rho value in rad/s by which
to judge insignificance. If the maximum difference between two points on all
dispersion curves for a spin is less than this value, that spin will be
deselected.
+ @type insignificance: float
@keyword numeric_only: The class of models to use in the model
selection. The default of False allows all dispersion models to be used in
the analysis (no exchange, the analytic models and the numeric models). The
value of True will activate a pure numeric solution - the analytic models
will be optimised, as they are very useful for replacing the grid search for
the numeric models, but the final model selection will not include them.
@type numeric_only: bool
@keyword mc_sim_all_models: A flag which if True will cause Monte
Carlo simulations to be performed for each individual model. Otherwise Monte
Carlo simulations will be reserved for the final model.
@@ -91,6 +93,7 @@
self.mc_sim_num = mc_sim_num
self.modsel = modsel
self.pre_run_dir = pre_run_dir
+ self.insignificance = insignificance
self.numeric_only = numeric_only
self.mc_sim_all_models = mc_sim_all_models
@@ -273,6 +276,10 @@
@type model: str
"""
+ # Deselect insignificant spins.
+ if model not in ['R2eff', 'No Rex']:
+
self.interpreter.relax_disp.insignificance(level=self.insignificance)
+
# Use pre-run results as the optimisation starting point.
if self.pre_run_dir:
self.pre_run_parameters(model=model)
r21284 - /branches/relax_disp/auto_analyses/relax_disp.py