Author: bugman
Date: Fri Oct 18 12:36:58 2013
New Revision: 21173
URL: http://svn.gna.org/viewcvs/relax?rev=21173&view=rev
Log:
Changed the new dispersion auto-analysis class variable model_class to the
numeric_only flag.
Modified:
branches/relax_disp/auto_analyses/relax_disp.py
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.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=21173&r1=21172&r2=21173&view=diff
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (original)
+++ branches/relax_disp/auto_analyses/relax_disp.py Fri Oct 18 12:36:58 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, model_class='mixed', 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, 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.
@@ -66,8 +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 model_class: The class of models to use in the model
selection. The default of 'mixed' allows all dispersion models to be used in
the analysis. The value of 'numeric' will activate a pure numeric solution -
the analytic models can be optimised, as they are very useful for replacing
the grid search for the numeric models, but the final model selection will
only use the 'No Rex' and numeric solutions exclusively.
- @type model_class: str
+ @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.
@type mc_sim_all_models: bool
"""
@@ -91,6 +91,7 @@
self.mc_sim_num = mc_sim_num
self.modsel = modsel
self.pre_run_dir = pre_run_dir
+ self.numeric_only = numeric_only
self.mc_sim_all_models = mc_sim_all_models
# No results directory, so default to the current directory.
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=21173&r1=21172&r2=21173&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Fri Oct 18
12:36:58 2013
@@ -487,7 +487,7 @@
MODEL_CR72,
MODEL_NS_CPMG_2SITE_EXPANDED
]
- ds.numeric_flag = True
+ ds.numeric_only = True
# Execute the script.
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py')
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py?rev=21173&r1=21172&r2=21173&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
Fri Oct 18 12:36:58 2013
@@ -19,10 +19,8 @@
ds.tmpdir = 'temp'
# The numeric flag.
-if hasattr(ds, 'numeric_flag') and ds.numeric_flag:
- model_class = 'numeric'
-else:
- model_class = 'mixed'
+if not hasattr(ds, 'numeric_flag'):
+ ds.numeric_only = False
# The grid search size (the number of increments per dimension).
GRID_INC = 5
@@ -60,7 +58,4 @@
Relax_disp.opt_max_iterations = 10000
# Do not change!
-Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
model_class=model_class)
-
-# Save the program state.
-state.save('devnull', force=True)
+Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
numeric_only=ds.numeric_only)
r21173 - in /branches/relax_disp: auto_analyses/ test_suite/system_tests/ test_suite/system_tests/scripts/relax_disp/