Author: bugman
Date: Tue Jan 27 15:00:53 2015
New Revision: 27329
URL: http://svn.gna.org/viewcvs/relax?rev=27329&view=rev
Log:
Introduced the nested_params_ave_dom_pos argument to the frame order
auto-analysis.
This allows the average domain position to be set to no rotations and
translations rather than
taking the average position from the rotor or free-rotor model. This can be
useful when large
motions are present causing the rigid model to have unreasonable domain
positions.
Modified:
branches/frame_order_cleanup/auto_analyses/frame_order.py
Modified: branches/frame_order_cleanup/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/frame_order.py?rev=27329&r1=27328&r2=27329&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/frame_order.py (original)
+++ branches/frame_order_cleanup/auto_analyses/frame_order.py Tue Jan 27
15:00:53 2015
@@ -385,43 +385,45 @@
# Debugging and test suite variables.
_final_state = True
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_dir=None, opt_rigid=None,
opt_subset=None, opt_full=None, opt_mc=None, mc_sim_num=500,
models=MODEL_LIST_NONREDUNDANT, brownian_step_size=2.0, brownian_snapshot=10,
brownian_total=1000, results_compress_type=0, rigid_grid_split=False,
store_intermediate=True):
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, pre_run_dir=None, opt_rigid=None,
opt_subset=None, opt_full=None, opt_mc=None, mc_sim_num=500,
models=MODEL_LIST_NONREDUNDANT, brownian_step_size=2.0, brownian_snapshot=10,
brownian_total=1000, results_compress_type=0, rigid_grid_split=False,
store_intermediate=True, nested_params_ave_dom_pos=True):
"""Perform the full frame order analysis.
- @param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
- @type data_pipe_full: str
- @param data_pipe_subset: The name of the data pipe containing
all of the RDC data but only a small subset of ~5 PCS points. This optional
argument is used to massively speed up the analysis.
- @type data_pipe_subset: str or None
- @keyword pipe_bundle: The data pipe bundle to associate
all spawned data pipes with.
- @type pipe_bundle: str
- @keyword results_dir: The directory where files are saved
in.
- @type results_dir: str
- @keyword pre_run_dir: The optional directory containing
the frame order auto-analysis results from a previous run. If supplied, then
the 'data_pipe_full', 'data_pipe_subset', and 'opt_subset' arguments will be
ignored. The results will be loaded from the results files in this
directory, and then optimisation starts from there. The model nesting
algorithm will also be deactivated.
- @keyword opt_rigid: The grid search, zooming grid search
and minimisation settings object for the rigid frame order model.
- @type pre_run_dir: None or str
- @type opt_rigid: Optimisation_settings instance
- @keyword opt_subset: The grid search, zooming grid search
and minimisation settings object for optimisation of all models, excluding
the rigid model, for the PCS data subset.
- @type opt_subset: Optimisation_settings instance
- @keyword opt_full: The grid search, zooming grid search
and minimisation settings object for optimisation of all models, excluding
the rigid model, for the full data set.
- @type opt_full: Optimisation_settings instance
- @keyword opt_mc: The grid search, zooming grid search
and minimisation settings object for optimisation of the Monte Carlo
simulations. Any grid search settings will be ignored, as only the
minimise.execute user function is run for the simulations. And only the
settings for the first iteration of the object will be accessed and used -
iterative optimisation will be ignored.
- @type opt_mc: Optimisation_settings instance
- @keyword mc_sim_num: The number of Monte Carlo
simulations to be used for error analysis at the end of the analysis.
- @type mc_sim_num: int
- @keyword models: The frame order models to use in the
analysis. The 'rigid' model must be included as this is essential for the
analysis.
- @type models: list of str
- @keyword brownian_step_size: The step_size argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
- @type brownian_step_size: float
- @keyword brownian_snapshot: The snapshot argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
- @type brownian_snapshot: int
- @keyword brownian_total: The total argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
- @type brownian_total: int
- @keyword results_compress_type: The type of compression to use when
creating the results files. See the results.write user function for details.
- @type results_compress_type: int
- @keyword rigid_grid_split: A flag which if True will cause the
grid search for the rigid model to be split so that the rotation is optimised
first followed by the translation. When combined with grid zooming, this can
save optimisation time. However it may result in the global minimum being
missed.
- @type rigid_grid_split: bool
- @keyword store_intermediate: A flag which if True will cause all
intermediate optimisation results to be stored in the 'intermediate_results'
directory. These can then be used for studying the optimisation settings or
loaded for subsequent analyses.
- @type store_intermediate: bool
+ @param data_pipe_full: The name of the data pipe
containing all of the RDC and PCS data.
+ @type data_pipe_full: str
+ @param data_pipe_subset: The name of the data pipe
containing all of the RDC data but only a small subset of ~5 PCS points.
This optional argument is used to massively speed up the analysis.
+ @type data_pipe_subset: str or None
+ @keyword pipe_bundle: The data pipe bundle to
associate all spawned data pipes with.
+ @type pipe_bundle: str
+ @keyword results_dir: The directory where files are
saved in.
+ @type results_dir: str
+ @keyword pre_run_dir: The optional directory
containing the frame order auto-analysis results from a previous run. If
supplied, then the 'data_pipe_full', 'data_pipe_subset', and 'opt_subset'
arguments will be ignored. The results will be loaded from the results files
in this directory, and then optimisation starts from there. The model
nesting algorithm will also be deactivated.
+ @keyword opt_rigid: The grid search, zooming grid
search and minimisation settings object for the rigid frame order model.
+ @type pre_run_dir: None or str
+ @type opt_rigid: Optimisation_settings instance
+ @keyword opt_subset: The grid search, zooming grid
search and minimisation settings object for optimisation of all models,
excluding the rigid model, for the PCS data subset.
+ @type opt_subset: Optimisation_settings instance
+ @keyword opt_full: The grid search, zooming grid
search and minimisation settings object for optimisation of all models,
excluding the rigid model, for the full data set.
+ @type opt_full: Optimisation_settings instance
+ @keyword opt_mc: The grid search, zooming grid
search and minimisation settings object for optimisation of the Monte Carlo
simulations. Any grid search settings will be ignored, as only the
minimise.execute user function is run for the simulations. And only the
settings for the first iteration of the object will be accessed and used -
iterative optimisation will be ignored.
+ @type opt_mc: Optimisation_settings instance
+ @keyword mc_sim_num: The number of Monte Carlo
simulations to be used for error analysis at the end of the analysis.
+ @type mc_sim_num: int
+ @keyword models: The frame order models to use in
the analysis. The 'rigid' model must be included as this is essential for
the analysis.
+ @type models: list of str
+ @keyword brownian_step_size: The step_size argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
+ @type brownian_step_size: float
+ @keyword brownian_snapshot: The snapshot argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
+ @type brownian_snapshot: int
+ @keyword brownian_total: The total argument for the
pseudo-Brownian dynamics simulation frame_order.simulate user function.
+ @type brownian_total: int
+ @keyword results_compress_type: The type of compression to use
when creating the results files. See the results.write user function for
details.
+ @type results_compress_type: int
+ @keyword rigid_grid_split: A flag which if True will cause
the grid search for the rigid model to be split so that the rotation is
optimised first followed by the translation. When combined with grid
zooming, this can save optimisation time. However it may result in the
global minimum being missed.
+ @type rigid_grid_split: bool
+ @keyword store_intermediate: A flag which if True will cause
all intermediate optimisation results to be stored in the
'intermediate_results' directory. These can then be used for studying the
optimisation settings or loaded for subsequent analyses.
+ @type store_intermediate: bool
+ @keyword nested_params_ave_dom_pos: A flag which if True will cause
the average domain position parameters to be taken from the rigid or
free-rotor models. If False, then these parameters will be set to zero.
+ @type nested_params_ave_dom_pos: bool
"""
# Execution lock.
@@ -447,6 +449,7 @@
self.results_compress_type = results_compress_type
self.rigid_grid_split = rigid_grid_split
self.store_intermediate = store_intermediate
+ self.flag_nested_params_ave_dom_pos = nested_params_ave_dom_pos
# Re-order the models to enable the parameter nesting protocol.
self.models = self.reorder_models(models)
@@ -713,6 +716,16 @@
@param model: The frame order model.
@type model: str
"""
+
+ # No nesting, so set all parameters to zero.
+ if not self.flag_nested_params_ave_dom_pos:
+ self.interpreter.value.set(param='ave_pos_x', val=0.0)
+ self.interpreter.value.set(param='ave_pos_y', val=0.0)
+ self.interpreter.value.set(param='ave_pos_z', val=0.0)
+ self.interpreter.value.set(param='ave_pos_alpha', val=0.0)
+ self.interpreter.value.set(param='ave_pos_beta', val=0.0)
+ self.interpreter.value.set(param='ave_pos_gamma', val=0.0)
+ return
# Skip the following models to allow for full optimisation.
if model in [MODEL_RIGID, MODEL_FREE_ROTOR]:
r27329 - /branches/frame_order_cleanup/auto_analyses/frame_order.py