__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=[ ' rigid ' , ' rotor ' , ' free rotor ' , ' iso cone, torsionless ' , ' iso ... ,
brownian_step_size=2.0,
brownian_snapshot=10,
brownian_total=1000,
dist_total=1000,
dist_max_rotations=1000000,
results_compress_type=1,
rigid_grid_split=False,
store_intermediate=True,
nested_params_ave_dom_pos=True)
(Constructor)
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Perform the full frame order analysis.
- Parameters:
data_pipe_full (str) - The name of the data pipe containing all of the RDC and PCS data.
data_pipe_subset (str or None) - 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.
pipe_bundle (str) - The data pipe bundle to associate all spawned data pipes with.
results_dir (str) - The directory where files are saved in.
pre_run_dir (None or str) - 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.
opt_rigid (Optimisation_settings instance) - The grid search, zooming grid search and minimisation settings
object for the rigid frame order model.
opt_subset (Optimisation_settings instance) - The grid search, zooming grid search and minimisation settings
object for optimisation of all models, excluding the rigid model,
for the PCS data subset.
opt_full (Optimisation_settings instance) - The grid search, zooming grid search and minimisation settings
object for optimisation of all models, excluding the rigid model,
for the full data set.
opt_mc (Optimisation_settings instance) - 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.
mc_sim_num (int) - The number of Monte Carlo simulations to be used for error
analysis at the end of the analysis.
models (list of str) - The frame order models to use in the analysis. The 'rigid' model
must be included as this is essential for the analysis.
brownian_step_size (float) - The step_size argument for the pseudo-Brownian dynamics
simulation frame_order.simulate user function.
brownian_snapshot (int) - The snapshot argument for the pseudo-Brownian dynamics simulation
frame_order.simulate user function.
brownian_total (int) - The total argument for the pseudo-Brownian dynamics simulation
frame_order.simulate user function.
dist_total (int) - The total argument for the uniform distribution
frame_order.distribute user function.
dist_max_rotations (int) - The max_rotations argument for the uniform distribution
frame_order.distribute user function.
results_compress_type (int) - The type of compression to use when creating the results files.
See the results.write user function for details.
rigid_grid_split (bool) - 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.
store_intermediate (bool) - 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.
nested_params_ave_dom_pos (bool) - 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.
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