Class dAuvergne_protocol

The model-free auto-analysis.

Instance Methods

__init__(self, pipe_name=None, results_dir=None, diff_model=None, mf_models=['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'], local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8'..., grid_inc=11, diff_tensor_grid_inc={'ellipsoid': 6, 'oblate': 11, 'prolate': 11, 'sphere': 11}, min_algor='newton', mc_sim_num=500, max_iter=None, user_fns=None, conv_loop=True)
Perform the full model-free analysis protocol of d'Auvergne and Gooley, 2008b.

check_vars(self)
Check that the user has set the variables correctly.

convergence(self)
Test for the convergence of the global model.

determine_rnd(self, model=None)
Function for returning the name of next round of optimisation.

execute(self)
Execute the protocol.

load_tensor(self)
Function for loading the optimised diffusion tensor.

model_selection(self, modsel_pipe=None, dir=None, write_flag=True)
Model selection function.

multi_model(self, local_tm=False)
Function for optimisation of all model-free models.

status_setup(self)
Initialise the status object.

write_results(self)
Create Grace plots of the final model-free results.

Class Variables

opt_func_tol = 1e-25

opt_max_iterations = 10000000

Method Details

__init__(self, pipe_name=None, results_dir=None, diff_model=None, mf_models=['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'], local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8'..., grid_inc=11, diff_tensor_grid_inc={'ellipsoid': 6, 'oblate': 11, 'prolate': 11, 'sphere': 11}, min_algor='newton', mc_sim_num=500, max_iter=None, user_fns=None, conv_loop=True)
(Constructor)

Perform the full model-free analysis protocol of d'Auvergne and Gooley, 2008b.

Parameters:

• pipe_name - The name of the data pipe containing the sequence info. This data pipe should have all values set including the CSA value, the bond length, the heteronucleus name and proton name. It should also have all relaxation data loaded.
• results_dir (str) - The directory, where files are saved in.
• diff_model (str or list of str) - The global diffusion model to optimise. This can be one of 'local_tm', 'sphere', 'oblate', 'prolate', 'ellipsoid', or 'final'. If all or a subset of these are supplied as a list, then these will be automatically looped over and calculated.
• mf_models (list of str) - The model-free models.
• local_tm_models (list of str) - The model-free models.
• grid_inc (int) - The grid search size (the number of increments per dimension).
• diff_tensor_grid_inc (list of int) - A list of grid search sizes for the optimisation of the sphere, prolate spheroid, oblate spheroid, and ellipsoid.
• min_algor (str) - The minimisation algorithm (in most cases this should not be changed).
• mc_sim_num (int) - The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
• max_iter (int or None.) - The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence.
• user_fns (dict) - A dictionary of replacement user functions. These will overwrite the standard user functions. The key should be the name of the user function or user function class and the value should be the function or class instance.
• conv_loop (bool) - Automatic looping over all rounds until convergence.