Class Consistency_tests

Class containing functions specific to consistency testing.

Instance Methods

__init__(self)
Initialise the class by placing API_common methods into the API.

_set_frq(self, frq=None)
Function for selecting which relaxation data to use in the consistency tests.

calculate(self, spin_id=None, verbosity=1, sim_index=None)
Calculation of the consistency functions.

data_init(self, data_cont, sim=False)
Initialise the data structures.

list of str data_names(self, set=None, error_names=False, sim_names=False)
Return a list of all spin container specific consistency testing object names.

overfit_deselect(self)
Deselect spins which have insufficient data to support calculation.

set_error(self, model_info, index, error)
Set the parameter errors.

list of float sim_return_param(self, model_info, index)
Return the array of simulation parameter values.

list of int sim_return_selected(self, model_info)
Return the array of selected simulation flags.

Inherited from api_base.API_base: back_calc_ri, base_data_loop, bmrb_read, bmrb_write, create_mc_data, data_type, default_value, deselect, duplicate_data, eliminate, get_param_names, get_param_values, grid_search, has_errors, is_spin_param, map_bounds, minimise, model_desc, model_loop, model_statistics, model_type, molmol_macro, num_instances, pymol_macro, read_columnar_results, return_conversion_factor, return_data, return_data_desc, return_data_name, return_error, return_grace_string, return_units, return_value, set_param_values, set_selected_sim, set_update, sim_init_values, sim_pack_data, sim_return_chi2, skip_function, test_grid_ops

Inherited from api_common.API_common (private): _base_data_loop_spin, _create_mc_relax_data, _data_init_dummy, _default_value_spin, _eliminate_false, _has_errors_spin, _is_spin_param_true, _model_loop_single_global, _model_loop_spin, _num_instances_spin, _overfit_deselect_dummy, _return_conversion_factor_spin, _return_data_desc_spin, _return_data_name, _return_data_name_global, _return_data_name_spin, _return_data_relax_data, _return_error_relax_data, _return_grace_string_spin, _return_no_conversion_factor, _return_units_global, _return_units_spin, _return_value_general, _set_error_spin, _set_param_values_global, _set_param_values_spin, _set_selected_sim_global, _set_selected_sim_spin, _set_update, _sim_init_values_spin, _sim_pack_relax_data, _sim_return_chi2_spin, _sim_return_param_spin, _sim_return_selected_global, _sim_return_selected_spin, _test_grid_ops_general

Class Variables

default_value_doc = '\n Consistency testing default val...

return_data_name_doc = '\n Consistency testing data typ...

set_doc = '\n Consistency testing set details\n ...

Inherited from api_base.API_base: GLOBAL_PARAMS, SPIN_PARAMS, eliminate_doc

Method Details

calculate(self, spin_id=None, verbosity=1, sim_index=None)

Calculation of the consistency functions.

Parameters:

• spin_id (None or str) - The spin identification string.
• verbosity (int) - The amount of information to print. The higher the value, the greater the verbosity.
• sim_index (None or int) - The optional MC simulation index.

Overrides: api_base.API_base.calculate

data_init(self, data_cont, sim=False)

Initialise the data structures.

Parameters:

• data_cont (instance) - The data container.
• sim (bool) - The Monte Carlo simulation flag, which if true will initialise the simulation data structure.

Overrides: api_base.API_base.data_init

data_names(self, set=None, error_names=False, sim_names=False)

Return a list of all spin container specific consistency testing object names.

Description

The names are as follows:

• 'r', bond length.
• 'csa', CSA value.
• 'heteronuc_type', the heteronucleus type.
• 'orientation', angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor.
• 'tc', correlation time.
• 'j0', spectral density value at 0 MHz (from Farrow et al. (1995) JBNMR, 6: 153-162).
• 'f_eta', eta-test (from Fushman et al. (1998) JACS, 120: 10947-10952).
• 'f_r2', R2-test (from Fushman et al. (1998) JACS, 120: 10947-10952).

Parameters:

• set (ignored) - An unused variable.
• error_names (bool) - A flag which if True will add the error object names as well.
• sim_names (bool) - A flag which if True will add the Monte Carlo simulation object names as well.

Returns: list of str

The list of object names.

Overrides: api_base.API_base.data_names

overfit_deselect(self)

Deselect spins which have insufficient data to support calculation.

Overrides: api_base.API_base.overfit_deselect

set_error(self, model_info, index, error)

Set the parameter errors.

Parameters:

• model_info (SpinContainer instance) - The spin container originating from model_loop().
• index (int) - The index of the parameter to set the errors for.
• error (float) - The error value.

Overrides: api_base.API_base.set_error

sim_return_param(self, model_info, index)

Return the array of simulation parameter values.

Parameters:

• model_info (SpinContainer instance) - The spin container originating from model_loop().
• index (int) - The index of the parameter to return the array of values for.

Returns: list of float

The array of simulation parameter values.

Overrides: api_base.API_base.sim_return_param

sim_return_selected(self, model_info)

Return the array of selected simulation flags.

Parameters:

• model_info (SpinContainer instance) - The spin container originating from model_loop().

Returns: list of int

The array of selected simulation flags.

Overrides: api_base.API_base.sim_return_selected

Class Variable Details

default_value_doc

Value:

'''
        Consistency testing default values
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        These default values are found in the file \'physical_constant
s.py\'.

         _____________________________________________________________
_________________________
...

return_data_name_doc

Value:

'''
        Consistency testing data type string matching patterns
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

         ___________________________________________
        |                       |                  |
        | Data type             | Object name      |
        |_______________________|__________________|
...

set_doc

Value:

'''
        Consistency testing set details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

        In consistency testing, only four values can be set, the bond 
length, CSA, angle
        Theta (\'orientation\') and correlation time values. These mus
t be set prior to the
...