Class Jw_mapping

Class containing functions specific to reduced spectral density mapping.

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 J(w) mapping.

calculate(self, spin_id=None, verbosity=1, sim_index=None)
Calculation of the spectral density values.

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 J(w) mapping 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 = ['Reduced spectral density mapping default...

return_data_name_doc = ['Reduced spectral density mapping data...

set_doc = ['Reduced spectral density mapping 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 spectral density values.

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 J(w) mapping object names.

Description

The names are as follows:

• 'r', bond length.
• 'csa', CSA value.
• 'heteronuc_type', the heteronucleus type.
• 'j0', spectral density value at 0 MHz.
• 'jwx', spectral density value at the frequency of the heteronucleus.
• 'jwh', spectral density value at the frequency of the heteronucleus.

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:

['Reduced spectral density mapping default values',
 '''
        These default values are found in the file \'physical_constant
s.py\'.

        ______________________________________________________________
_________________________
        |                                       |                    |
...

return_data_name_doc

Value:

['Reduced spectral density mapping data type string matching patterns'
,
 '''
        _____________________________________________
        |                        |                  |
        | Data type              | Object name      |
        |________________________|__________________|
        |                        |                  |
...

set_doc

Value:

['Reduced spectral density mapping set details',
 '''
        In reduced spectral density mapping, three values must be set 
prior to the calculation of spectral density values:  the bond length,
 CSA, and heteronucleus type.
        ''']