type 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.

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

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

list of str get_param_names(self, model_info=None)
Return a vector of parameter names.

overfit_deselect(self, data_check=True, verbose=True)
Deselect spins which have insufficient data to support calculation.

set_error(self, index, error, model_info=None)
Set the parameter errors.

list of float sim_return_param(self, index, model_info=None)
Return the array of simulation parameter values.

list of int sim_return_selected(self, model_info=None)
Return the array of selected simulation flags.

Inherited from api_base.API_base: back_calc_ri, base_data_loop, bmrb_read, bmrb_write, constraint_algorithm, covariance_matrix, create_mc_data, data_names, data_type, default_value, deselect, duplicate_data, eliminate, get_model_container, 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, print_model_title, pymol_macro, return_conversion_factor, return_data, return_data_desc, return_error, return_error_red_chi2, return_grace_string, return_grace_units, return_units, return_value, set_param_values, set_selected_sim, set_update, sim_init_values, sim_pack_data, sim_return_chi2, skip_function

Inherited from api_common.API_common (private): _base_data_loop_spin, _create_mc_relax_data, _data_init_dummy, _data_init_spin, _deselect_global, _eliminate_false, _get_model_container_cdp, _has_errors_spin, _is_spin_param_false, _is_spin_param_true, _model_loop_single_global, _model_loop_spin, _model_type_global, _model_type_local, _num_instances_spin, _overfit_deselect_dummy, _print_model_title_global, _print_model_title_spin, _return_data_relax_data, _return_error_relax_data, _return_no_conversion_factor, _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

Static Methods

Inherited from api_base.API_base: __new__

Class Variables

instance = None

Method Details

__init__(self)
(Constructor)

Initialise the class by placing API_common methods into the API.

Overrides: object.__init__

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

Calculation of the spectral density values.

Parameters:

• spin_id (None or str) - The spin identification string.
• scaling_matrix (list of numpy rank-2, float64 array or list of None) - The per-model list of diagonal and square scaling matrices.
• 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, sim=False)

Initialise the data structures.

Parameters:

• data (str) - The spin ID string from the _base_data_loop_spin() method.
• sim (bool) - The Monte Carlo simulation flag, which if true will initialise the simulation data structure.

Overrides: api_base.API_base.data_init

get_param_names(self, model_info=None)

Return a vector of parameter names.

Parameters:

• model_info (SpinContainer instance, str) - The spin container and the spin ID string from the _model_loop_spin() method.

Returns: list of str

The vector of parameter names.

Overrides: api_base.API_base.get_param_names

overfit_deselect(self, data_check=True, verbose=True)

Deselect spins which have insufficient data to support calculation.

Parameters:

• data_check (bool) - A flag to signal if the presence of base data is to be checked for.
• verbose (bool) - A flag which if True will allow printouts.

Overrides: api_base.API_base.overfit_deselect

set_error(self, index, error, model_info=None)

Set the parameter errors.

Parameters:

• index (int) - The index of the parameter to set the errors for.
• error (float) - The error value.
• model_info (SpinContainer instance, str) - The spin container and the spin ID string from the _model_loop_spin() method.

Overrides: api_base.API_base.set_error

sim_return_param(self, index, model_info=None)

Return the array of simulation parameter values.

Parameters:

• index (int) - The index of the parameter to return the array of values for.
• model_info (SpinContainer instance, str) - The spin container and the spin ID string from the _model_loop_spin() method.

Returns: list of float

The array of simulation parameter values.

Overrides: api_base.API_base.sim_return_param

sim_return_selected(self, model_info=None)

Return the array of selected simulation flags.

Parameters:

• model_info (SpinContainer instance, str) - The spin container and the spin ID string from the _model_loop_spin() method.

Returns: list of int

The array of selected simulation flags.

Overrides: api_base.API_base.sim_return_selected