Package specific_analyses :: Package noe :: Module api :: Class Noe
[hide private]
[frames] | no frames]

Class Noe

source code


Specific analysis API class for the steady-state heternuclear NOE analysis.

Instance Methods [hide private]
 
__init__(self)
Initialise the class by placing API_common methods into the API.
source code
 
calculate(self, spin_id=None, scaling_matrix=None, verbosity=1, sim_index=None)
Calculate the NOE and its error.
source code
list of str
get_param_names(self, model_info=None)
Return a vector of parameter names.
source code
 
overfit_deselect(self, data_check=True, verbose=True)
Deselect spins which have insufficient data to support calculation.
source code

Inherited from api_base.API_base: back_calc_ri, base_data_loop, bmrb_read, bmrb_write, constraint_algorithm, covariance_matrix, create_mc_data, data_init, 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_error, set_param_values, set_selected_sim, set_update, sim_init_values, sim_pack_data, sim_return_chi2, sim_return_param, sim_return_selected, skip_function

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods [hide private]

Inherited from api_base.API_base: __new__

Class Variables [hide private]
  instance = None
hash(x)
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 

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)

source code 

Calculate the NOE and its error.

The error for each peak is calculated using the formula:

                 ___________________________________________
              \/ {sd(sat)*I(unsat)}^2 + {sd(unsat)*I(sat)}^2
   sd(NOE) = -----------------------------------------------
                                 I(unsat)^2
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) - The MC simulation index (unused).
Overrides: api_base.API_base.calculate

get_param_names(self, model_info=None)

source code 

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)

source code 

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