Class Noe_main

Class containing functions for relaxation data.

Instance Methods

_assign_function(self, spin=None, intensity=None, spectrum_type=None)
Place the peak intensity data into the spin container.

_spectrum_type(self, spectrum_type=None, spectrum_id=None)
Set the spectrum type corresponding to the spectrum_id.

calculate(self, spin_id=None, verbosity=1, sim_index=None)
Calculate the NOE and its error.

list of str data_names(self, set='all', error_names=False, sim_names=False)
Return a list of all spin container specific model-free object names.

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

None return_units(self, param)
Dummy function which returns None as the stats have no units.

Class Variables

return_data_name_doc = ['NOE calculation data type string matc...

Method Details

_assign_function(self, spin=None, intensity=None, spectrum_type=None)

Place the peak intensity data into the spin container.

The intensity data can be either that of the reference or saturated spectrum.

Parameters:

• spin (SpinContainer instance) - The spin container.
• intensity (float) - The intensity value.
• spectrum_type (str) - The type of spectrum, one of 'ref' or 'sat'.

_spectrum_type(self, spectrum_type=None, spectrum_id=None)

Set the spectrum type corresponding to the spectrum_id.

Parameters:

• spectrum_type (str) - The type of NOE spectrum, one of 'ref' or 'sat'.
• spectrum_id (str) - The spectrum id string.

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

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.
• verbosity (int) - The amount of information to print. The higher the value, the greater the verbosity.
• sim_index (None) - The MC simulation index (unused).

data_names(self, set='all', error_names=False, sim_names=False)

Return a list of all spin container specific model-free object names.

Description

The names are as follows:

• 'model', the model-free model name.
• 'equation', the model-free equation type.
• 'params', an array of the model-free parameter names associated with the model.
• 's2', S2.
• 's2f', S2f.
• 's2s', S2s.
• 'local_tm', local tm.
• 'te', te.
• 'tf', tf.
• 'ts', ts.
• 'rex', Rex.
• 'r', bond length.
• 'csa', CSA value.
• 'nucleus', the heteronucleus type.
• 'chi2', chi-squared value.
• 'iter', iterations.
• 'f_count', function count.
• 'g_count', gradient count.
• 'h_count', hessian count.
• 'warning', minimisation warning.

Parameters:

• set (str) - The set of object names to return. This can be set to 'all' for all names, to 'generic' for generic object names, 'params' for model-free parameter names, or to 'min' for minimisation specific object names.
• 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.

return_units(self, param)

Dummy function which returns None as the stats have no units.

Parameters:

• param (str) - The name of the parameter to return the units string for.

Returns: None

Nothing.

Class Variable Details

return_data_name_doc

Value:

['NOE calculation data type string matching patterns',
 '''
        _________________________________________
        |                        |              |
        | Data type              | Object name  |
        |________________________|______________|
        |                        |              |
        | Reference intensity    | \'ref\'        |
...