Class Jw_mapping

Instance Methods

__init__(self, relax)
Class containing functions specific to reduced spectral density mapping.

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

data_init(self, data, sim=0)
Function for initialising the data structures.

data_names(self)
Function for returning a list of names of data structures.

default_value(self, param)
Reduced spectral density mapping default values ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

num_instances(self, run=None)
Function for returning the number of instances.

overfit_deselect(self, run)
Function for deselecting residues without sufficient data to support calculation

return_conversion_factor(self, stat_type)
Dummy function for returning 1.0.

return_data_name(self, name)
Reduced spectral density mapping data type string matching patterns ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

return_grace_string(self, data_type)
Function for returning the Grace string representing the data type for axis labelling.

return_units(self, data_type)
Function for returning a string representing the parameters units.

set(self, run=None, value=None, error=None, param=None, index=None)
Reduced spectral density mapping set details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

set_frq(self, run=None, frq=None)
Function for selecting which relaxation data to use in the J(w) mapping.

set_error(self, run, instance, index, error)
Function for setting parameter errors.

sim_return_param(self, run, instance, index)
Function for returning the array of simulation parameter values.

sim_return_selected(self, run, instance)
Function for returning the array of selected simulation flags.

set_selected_sim(self, run, instance, select_sim)
Function for returning the array of selected simulation flags.

sim_pack_data(self, run, i, sim_data)
Function for packing Monte Carlo simulation data.

write_columnar_line(self, file=None, num=None, name=None, select=None, data_set=None, nucleus=None, wH=None, j0=None, jwx=None, jwh=None, r=None, csa=None, ri_labels=None, remap_table=None, frq_labels=None, frq=None, ri=None, ri_error=None)
Function for printing a single line of the columnar formatted results.

write_columnar_results(self, file, run)
Function for printing the results into a file.

Inherited from base_class.Common_functions: has_errors, return_data, return_error, return_value, set_update, sim_init_values

Method Details

__init__(self, relax)
(Constructor)

Class containing functions specific to reduced spectral density mapping.

Overrides: base_class.Common_functions.__init__

data_names(self)

Function for returning a list of names of data structures.

Description
~~~~~~~~~~~

r:  Bond length.

csa:  CSA value.

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.

default_value(self, param)

Reduced spectral density mapping default values
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

_______________________________________________________________________________________
|                                       |              |                              |
| Data type                             | Object name  | Value                        |
|_______________________________________|______________|______________________________|
|                                       |              |                              |
| Bond length                           | 'r'          | 1.02 * 1e-10                 |
|                                       |              |                              |
| CSA                                   | 'csa'        | -172 * 1e-6                  |
|_______________________________________|______________|______________________________|

return_data_name(self, name)

Reduced spectral density mapping data type string matching patterns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

____________________________________________________________________________________________
|                        |              |                                                  |
| Data type              | Object name  | Patterns                                         |
|________________________|______________|__________________________________________________|
|                        |              |                                                  |
| J(0)                   | 'j0'         | '^[Jj]0$' or '[Jj]\(0\)'                         |
|                        |              |                                                  |
| J(wX)                  | 'jwx'        | '^[Jj]w[Xx]$' or '[Jj]\(w[Xx]\)'                 |
|                        |              |                                                  |
| J(wH)                  | 'jwh'        | '^[Jj]w[Hh]$' or '[Jj]\(w[Hh]\)'                 |
|                        |              |                                                  |
| Bond length            | 'r'          | '^r$' or '[Bb]ond[ -_][Ll]ength'                 |
|                        |              |                                                  |
| CSA                    | 'csa'        | '^[Cc][Ss][Aa]$'                                 |
|________________________|______________|__________________________________________________|

return_units(self, data_type)

Function for returning a string representing the parameters units.

For example, the internal representation of te is in seconds, whereas the external representation is in picoseconds, therefore this function will return the string 'picoseconds' for te.

set(self, run=None, value=None, error=None, param=None, index=None)

Reduced spectral density mapping set details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In reduced spectral density mapping, only two values can be set, the bond length and CSA
value.  These must be set prior to the calculation of spectral density values.

Overrides: base_class.Common_functions.set

set_error(self, run, instance, index, error)

Function for setting parameter errors.

Overrides: base_class.Common_functions.set_error

sim_return_param(self, run, instance, index)

Function for returning the array of simulation parameter values.

Overrides: base_class.Common_functions.sim_return_param

sim_return_selected(self, run, instance)

Function for returning the array of selected simulation flags.

Overrides: base_class.Common_functions.sim_return_selected