Class Consistency_tests

Instance Methods

__init__(self, relax)
Class containing functions specific to consistency testing.

calculate(self, run=None, print_flag=1, sim_index=None)
Calculation of the consistency functions.

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)
Consistency testing 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)
Consistency testing 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)
Consistency testing set details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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, f_eta=None, f_r2=None, r=None, csa=None, orientation=None, tc=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 consistency testing.

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.

orientation:  Angle between the 15N-1H vector and the principal axis of the 15N chemical
             shift tensor.

tc:  Correlation time.

j0:  Spectral density value at the zero frequency.

f_eta:  Eta-test (from Fushman D. et al. (1998) JACS, 120: 10947-10952).

f_r2:  R2-test (from Fushman D. et al. (1998) JACS, 120: 10947-10952).

default_value(self, param)

Consistency testing default values
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

_______________________________________________________________________________________
|                                       |               |                             |
| Data type                             | Object name   | Value                       |
|_______________________________________|_______________|_____________________________|
|                                       |               |                             |
| Bond length                           | 'r'           | 1.02 * 1e-10                |
|                                       |               |                             |
| CSA                                   | 'csa'         | -172 * 1e-6                 |
|                                       |               |                             |
| Angle Theta                           | 'orientation' | 15.7                        |
|                                       |               |                             |
| Correlation time                      | 'tc'          | 13 * 1e-9                   |
|_______________________________________|_______________|_____________________________|

return_conversion_factor(self, stat_type)

Dummy function for returning 1.0. This function is essential when writing grace files

return_data_name(self, name)

Consistency testing data type string matching patterns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

____________________________________________________________________________________________
|                       |               |                                                  |
| Data type             | Object name   | Patterns                                         |
|_______________________|_______________|__________________________________________________|
|                       |               |                                                  |
| J(0)                  | 'j0'          | '^[Jj]0$' or '[Jj]\(0\)'                         |
|                       |               |                                                  |
| F_eta                 | 'f_eta'       | '^[Ff]_[Ee][Tt][Aa]$'                            |
|                       |               |                                                  |
| F_R2                  | 'f_r2'        | '^[Ff]_[Rr]2$'                                   |
|                       |               |                                                  |
| Bond length           | 'r'           | '^r$' or '[Bb]ond[ -_][Ll]ength'                 |
|                       |               |                                                  |
| CSA                   | 'csa'         | '^[Cc][Ss][Aa]$'                                 |
|                       |               |                                                  |
| Angle Theta           | 'orientation' | '^[Oo][Rr][Ii][Ee][Nn][Tt][Aa][Tt][Ii][Oo][Nn]$' |
|                       |               |                                                  |
| Correlation time      | 'tc'          | '^[Tt]c$'                                        |
|_______________________|_______________|__________________________________________________|

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)

Consistency testing set details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In consistency testing, only four values can be set, the bond length, CSA, angle
Theta ('orientation') and correlation time values. These must be set prior to the
calculation of consistency functions.

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