Module rdc

Module for the manipulation of RDC data.

Functions

back_calc(align_id=None)
Back calculate the RDC from the alignment tensor and unit bond vectors.

float or None convert(value, align_id, to_intern=False)
Convert the RDC based on the 'D' or '2D' data type.

corr_plot(format=None, file=None, dir=None, force=False)
Generate a correlation plot of the measured vs.

delete(align_id=None)
Delete the RDC data corresponding to the alignment ID.

display(align_id=None, bc=False)
Display the RDC data corresponding to the alignment ID.

q_factors(spin_id=None)
Calculate the Q-factors for the RDC data.

read(align_id=None, file=None, dir=None, file_data=None, data_type='D', spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None, neg_g_corr=False)
Read the RDC data from file.

weight(align_id=None, spin_id=None, weight=1.0)
Set optimisation weights on the RDC data.

write(align_id=None, file=None, dir=None, bc=False, force=False)
Display the RDC data corresponding to the alignment ID.

Variables

__package__ = 'generic_fns'

Imports: deepcopy, pi, sqrt, float64, ones, zeros, norm, sys, warn, nan, grace, pipes, get_tensor_index, exists_mol_res_spin_data, return_spin, spin_loop, ave_rdc_tensor, dipolar_constant, return_gyromagnetic_ratio, RelaxError, RelaxNoRDCError, RelaxNoSequenceError, RelaxSpinTypeError, open_write_file, read_spin_data, write_spin_data, RelaxWarning, RelaxNoSpinWarning

Function Details

back_calc(align_id=None)

Back calculate the RDC from the alignment tensor and unit bond vectors.

Parameters:

• align_id (str) - The alignment tensor ID string.

convert(value, align_id, to_intern=False)

Convert the RDC based on the 'D' or '2D' data type.

Parameters:

• value (float or None) - The value or error to convert.
• align_id (str) - The alignment tensor ID string.
• to_intern (bool) - A flag which if True will convert to the internal D notation if needed, or if False will convert from the internal D notation to the external D or 2D format.

Returns: float or None

The converted value.

corr_plot(format=None, file=None, dir=None, force=False)

Generate a correlation plot of the measured vs. back-calculated RDCs.

Parameters:

• format (str or None) - The format for the plot file. The following values are accepted: 'grace', a Grace plot; None, a plain text file.
• file (str or file object) - The file name or object to write to.
• dir (str) - The name of the directory to place the file into (defaults to the current directory).
• force (bool) - A flag which if True will cause any pre-existing file to be overwritten.

delete(align_id=None)

Delete the RDC data corresponding to the alignment ID.

Parameters:

• align_id (str or None) - The alignment tensor ID string. If not specified, all data will be deleted.

display(align_id=None, bc=False)

Display the RDC data corresponding to the alignment ID.

Parameters:

• align_id (str) - The alignment tensor ID string.
• bc (bool) - The back-calculation flag which if True will cause the back-calculated rather than measured data to be displayed.

q_factors(spin_id=None)

Calculate the Q-factors for the RDC data.

Parameters:

• spin_id (None or str) - The spin ID string used to restrict the Q-factor calculation to a subset of all spins.

read(align_id=None, file=None, dir=None, file_data=None, data_type='D', spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None, neg_g_corr=False)

Read the RDC data from file.

Parameters:

• align_id (str) - The alignment tensor ID string.
• file (str) - The name of the file to open.
• dir (str or None) - The directory containing the file (defaults to the current directory if None).
• file_data (list of lists) - An alternative to opening a file, if the data already exists in the correct format. The format is a list of lists where the first index corresponds to the row and the second the column.
• data_type - A string which is set to 'D' means that the splitting in the aligned sample was assumed to be J + D, or if set to '2D' then the splitting was taken as J + 2D.
• spin_id_col (int or None) - The column containing the spin ID strings. If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
• mol_name_col (int or None) - The column containing the molecule name information. If supplied, spin_id_col must be None.
• res_name_col (int or None) - The column containing the residue name information. If supplied, spin_id_col must be None.
• res_num_col (int or None) - The column containing the residue number information. If supplied, spin_id_col must be None.
• spin_name_col (int or None) - The column containing the spin name information. If supplied, spin_id_col must be None.
• spin_num_col (int or None) - The column containing the spin number information. If supplied, spin_id_col must be None.
• data_col (int or None) - The column containing the RDC data in Hz.
• error_col (int or None) - The column containing the RDC errors.
• sep (str or None) - The column separator which, if None, defaults to whitespace.
• spin_id (None or str) - The spin ID string used to restrict data loading to a subset of all spins.
• neg_g_corr (bool) - A flag which is used to correct for the negative gyromagnetic ratio of 15N. If True, a sign inversion will be applied to all RDC values to be loaded.

weight(align_id=None, spin_id=None, weight=1.0)

Set optimisation weights on the RDC data.

Parameters:

• align_id (str) - The alignment tensor ID string.
• spin_id (None or str) - The spin ID string.
• weight (float or int.) - The optimisation weight. The higher the value, the more importance the RDC will have.

write(align_id=None, file=None, dir=None, bc=False, force=False)

Display the RDC data corresponding to the alignment ID.

Parameters:

• align_id (str) - The alignment tensor ID string.
• file (str or file object) - The file name or object to write to.
• dir (str) - The name of the directory to place the file into (defaults to the current directory).
• bc (bool) - The back-calculation flag which if True will cause the back-calculated rather than measured data to be written.
• force (bool) - A flag which if True will cause any pre-existing file to be overwritten.