Module pcs

Module for the manipulation of pseudocontact shift data.

Functions

back_calc(align_id=None)
Back calculate the PCS from the alignment tensor.

centre(pos=None, atom_id=None, pipe=None, verbosity=1, ave_pos=False, force=False)
Specify the atom in the loaded structure corresponding to the paramagnetic centre.

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

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

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

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

read(align_id=None, file=None, dir=None, file_data=None, 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)
Read the PCS data from file.

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

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

Variables

__package__ = 'generic_fns'

Imports: deepcopy, pi, sqrt, array, float64, ones, zeros, norm, sys, warn, grace, pipes, get_tensor_index, exists_mol_res_spin_data, return_spin, spin_loop, ave_pcs_tensor, g1H, pcs_constant, RelaxError, RelaxNoPdbError, RelaxNoSequenceError, open_write_file, read_spin_data, write_spin_data, RelaxWarning, RelaxNoSpinWarning

Function Details

back_calc(align_id=None)

Back calculate the PCS from the alignment tensor.

Parameters:

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

centre(pos=None, atom_id=None, pipe=None, verbosity=1, ave_pos=False, force=False)

Specify the atom in the loaded structure corresponding to the paramagnetic centre.

Parameters:

• pos (list of float) - The atomic position. If set, the atom_id string will be ignored.
• atom_id (str) - The atom identification string.
• pipe (None or str) - An alternative data pipe to extract the paramagnetic centre from.
• verbosity (int) - The amount of information to print out. The bigger the number, the more information.
• ave_pos (bool) - A flag which if True causes the atomic positions from multiple models to be averaged.
• force - A flag which if True will cause the current PCS centre to be overwritten.

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

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

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 PCS 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 PCS 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 PCS 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, 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)

Read the PCS 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 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.
• 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 PCS data in Hz.
• error_col (int or None) - The column containing the PCS 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.

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

Set optimisation weights on the PCS 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 PCS will have.

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

Display the PCS 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.