Module dipole_pair

Module for the manipulation of relaxation data.

Functions

define(spin_id1=None, spin_id2=None, pipe=None, direct_bond=False, verbose=True)
Set up the magnetic dipole-dipole interaction.

read_dist(file=None, dir=None, unit='meter', spin_id1_col=None, spin_id2_col=None, data_col=None, sep=None)
Set up the magnetic dipole-dipole interaction.

set_dist(spin_id1=None, spin_id2=None, ave_dist=None, unit='meter')
Set up the magnetic dipole-dipole interaction.

unit_vectors(ave=True)
Extract the bond vectors from the loaded structures and store them in the spin container.

Variables

__package__ = 'generic_fns'

Imports: float64, zeros, norm, sys, warn, is_float, create_interatom, exists_data, interatomic_loop, return_interatom, Selection, exists_mol_res_spin_data, return_spin, spin_loop, pipes, RelaxError, RelaxNoInteratomError, extract_data, write_data, RelaxWarning, RelaxZeroVectorWarning

Function Details

define(spin_id1=None, spin_id2=None, pipe=None, direct_bond=False, verbose=True)

Set up the magnetic dipole-dipole interaction.

Parameters:

• spin_id1 (str) - The spin identifier string of the first spin of the pair.
• spin_id2 (str) - The spin identifier string of the second spin of the pair.
• pipe (str) - The data pipe to operate on. Defaults to the current data pipe.
• direct_bond (bool) - A flag specifying if the two spins are directly bonded.
• verbose (bool) - A flag which if True will result in printouts of the created interatomoic data containers.

read_dist(file=None, dir=None, unit='meter', spin_id1_col=None, spin_id2_col=None, data_col=None, sep=None)

Set up the magnetic dipole-dipole interaction.

Parameters:

• 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).
• unit (str) - The measurement unit. This can be either 'meter' or 'Angstrom'.
• spin_id1_col (int) - The column containing the spin ID strings of the first spin.
• spin_id2_col (int) - The column containing the spin ID strings of the second spin.
• data_col (int or None) - The column containing the averaged distances in meters.
• sep (str or None) - The column separator which, if None, defaults to whitespace.

set_dist(spin_id1=None, spin_id2=None, ave_dist=None, unit='meter')

Set up the magnetic dipole-dipole interaction.

Parameters:

• spin_id1 (str) - The spin identifier string of the first spin of the pair.
• spin_id2 (str) - The spin identifier string of the second spin of the pair.
• ave_dist (float) - The r^-3 averaged interatomic distance.
• unit (str) - The measurement unit. This can be either 'meter' or 'Angstrom'.

unit_vectors(ave=True)

Extract the bond vectors from the loaded structures and store them in the spin container.

Parameters:

• ave (bool) - A flag which if True will cause the average of all vectors to be calculated.