Module superimpose

Module for handling all types of structural superimpositions.

Classes

Pivot_finder
Class for finding the optimal pivot point for motions between the given models.

Functions

atomic_rmsd(coord)
Determine the RMSD for the given atomic coordinates.

calc_mean_structure(coord=None, mean=None)
Average the coordinates.

numpy rank-1, 3D array find_centroid(coords)
Calculate the centroid of the structural coordinates.

list of numpy rank-1 3D arrays, list of numpy rank-2 3D arrays, list of numpy rank-1 3D arrays fit_to_first(models=None, coord=None, centroid=None)
Superimpose a set of structural models using the fit to first algorithm.

list of numpy rank-1 3D arrays, list of numpy rank-2 3D arrays, list of numpy rank-1 3D arrays fit_to_mean(models=None, coord=None, centroid=None, verbosity=1)
Superimpose a set of structural models using the fit to first algorithm.

numpy rank-1 3D array, float, numpy rank-2 3D array, numpy rank-1 3D array, float, numpy rank-1 3D array kabsch(name_from=None, name_to=None, coord_from=None, coord_to=None, centroid=None, verbosity=1)
Calculate the rotational and translational displacements between the two given coordinate sets.

numpy rank-2, 3D array kabsch_rotation(coord_from=None, coord_to=None, centroid_from=None, centroid_to=None)
Calculate the rotation via SVD.

Variables

__package__ = 'generic_fns.structure'

Imports: deepcopy, pi, diag, dot, eye, float64, outer, sign, sqrt, transpose, zeros, det, norm, svd, R_to_axis_angle

Function Details

atomic_rmsd(coord)

Determine the RMSD for the given atomic coordinates.

This is the per atom RMSD to the mean structure.

Parameters:

• coord (rank-3 numpy array) - The array of molecular coordinates. The first dimension corresponds to the model, the second the atom, the third the coordinate.

calc_mean_structure(coord=None, mean=None)

Average the coordinates.

Parameters:

• coord (list of numpy rank-2, Nx3 arrays) - The list of coordinates of all models to superimpose. The first index is the models, the second is the atomic positions, and the third is the xyz coordinates.
• mean (numpy rank-2, Nx3 array) - The data storage for the mean structure.

find_centroid(coords)

Calculate the centroid of the structural coordinates.

Parameters:

• coord (numpy rank-2, Nx3 array) - The atomic coordinates.

Returns: numpy rank-1, 3D array

The centroid.

fit_to_first(models=None, coord=None, centroid=None)

Superimpose a set of structural models using the fit to first algorithm.

Parameters:

• models (list of int) - The list of models to superimpose.
• coord (list of numpy rank-2, Nx3 arrays) - The list of coordinates of all models to superimpose. The first index is the models, the second is the atomic positions, and the third is the xyz coordinates.
• centroid (list of float or numpy rank-1, 3D array) - An alternative position of the centroid to allow for different superpositions, for example of pivot point motions.

Returns: list of numpy rank-1 3D arrays, list of numpy rank-2 3D arrays, list of numpy rank-1 3D arrays

The lists of translation vectors, rotation matrices, and rotation pivots.

fit_to_mean(models=None, coord=None, centroid=None, verbosity=1)

Superimpose a set of structural models using the fit to first algorithm.

Parameters:

• models (list of int) - The list of models to superimpose.
• coord (list of numpy rank-2, Nx3 arrays) - The list of coordinates of all models to superimpose. The first index is the models, the second is the atomic positions, and the third is the xyz coordinates.
• centroid (list of float or numpy rank-1, 3D array) - An alternative position of the centroid to allow for different superpositions, for example of pivot point motions.
• verbosity (int) - The amount of information to print out. If 0, nothing will be printed.

Returns: list of numpy rank-1 3D arrays, list of numpy rank-2 3D arrays, list of numpy rank-1 3D arrays

The lists of translation vectors, rotation matrices, and rotation pivots.

kabsch(name_from=None, name_to=None, coord_from=None, coord_to=None, centroid=None, verbosity=1)

Calculate the rotational and translational displacements between the two given coordinate sets.

This uses the Kabsch algorithm (http://en.wikipedia.org/wiki/Kabsch_algorithm).

Parameters:

• name_from (str) - The name of the starting structure, used for the print outs.
• name_to (str) - The name of the ending structure, used for the print outs.
• coord_from (numpy rank-2, Nx3 array) - The list of atomic coordinates for the starting structure.
• coord_to (numpy rank-2, Nx3 array) - The list of atomic coordinates for the ending structure.
• centroid (list of float or numpy rank-1, 3D array) - An alternative position of the centroid, used for studying pivoted systems.

Returns: numpy rank-1 3D array, float, numpy rank-2 3D array, numpy rank-1 3D array, float, numpy rank-1 3D array

The translation vector T, translation distance d, rotation matrix R, rotation axis r, rotation angle theta, and the rotational pivot defined as the centroid of the ending structure.

kabsch_rotation(coord_from=None, coord_to=None, centroid_from=None, centroid_to=None)

Calculate the rotation via SVD.

Parameters:

• coord_from (numpy rank-2, Nx3 array) - The list of atomic coordinates for the starting structure.
• coord_to (numpy rank-2, Nx3 array) - The list of atomic coordinates for the ending structure.
• centroid_from (numpy rank-1, 3D array) - The starting centroid.
• centroid_to (numpy rank-1, 3D array) - The ending centroid.

Returns: numpy rank-2, 3D array

The rotation matrix.