Bio.PDB.QCPSuperimposer package

Module contents

Structural alignment using Quaternion Characteristic Polynomial (QCP).

QCPSuperimposer finds the best rotation and translation to put two point sets on top of each other (minimizing the RMSD). This is eg. useful to superimpose crystal structures. QCP stands for Quaternion Characteristic Polynomial, which is used in the algorithm.

class Bio.PDB.QCPSuperimposer.QCPSuperimposer

Bases: object

Quaternion Characteristic Polynomial (QCP) Superimposer.

QCPSuperimposer finds the best rotation and translation to put two point sets on top of each other (minimizing the RMSD). This is eg. useful to superimposing 3D structures of proteins.

QCP stands for Quaternion Characteristic Polynomial, which is used in the algorithm.

Reference:

Douglas L Theobald (2005), “Rapid calculation of RMSDs using a quaternion-based characteristic polynomial.”, Acta Crystallogr A 61(4):478-480

__init__(self)

Initialize the class.

set(self, reference_coords, coords)

Set the coordinates to be superimposed.

coords will be put on top of reference_coords.

• reference_coords: an NxDIM array

• coords: an NxDIM array

DIM is the dimension of the points, N is the number of points to be superimposed.

run(self)

Superimpose the coordinate sets.

get_transformed(self)

Get the transformed coordinate set.

get_rotran(self)

Right multiplying rotation matrix and translation.

get_init_rms(self)

Root mean square deviation of untransformed coordinates.

get_rms(self)

Root mean square deviation of superimposed coordinates.