Package Bio :: Package PDB :: Package QCPSuperimposer :: Class QCPSuperimposer
[hide private]
[frames] | no frames]

Class QCPSuperimposer

source code

object --+
         |
        QCPSuperimposer

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

Instance Methods [hide private]
 
__init__(self)
Initialize the class.
source code
 
_clear(self) source code
 
_rms(self, coords1, coords2)
Return rms deviations between coords1 and coords2 (PRIVATE).
source code
 
_inner_product(self, coords1, coords2) source code
 
_align(self, centered_coords1, centered_coords2) source code
 
set(self, reference_coords, coords)
Set the coordinates to be superimposed.
source code
 
run(self)
Superimpose the coordinate sets.
source code
 
get_transformed(self)
Get the transformed coordinate set.
source code
 
get_rotran(self)
Right multiplying rotation matrix and translation.
source code
 
get_init_rms(self)
Root mean square deviation of untransformed coordinates.
source code
 
get_rms(self)
Root mean square deviation of superimposed coordinates.
source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 
Initialize the class.
Overrides: object.__init__

set(self, reference_coords, coords)

source code 

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.