Package Bio :: Package SVDSuperimposer :: Class SVDSuperimposer
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Class SVDSuperimposer

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object --+
         |
        SVDSuperimposer


SVDSuperimposer 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.

SVD stands for Singular Value Decomposition, which is used to calculate
the superposition.

Reference:

Matrix computations, 2nd ed. Golub, G. & Van Loan, CF., The Johns
Hopkins University Press, Baltimore, 1989

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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_clear(self) source code
 
_rms(self, coords1, coords2)
Return rms deviations between coords1 and coords2.
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set(self, reference_coords, coords)
Set the coordinates to be superimposed.
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run(self)
Superimpose the coordinate sets.
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get_transformed(self)
Get the transformed coordinate set.
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get_rotran(self)
Right multiplying rotation matrix and translation.
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get_init_rms(self)
Root mean square deviation of untransformed coordinates.
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get_rms(self)
Root mean square deviation of superimposed coordinates.
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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 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

set(self, reference_coords, coords)

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Set the coordinates to be superimposed.
coords will be put on top of reference_coords.

o reference_coords: an NxDIM array
o coords: an NxDIM array

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