Package Bio :: Package SVDSuperimposer :: Module SVDSuperimposer' :: Class SVDSuperimposer
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Class SVDSuperimposer

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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) source code
 
_clear(self) source code
 
_rms(self, coords1, coords2)
Return rms deviations between coords1 and coords2.
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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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get_rotran(self)
Right multiplying rotation matrix and translation.
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get_transformed(self)
Get the transformed coordinate set.
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run(self)
Superimpose the coordinate sets.
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set(self, reference_coords, coords)
Set the coordinates to be superimposed.
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Method Details [hide private]

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.