rmsFit¶
superimpose 2 structures iteratively
Functions Overview
findTransformation |
Match two arrays by rotation and translation. |
match |
Matches two arrays onto each other, while iteratively removing outliers. |
rowDistances |
Calculate the distances between the items of two arrays (of same shape) after least-squares superpositioning. |
svd |
Singular Value Decomposition. |
Classes Overview
rmsFit Module Details
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biskit.rmsFit.
findTransformation
(x, y)[source]¶ Match two arrays by rotation and translation. Returns the rotation matrix and the translation vector.
Parameters: - x (array('f')) – first set of coordinates
- y (array('f')) – second set of coordinates
Returns: rotation matrix (3x3) and translation vector (1x3)
Return type: array, array
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biskit.rmsFit.
match
(x, y, n_iterations=1, z=2, eps_rmsd=0.5, eps_stdv=0.05)[source]¶ Matches two arrays onto each other, while iteratively removing outliers. Superimposed array y would be C{ N0.dot(y, N0.transpose(r)) + t }.
Parameters: - n_iterations (1|0) – number of calculations:: 1 .. no iteration 0 .. until convergence
- z (float) – number of standard deviations for outlier definition (default: 2)
- eps_rmsd (float) – tolerance in rmsd (default: 0.5)
- eps_stdv (float) – tolerance in standard deviations (default: 0.05)
Returns: (r,t), [ [percent_considered, rmsd_for_it, outliers] ]
Return type: (array, array), [float, float, int]
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biskit.rmsFit.
rowDistances
(x, y)[source]¶ Calculate the distances between the items of two arrays (of same shape) after least-squares superpositioning.
Parameters: - x (array('f')) – first set of coordinates
- y (array('f')) – second set of coordinates
Returns: array( len(x), ‘f’ ), distance between x[i] and y[i] for all i
Return type: array