Module rmsFit

source code

superimpose 2 structures iteratively

Classes

[hide private]

Test
Test class

Functions

[hide private]

array, array findTransformation(x, y)
Match two arrays by rotation and translation.

(array, array), [float, float, int] match(x, y, n_iterations=1, z=2, eps_rmsd=0.5, eps_stdv=0.05)
Matches two arrays onto each other, while iteratively removing outliers.

array rowDistances(x, y)
Calculate the distances between the items of two arrays (of same shape) after least-squares superpositioning.

Variables

[hide private]

test = Test()

Function Details

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findTransformation(x, y)

source code

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: array, array: rotation matrix (3x3) and translation vector (1x3)

match(x, y, n_iterations=1, z=2, eps_rmsd=0.5, eps_stdv=0.05)

source code

Matches two arrays onto each other, while iteratively removing outliers. Superimposed array y would be

 N.dot(y, N.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: (array, array), [float, float, int]: (r,t), [ [percent_considered, rmsd_for_it, outliers] ]

rowDistances(x, y)

source code

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: array( len(x), 'f' ), distance between x[i] and y[i] for all i

Variables Details

[hide private]

test

Value:

Test()