Package Biskit :: Module rmsFit
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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 [hide private]

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()