Package mmLib :: Module Superposition
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Module mmLib.Superposition

Class for least-squares structural superposition. Uses a quaternion method which avoids improper rotations.
Classes
SuperpositionResults Returns the results of a superposition.

Function Summary
  QuaternionToRotationMatrix(q)
Create a rotation matrix from q quaternion rotation.
  SuperimposeAtoms(atom_pair_list)
Superimposes a list of 2-tuple atom pairs.
  SuperimposeAtomsOutlierRejection(alist, rmsd_cutoff, max_cycles)
Superimpose two homologus protein chains.
  SuperimposePoints(src_points, dst_points)
Takes two 1:1 set of points and returns a 3x3 rotation matrix and translation vector.
  SuperimposePositions(position_tuple_list)
Superimposes a list of 2-tuple atom pairs.
  test_module()

Function Details

QuaternionToRotationMatrix(q)

Create a rotation matrix from q quaternion rotation. Quaternions are typed as Numeric Python arrays of length 4.

SuperimposeAtoms(atom_pair_list)

Superimposes a list of 2-tuple atom pairs.

SuperimposeAtomsOutlierRejection(alist, rmsd_cutoff=1.0, max_cycles=100)

Superimpose two homologus protein chains. The argument alist is a list of 2-tuples. The 2-tuples are the 1:1 atoms to superimpose. The alignment procedure incrementally omits atoms with large deviations until the rmsd of the least squares superposition is less than or equal to rmsd_cutoff, or the number of cycles exceeds max_cycles.

SuperimposePoints(src_points, dst_points)

Takes two 1:1 set of points and returns a 3x3 rotation matrix and translation vector.

SuperimposePositions(position_tuple_list)

Superimposes a list of 2-tuple atom pairs.

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