Package mmLib :: Module Superposition
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Module Superposition

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Class for least-squares structural superposition. Uses a quaternion method which avoids improper rotations.

Classes [hide private]
  SuperpositionResults
Returns the results of a superposition.
Functions [hide private]
 
QuaternionToRotationMatrix(q)
Create a rotation matrix from q quaternion rotation.
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SuperimposePoints(src_points, dst_points)
Takes two 1:1 set of points and returns a 3x3 rotation matrix and translation vector.
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SuperimposePositions(position_tuple_list)
Superimposes a list of 2-tuple atom pairs.
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SuperimposeAtoms(atom_pair_list)
Superimposes a list of 2-tuple atom pairs.
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SuperimposeAtomsOutlierRejection(alist, rmsd_cutoff=1.0, max_cycles=100)
Superimpose two homologous protein chains.
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test_module() source code
Variables [hide private]
  __package__ = 'mmLib'
Function Details [hide private]

QuaternionToRotationMatrix(q)

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

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

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Superimpose two homologous 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.