mmLib.Superposition

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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