eigenMatrix ( q=None )

Return the matrix form of an eigenvector, q. If q, is not specified, return a zero matrix

matchPositions ( fixedPositions,  movablePositions )

Computes rotation and translation to align one set of positions with another. The sum of the squares of the distances between corresponding positions is minimized. The xyz positions are specified as n by 3 numpy arrays. Returns Chimera Xform and rms value.

matchAtoms (
        fixedAtoms,
        movableAtoms,
        fCoordSet=None,
        mCoordSet=None,
        )

Computes rotation and translation to align one set of atoms with another. The sum of the squares of the distances between corresponding atoms is minimized. Returns Chimera Xform and rms value.

Match

XXX: This does not need to be a class. A function which does it