Pymol stores a transformation matrix for each object relative to it's initial position when loaded in. get_object_matrix will return a list of floats with that matrix for a named object.
The matrix is 4X4, with the upper left 3x3 forming a rotation matrix, the fourth column and row representing pre-rotation and post-rotation translation vectors respectively, and the 16th element always being 1.0.
cmd.get_object_matrix(object, state=1)
cmd.load("prot1.pdb", "prot1")
cmd.load("prot2.pdb", "prot2")
cmd.super("prot1", "prot2") #align prot1 to prot 2
transformation = cmd.get_object_matrix("prot1") #translation and rotation to align the two proteins
