Structural comparisons using restrained inhomogeneous transformations

Comparisons between structures with similar atomic skeletons are made by mathematically deforming one over the other using inhomogeneous transformations. Removal of shallow bending and twisting distortions between the structures reveals local differences that are masked by comparisons using homogeneous transformations. Inhomogenous deformations are restrained to prevent unrealistic changes in local atomic bonding geometry by the addition of penalty functions similar in form to the potentials used in empirical molecular mechanics calculations.