A central partition of molecular conformational space. II. embedding 3D structures

A combinatorial model of molecular conformational space that was previously developed, had the drawback that structures could not be properly embedded because it lacked explicit rotational symmetry. The problem can be circumvented by sorting the elementary 3D components of a molecular system into a finite set of classes that can be separately embedded. This also opens up the possibility of encoding the dynamical states into a graph structure.