1. A computer-implemented method for maintaining semantics of a graph that corresponds to a model of a three-dimensional (3-D) structure, the method comprising: creating node data structures by a processor of a computer executing a modeling application for storage in a memory of the computer, instantiations of which store data that describes primitive nodes and group nodes of the graph, each node data structure that describes a primitive node to store a node name of a primitive node that represents a portion of the 3-D structure, and each node data structure that describes a group node to store a node name of a group node that represents a collection of portions of the 3-D and a node reference object that lists a set of nodes subsumed by the group node and a set of links subsumed by the group node; creating link data structures by the processor for storage in the memory of the computer, instantiations of which store data that describes primitive links and group links of the graph, each link data structure that describes a primitive link to represent a relationship between portions of the 3-D structure and to store an indication of where the primitive link extends from and an indication of where the primitive link extends to, and each link data structure that describes a group link to represent a relationship between collections of portions of the 3-D structure, and to store an indication of where the group link extends from, an indication of where the group link extends to, and a link reference object that lists a set of links subsumed or replaced by the group link; and storing the node data structures and the link data structures in the memory of the computer to maintain the semantics of the graph.