In this paper we propose a generic and integrated data structure that is decoupled form the product model database in order to manage and update the geometric elements (parts) related with topological constraints. We present a practical application in the case of ship design. In ship design it is necessary to manage and to deal with a huge number of components and relationships. The data structure is based on a directed graph. The software design follows object oriented techniques and pattern-based design. Using class patterns to implement the graph and to manage the topological constraints performs high reusability of the proposed solution.