Object Command Language: a formalism to build molecular models and to analyze structural parameters in...

We have written a programming language OCL (Object Command Language) to solve, in a general way, two recurring problems that arise during the construction of molecular models and during the geometrical characterization of macromolecules: how to move precisely and reproducibly any part of a molecular model in any user-defined local reference axes; and how to calculate standard or user-defined structural parameters that characterize the complex geometries of any macromolecule. OCL endows the user with three main capabilities: the definition of subsets of the macromolecule, called objects in OCL, with a formalism from elementary set theory or lexical analysis; the definition of sequences of elementary geometrical operations, called procedures in OCL, enabling one to build arbitrary three-dimensional (3D) orthonormal reference frames, to be associated with previously defined objects; and the transmission of these definitions to programs that allow one to display, to modify and to analyze interactively the molecular structure, or to programs that perform energy minimizations or molecular dynamics. Several applications to nucleic acids are presented.