An object-oriented programming suite for electrostatic effects in biological molecules An experience report on the MEAD project

Abstract

We have developed a set of object-oriented classes and programs in C++ that implement molecular electrostatic models that can be described by the term, Macroscopic Electrostatics with Atomic Detail (MEAD). In the course of developing the MEAD suite, we have shifted from a class hierarchy rooted in atoms and molecules, to a system in which the top-level classes are the electrostatic potential and the entities that determine the potential in the equations of electrostatics: the charge distribution, the dielectric environment and the electrolyte environment. Atoms and molecules are then seen as objects giving rise to, or occurring as subclasses of, charge distributions, dielectric environments, etc. This shift in focus from the physical objects (molecules) to the more abstract objects that appear in the underlying physics has facilitated the development of alternative approximation schemes and numerical methods through subclassing. It also provides a natural way of writing high level programs in terms of potentials and distributions. Some of the newer elements of C++, such as templates and RTTI, have proven useful to solve multi-method and default method problems. MEAD is distributed as free software.

The author gratefully acknowledges support from the National Institutes of Health (GM45607)