A rapid method for the computation, comparison and display of molecular volumes

This paper presents a method for the rapid computation of approximate molecular van der Waals volumes and their subsequent display. The procedure relies on bit representation of individual volume elements that are mapped into an array that stores the total molecular volume. Our method differs from previously described algorithms in its use of bit-encoded templates that define atomic van der Waals radii. For each atom in the molecule, for which the volume is to be computed, the relevant template is mapped into a bit array with an offset corresponding to the appropriate atomic position. Bit-wise Boolean operations can be used for volume comparisons (e.g., common volume and excluded volume). An algorithm for the graphical display of the molecular surface encompassing the computed volumes is also described. The speed of the method enables users to perform volume computations in a reasonable period of time with VAX-class computers on molecules containing as many as several hundred atoms.