Bohacek R S, Guida W C
Pharmaceuticals Division, CIBA-GEIGY Corporation, Summit, NJ.
J Mol Graph. 1989 Jun;7(2):113-7. doi: 10.1016/s0263-7855(89)80015-3.
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.
本文提出了一种快速计算近似分子范德华体积并随后进行显示的方法。该过程依赖于将各个体积元素进行位表示，这些元素被映射到一个存储分子总体积的数组中。我们的方法与先前描述的算法不同之处在于，它使用了定义原子范德华半径的位编码模板。对于要计算体积的分子中的每个原子，将相关模板映射到位数组中，其偏移量对应于适当的原子位置。按位布尔运算可用于体积比较（例如，公共体积和排除体积）。本文还描述了一种用于图形显示包含计算出的体积的分子表面的算法。该方法的速度使用户能够在合理的时间内，使用VAX级计算机对包含多达几百个原子的分子进行体积计算。
