Abstract
Ray-representation or ray-rep formalism provides a comprehensive and simple approach for geometric computations on molecular solid models. These methods allow model formulation in terms of simple constructive solid geometry. In particular, the van der Waals exclusion volume is described by computing the ray-representation of a union of spheres and the solvent exclusion volume is computed by Minkowski dilation and erosion. Volume and area properties are calculated, respectively, by a ”pile-of-bricks” and ”collocation-of-tiles” interpretation of the rayrep. Labeling the chemical character of surface patches is facilitated by the intrinsic point ordering of the ray-rep. Definition of internal cavities can be accomplished by equivalence-set clustering of internal void segments. Finally, a Boolean intersection procedure determines placement of crystallographic waters with respect to the protein solvent excluded volume.
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Prisant, M.G. (1996). Ray-representation formalism for geometric computations on protein solid models. In: Lin, M.C., Manocha, D. (eds) Applied Computational Geometry Towards Geometric Engineering. WACG 1996. Lecture Notes in Computer Science, vol 1148. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0014487
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DOI: https://doi.org/10.1007/BFb0014487
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