Figure 1.

p3d data structures. The p3d data structures are a) a list of all atom objects that can be treated as vectors, b) a variety of sets, where each atom can be member of several sets and c) a Binary space-partitioning (BSP) tree that allows fast spatial queries to the protein structure. Illustrated are the recursive divisions performed on an aquaporin structure (Chain A, 1RC2.pdb [12]). Finally, the implemented query functions allow the combination of all three hashes and custom user defined vectors or atoms to formulate complex queries in a human readable syntax.