A Central Partition of Molecular Conformational Space. V. The Hypergraph of 3D Partition Sequences

Details A Central Partition of Molecular Conformational Space. V. The Hypergraph of 3D Partition Sequences A Central Partition of Molecular Conformational Space. V. The Hypergraph of 3D Partition Sequences

2008-12-15

arxiv.org/abs/0812.2844v2

Physics

Computational Physics

Scientific paper

In a previous work a procedure was decribed for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells or G, encoding the set of cells in conformational space that are visited by the system in its thermal wandering. The information in G however, is encoded in a great number of fragments that must be aggregated. We describe here the algorithmic procedures 1) for aggregating the information from G into an hypergraph allowing to enumerate the relevant cells from conformational space, and 2) for puttting the data in a very compact format.

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