moleculaRnetworks is a bundled series of scripts, written in the software package R, for processing molecular simulations data. These scripts are intended for the frame-by-frame geometric and solvent network analysis of aqueous solutes only. The algorithms contained therein are based on graph theory and contain a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute, as well as an exploratory approach for describing H-bonding, based on the PageRank algorithm implemented by the Google search engine. The moleculaRnetworks codes include a preprocessor which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, correlation analyses and other data mining.
Any results obtained with moleculaRnetworks should refer to the following publication:
Mooney, B. L.; Corrales, L. R.; Clark, A. E. "moleculaRnetworks: an Integrated Graph Theoretic and Data Mining Tool to Explore Solvent Organization in Molecular Simulation", J. Comp. Chem. 2012, 33, 853-860.
This paper also has a detailed description of a typical user session and can act as a user manual.