How to cite this article: B. L. Mooney, L. R. Corrales, A. E. Clark, J. Comput. Chem. 2012, 33, 853-860. DOI: 10.1002/jcc.22917
Article first published online: 25 JAN 2012
Copyright © 2012 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 33, Issue 8, pages 853–860, 30 March 2012
How to Cite
Mooney, B. L., Corrales, L.René. and Clark, A. E. (2012), MoleculaRnetworks: An integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation. J. Comput. Chem., 33: 853–860. doi: 10.1002/jcc.22917
This article was published online on 25 January 2012 with an incorrect hyperlink, which was corrected on 23 February 2012.
- Issue published online: 21 FEB 2012
- Article first published online: 25 JAN 2012
- Manuscript Accepted: 3 DEC 2011
- Manuscript Received: 17 OCT 2011
- US Department of Energy, Basic Energy Sciences, Heavy Element program. Grant Number: DE-SC0001815
- simulation analysis;
- solvent lability
This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations. © 2012 Wiley Periodicals, Inc.