pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

TitlepyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data
Publication TypeJournal Article
Year of Publication2016
AuthorsShkurti, Ardita, Goni Ramon, Andrio Pau, Breitmoser Elena, Bethune Iain, Orozco Modesto, and Laughton Charles A.
JournalSoftwareX
Volume5
Pagination44 - 50
Date Published12/2016
ISBN Number2352-7110
KeywordsData analysis, molecular dynamics, Molecular simulation, Principal Component Analysis
Abstract

AbstractThe biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

URLhttp://www.sciencedirect.com/science/article/pii/S2352711016300036
Short TitleSoftwareX
Highlight: 
Review: