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


We are pleased to announce the publication of this paper, in the journal Software X.

Abstract

The 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.

 

Citation

Ardita Shkurti, Ramon Goni, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton, pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data, SoftwareX, Available online 19 April 2016, ISSN 2352-7110, http://dx.doi.org/10.1016/j.softx.2016.04.002.

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