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

Ardita Shkurti | Zendy; Ramón Goñi | Zendy; Pau Andrio | Zendy; Elena Breitmoser | Zendy; Iain Bethune | Zendy; Modesto Orozco | Zendy; Charles A. Laughton | Zendy

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

Author(s) -

Ardita Shkurti,

Ramón Goñi,

Pau Andrio,

Elena Breitmoser,

Iain Bethune,

Modesto Orozco,

Charles A. Laughton

Publication year - 2016

Publication title -

softwarex

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.528

H-Index - 21

ISSN - 2352-7110

DOI - 10.1016/j.softx.2016.04.002

Subject(s) - python (programming language) , computer science , unix , suite , software , software suite , computational science , data mining , operating system , parallel computing , archaeology , history

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.

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