Pteros: Fast and easy to use open‐source C++ library for molecular analysis
Open Access
- 27 April 2012
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 33 (19) , 1632-1636
Abstract
An open‐source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open‐source Artistic License from http://sourceforge.net/projects/pteros/.Keywords
This publication has 19 references indexed in Scilit:
- ProDy: Protein Dynamics Inferred from Theory and ExperimentsBioinformatics, 2011
- BALL - biochemical algorithms library 1.3BMC Bioinformatics, 2010
- Biopython: freely available Python tools for computational molecular biology and bioinformaticsBioinformatics, 2009
- GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationJournal of Chemical Theory and Computation, 2008
- Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters2006
- DL_POLY: Application to molecular simulationMolecular Simulation, 2002
- The molecular modeling toolkit: A new approach to molecular simulationsJournal of Computational Chemistry, 2000
- NAMD2: Greater Scalability for Parallel Molecular DynamicsJournal of Computational Physics, 1999
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983