Eur. Phys. J. E (2018) 41: 87
https://doi.org/10.1140/epje/i2018-11694-7

Regular Article

Implementing efficient concerted rotations using Mathematica and C code^⋆

¹ Computational Physics Department, University of Vienna, Sensengasse 8/10, 1090, Vienna, Austria
² Faculty of Science, Masaryk University, Kotlářská 2, 602 00, Brno, Czech Republic
³ CEITEC - Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic
⁴ CIC biomaGUNE Parque Cientfico y Tecnolgico de Gipuzkoa, Paseo Miramn 182, 20014, Donostia / San Sebastin, Gipuzkoa, Spain

^* e-mail: luca.tubiana@univie.ac.at

Received: 22 February 2018
Accepted: 28 June 2018
Published online: 20 July 2018

Abstract

In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.